From f0cd05e0184046f7370420646aa5c36440dfac0f Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Tue, 12 Dec 2023 14:13:26 +0100 Subject: [PATCH 001/121] Updated sativa build, incl. test case --- recipes/sativa/build.sh | 36 +---- recipes/sativa/meta.yaml | 15 ++- recipes/sativa/sequences.alnfna | 230 ++++++++++++++++++++++++++++++++ recipes/sativa/taxonomy.tsv | 5 + 4 files changed, 249 insertions(+), 37 deletions(-) create mode 100644 recipes/sativa/sequences.alnfna create mode 100644 recipes/sativa/taxonomy.tsv diff --git a/recipes/sativa/build.sh b/recipes/sativa/build.sh index 4c880d868a6ea..b983fcee56e33 100644 --- a/recipes/sativa/build.sh +++ b/recipes/sativa/build.sh @@ -1,32 +1,8 @@ #!/bin/bash -export USE_AVX=yes -export USE_AVX2=yes - -case `uname` in -Darwin) export DARWIN=1;; -Linux) export DARWIN=0;; -*) echo "Unknown architecture"; exit 1;; -esac - -make -C ./raxml CC="$CC" - -install -d ${PREFIX}/tmp -install -d ${PREFIX}/bin - -if [ $DARWIN -eq 1 ]; then - install sativa.cfg *.py ${PREFIX} -else - install -t ${PREFIX} *.py sativa.cfg -fi - -# Place a symlink to sativa.py in bin/ -( cd ${PREFIX}/bin; ln -s ../sativa.py . ) - -mkdir ${PREFIX}/raxml -cp ./raxml/raxmlHPC8* ./raxml/*.sh ${PREFIX}/raxml - -cp -r ./epac ${PREFIX} -cp -r ./tests ${PREFIX} -cp -r ./example ${PREFIX} - +mkdir ${PREFIX}/sativa/ +mv * ${PREFIX}/sativa/ +cd ${PREFIX}/sativa +./install.sh +cd ${PREFIX}/bin +ln -s ${PREFIX}/sativa/sativa.py . diff --git a/recipes/sativa/meta.yaml b/recipes/sativa/meta.yaml index 600f238ce24c5..181e24c1630be 100644 --- a/recipes/sativa/meta.yaml +++ b/recipes/sativa/meta.yaml @@ -6,11 +6,12 @@ package: version: {{ version }} source: - url: https://github.com/amkozlov/sativa/archive/refs/tags/v{{ version }}.zip - sha256: 14b772c7e1bc242655e1876e7492fd8d50d363058236bdf513aa5afca7d94841 + #url: https://github.com/amkozlov/sativa/archive/refs/tags/v{{ version }}.zip + #sha256: 14b772c7e1bc242655e1876e7492fd8d50d363058236bdf513aa5afca7d94841 + git_url: https://github.com/amkozlov/sativa build: - number: 1 + number: 2 requirements: build: @@ -23,11 +24,11 @@ requirements: - python >=3.0.0 test: - imports: - - unittest + files: + - sequences.alnfna + - taxonomy.tsv commands: -# - python sativa.py -h - - python -m unittest discover -v + - $PREFIX/sativa/sativa.py -s sequences.alnfna -t taxonomy.tsv -x bac -debug about: home: https://github.com/amkozlov/sativa diff --git a/recipes/sativa/sequences.alnfna b/recipes/sativa/sequences.alnfna new file mode 100644 index 0000000000000..7e0aa83c9190c --- /dev/null +++ b/recipes/sativa/sequences.alnfna @@ -0,0 +1,230 @@ +>RS_GCF_000019605.1~NC_010482.1 +---GGTTGATCCTGCCGGAGGGAAC-----CCCTATCGGGCTCGCACTAAGCCATGCGAG +TCTGCTGGGGG------------------------------------------------- +------------------------------------CCCCTGCCCCTGGCGGCGCACGGC +TCCGTAATACACGGTCAACCTGTCCTGGGGACCGGGATAA-------------------- +CCTCGGGAAACTGAGGTTAAT---ACCGGATAGGGGTGGATTCCTGGAATGGGTCCACCC +CTAAAGTAGGCGGGGGGACG-GCC-----CCGCTGAGGCCCCAGGGTGGGACCGTGGCCT +AT-CAGG----TAGTAGGTGGGGTA---------ACGGCCCACCTAGCCTAAGACGGGTA +CGGG------CTCTGAGAG-GAGG-AGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGC +C-CTACGGGGCGCAGCAG--------GCGGGAAACTTCCCCAATG-----CGCGCAAGCG +TGAGGGAGTGAGCCCGAGTGCCGCCCGCTGAGGG------CGGCTGTTCCCCTGTGTAA- +--------A-AAG-------CAGGGGGTAGGAAG-GGGAG-------GGTAAGGCTGGTG +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------CCAGCCGCCGCGGTAAAACCAGC---------TCC-CCGA-- +-GGG--GTTCCCACGCATACTGGGCCTAAAGCGTCCGTAGCCGGCCCCGTAAGTCCTCGG +TT---AAATCCGC--CTGAAGACAGG--CGGACCGCCGAGGAT------A--CTGCGGGG +C-TAGGGAGC--GGGAGGGGCCGAGGGTATTCCGGGGGGAGCGGTAAAATGCGT------ +------------------------------------------AGATCCCCGGAGGACC-- +-ACCAGTGGCGAAGGCGCTCGGCTGGAACGCGTCCGACGGTGAGGG--------ACGAAA +GCTGGG-GGAG------------------CAAACCGGATTAGATACCCGGGTAGTCCCAG +CCGTAAACGATGCCGG---CTAGGTGCCG---GCTGAGG---------TTTCGGCCTCAG +CCGGTGTCGA---------------------AGCGAAGGCATTAAGCCGGCCGC-CTGAG +GAGTACAGCCGCAAGGCCGAAA----------CTTAAAGGAATTG-ACGGGGGGGC---- +------------------------------------------------------------ +--------------------------ACCACAAGGGGTGAATGCCTGCGGCTCAATTGGA +CTCAACGCCGGGAATC-TTACCGGGGGCGACAGCAGGATGAAGGTCAGG----------- +------------------------------------------------------------ +--------------------------------------CTG-------AA---------- +-------GACCTTACCTGAC----GCGCTGAG--GG-GTGGTGCATGGC---------CG +TCGCCAGCTCGTGCCGTGAGGTGT--CCTGTTAAGTCAGGC-------AACGAGCGAGAC +-CCCCGCCCTC-AGTTGCCAGCGGGGCCTT-ACGGCTGG-C-CG-GGCAAACTGGGGGGA +CTGCCGGCGAAGA---GCCGGAGGAAGGAGGGGGCTACGGCAGGTCAGTATGCCCCTAAT +C---CCCCGGGCCGCACGCGGGCTGCAATGGGCGGGACA---GCGG---------G-ATG +CGAC-CCCGAGAGGGGGAGCAAATCCCTGAAACCCGCCCGT-G--GTTGGGATCGAGGGT +TGCAACTCGCCCTCGTGA-ACCCGGAATCCCTAGTAACCGCGGTTCTCC-ATAC------ +----------------------------CGCGGTGAATACGTCCCTGCCCCTTGTACACA +CCGCCCGTCAACCCACCCGAGTGGACTTGGGGCGAGGCCCAGCTCAA------------- +-------------------TGGCTGGGTCGAGCTTTGGGTCCGCGAGGGGGGGTAAGTCG +TAACAAGGTAGCCGTAG---GGGAACCTGCGGCTGGATCACCTCCC-------------- +------------------------------------------------------------ +------------------- +>RS_GCF_000092465.1~NC_014205.1 +------------------------------------------------------------ +------------------------------------------------------------ +----------------------AGGTGATCCA----GCCGCAGGTTCCCCTACGGCTACC +TTGTTACGACTTCTCCCCCCTTGGGAGGGGGGAGTTCGACCTGGCCCCC----CGGGTTT +CCCCGGGAGACCAGGCCTCAC---TCCCCCCTCCCTCGGGTGGAGCGACGGGCGGTGTGT +GCAAGGAGCAGGGA--CG---TATTC--ACCGC-GCGATGATGACGCGCGGTTACTAGGG +ATTCCACGTTCACGAGGG-CGAGTT------------------GCAGCCCTCGATCCCAA +CTGCGGCGGGGTTTGAGGGATTGCCTCCCCCTTAC-GGGGTCGGATCCCGCTGTCCCCGC +CATTGTAGCCC---------------GCGTGTAGCCCGGGGGATT-----CGGGGCATGC +TGAC-------------------------------------------------------- +---------------------------------------------CTGCCGTGGCCCCCT +CCTTCCTCCGCCTTATACGGCGGCAGTCCCCCTAGTGTG-CCCC-GG--AGCCGGAGCTC +CGGGTAGCAACTAGGGGCGGGGGT-CTCGCTCGTTGC------------CGGACTTAACC +GGACACCTCACGG----CACGAGCTGGCGACGGCCATGCACCTCCTCTCAGCGCG----- +-TCGGGCAA--------------------------------------------------- +------------------------------------------------------------ +---------------------------GGCCGTTAGCCTGGCCGTCATC-CTGCTG---- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------TCGCCCCCGGTGAGG------------TTCCCGG +CGTTGACTCCAATTAAACCG--CAGGCTCCACC---CCTTGTGGTGCTCCCCCGC----- +-------------------CAATTCCTTTAAGTTTCAGCCTTGCGGCCGTACTCCCCAG- +-GCGGCGGGCTTAACGGCTTCCCTGCGGCACTGGGCGGGCTCT-AA-G-CCCGCCCAACA +CCTAGCCCGCATCGT---------------TTACAGCCGGGACTACCCGGGTATCTAATC +CGGTTCGCTCCCCC------------------GGCTTTCGCCCCTCACCGTCG------- +----------------GGCGCGTTCCAGCCGAGCGCCTTCGCCACTGGTGGTCCTCCCGG +GATTATAGGATTTCGCCCCTAC-----------C------------------CCGGGAGT +ACCCTCGGCCTCTCCCGCCCCCTAGCCTGGCAGTTTCCCCTCCAGTC-C-CCGGGTTGAG +CCCGGGGATTTAGGAGGGGACTTG-CCAGGCCGGCTACGG------GCGCTTTAGGCCCA +ATAATCGTCCCGA----CCACTCGCGGGGCTGGTATTACCGCGGCGGCTGACACCAGTCT +TGCCCCCCGCTTATTCCCCC---------------------------------------- +------------------------------------------------------------ +-----GCCTTCTTACAGCGG-GGAAAAGCCCC------CT-AATTAGGGGGCACTCGGGG +TGACCCCGTCACGGTTGCCCGCAT--TGCGGAGGTTTCGCGCCTGGTGCACCCCGTAGGG +CCTGGGCCCTTGTCT--CAGTGCCCATCTG----GGGGC-----TCCCGCTCTCA-CGGC +CCCTACCCGTTATCGGCTTGGCGGGCCGTTACCCCGCCAACTACCTG-ATGGGCCGCAGC +CCCATCCTCGGGCTGCGCGGCGGCGATAACCCCCGCCGCA--CCC--TTTCGGGGAGGAA +CCCTTCCAGGCGTCCT---CCCCTATGG-GGGATTAGCACC-A--GTTTCCC---GG-TG +TTATCCCCCTCCCGAGGGTAGGTTAGCCACGTGTTACTCAGCCGTCCGCCACGCTCCGCA +GCGG----------CGGAGCGTACGACTCCCATGGCTTAGCCCCACCCCGATAGCGGTCG +GGTCCGGCAGGATCAACCGGAGTT------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------- +>RS_GCF_000970205.1~NZ_CP009512.1-#2 +------------------------------------------------------------ +------------------------------------------------------------ +---------------------GAGGTGATCCA----GCCGCAGATTCCCCTACGGCTACC +TTGTTACGACTTAACCCCCCTTGCAAAGCACAGGTTCGAACACGGCAC-G---------- +----A-AGTCCGTGCCCTCAC---CCATACCTCACTCGGGTGGTTTGACGGGCGGTGTGT +GCAAGGAGCAGGGA--CG---TATTC--ACCGC-GCTATATTGAAACGCGATTACTACGG +ATTCCAGCTTCACGA-GGGCGAGTT------------------ACAGCCCTCGATCCGAA +CTACGAATGGGTTTGTGAGATTAC-CAGCCCTTTTCAGGGGAGGGACCCATTGTCCCATC +CATTGTAGCCC---------------GCGTGTAGCCCGGGAGATT-----CGGGGCATAC +TGAC-------------------------------------------------------- +---------------------------------------------CTACCGTGGCCCGCA +CCTTCCTCCGATTTAACATCGGCGGTCCCCACAGAGTACCCATCGTCCC----GGAGGAC +ATGCTGGTAACAGTGGGCACGGGT-CTCGCTCGTTGC------------CTGACTTAACA +GGATGCTTCACAG----TACGAACTGGCGACGGCCATGCACCTCCTCTCAGCGAT----- +-TCAGGCAA--------------------------------------------------- +------------------------------------------------------------ +---------------------------AGTCTTCAGCTTGGCCTACATA-TTGCTG---- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------TCGCCCCCGGTGAGT------------TGTCCGG +CGTTGAGTCCAATTAAACCG--CAGGCTCCACC---CGTTGTTGTGCTCCCCCGC----- +-------------------CAATTCCTTTAAGTTTCAGCCTTGCGGCCGTACTTCCCAG- +-GTGGCTCGCTTCACGGCTTCCCTGCGGCACCAGACACGGTCG-CG-C-CATGCCTGACA +CCTAGCGAGCATCGT---------------TTACGGCTGGGACTACCCGGGTATCTAATC +CGGTTCGTGCCCCC------------------AGCTTTCGTCCCTCACCGTCG------- +----------------AACCCGTTCTGGTAAGACGCCTTCGCCACAGGTGGTCCCACAGG +GATTACAAGATTTCACTCCTAC-----------C------------------CCTGTAGT +ACCTCTTACCTCTCCCGGTTCCAAGTCTGGCAGTATCCCCCGAAAGCCT-AATAGTTGAG +CTATCAGATTTCCCGGAGGACTGA-CCAAACCGGCTACGG------ACCCTTTAGACCCA +ATAATCACGATCA----CCACTCGGGCCGCCGGTGTTACCGCGGCGGCTGGCACCGGTCT +TGCCCGGCCCTTGCTAACGG---------------------------------------- +------------------------------------------------------------ +-----ATGTATTTTACACATCCGGACAGCCA------GCATATGATGCTGGCACTCGGTG +TCCCCTTATCACGGTTTCCCGCAT--TGTAAAGTTTTCGCGCCTGCTGCGCCCCGTAGGG +CCTGGATTCATGTCT--CAGAATCCATCTC----CGGGC-----TCTTGCTCTCA-CAAC +CCGTACCCGTCGCTGGCTAGTAGGTACATTACACCCACTACTAC-CTGATAGGCCGCAGA +CCCATCCTTGGGCAGACGAATCCTT-------------------T--T--GACGCATAAA +GCATTCCAGCAAATAT---GCGTTATCC-GGAATTATCCCC-A--GTTTCCC---GG-GG +TTATGCCGGTCCCAAGGGCAGGTTATCCACGTGTTACTGAGCAGTACGCCATGTATT--- +---------------GCTACATATGACTCGCATGGCTTAGGCGAACACCGATAGCAGTAA +CCTCTGGCAGGATCAACCAGAATT------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------- +>RS_GCF_000302455.1~NZ_AMPO01000020.1 +-CCGTTTGATCCTGGCGGAGGCCAC-----TGCTATTGGGTTTCGATTAAGCCATGCAAG +TCGTACGATCCT------------------------------------------------ +-----------------------------------TTC----GGGGTCGTGGCATACGGC +TCAGTAACACGTGGATAACCTACCCTTAGGACTGGGATAA-------------------- +CCCCGGGAAACTGGGGACAAT---ACCGGATATGTAGAGTTGCCTGGAATTGGTACTCTA +TTGAAA-------------------T-GTATTCGTGCGCCTAAGGATGGATCTGCGGCAG +AT-TAGG----TAGTTGGCGGGGTA---------AATGCCCACCAAGCCAGTAATCTGTA +CGGG------TTGTGAGAG-CAAG-AGCCCGGAGATGGAACCTGAGACAAGGTTCCAGGC +C-CTACGGGGCGCAGCAG--------GCGCGAAACCTCCGCAATG-----CACGAAAGTG +CGACGGGGGAAACCCAAGTGCCACTCTTAACG--GG----GTGGCTTTTCTTAAGTGTA- +--------AAAAG-------CTTTTGGAATAAGA-GCTGG-------GC-AAGACCGGTG +C----------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------CAGCCGCCGCGGTAACACCGGC---------AGC-TCAA-- +-GTG--GTGGCCATTTTTATTGGGCCTAAAGCGTTCGTAGCCGGTTTGATAAGTCTCTGG +TG---AAATCTCA--CGGCTTAACCGTGAGAATTGCTGGAGAT------A--CTATTAGG +C-TTGAGGCC--GGGAGAGGTTAGCGGTACTCCCAGGGTAGGGGTGAAATCCTA------ +------------------------------------------TAATCCTGGGAGGACC-- +-ACCTGTGGCGAAGGCGGCTAACTGGAACGGACCTGACGGTGAGTA--------ACGAAA +GCCAGG-GGCG------------------CGAACCGGATTAGATACCCGGGTAGTCCTGG +CCGTAAACGATGTGGA---CTTGGTGTTG---GGATGGC--------------------- +------------------------------------------------------------ +---------------------------------TCCGAGCTGCCC-CAGTGCCGAAGGGA +AGCTGTTAAGTCCACC-------GCCTGGGAAGTACG-GTCGCAAGACTGAAACTTAAAG +G------AATTGGCGGGGGAG----CACCACAACGCGTGGAGCCT-GCGGTTTAATTGGA +TTCAACGCCGGACATC-TCACCAGGGGCGACAGCAGAATGATAGCCAGG----------- +------------------------------------------------------------ +--------------------------------------TTG-------AT---------- +-------GACCTTGCTTGAC----AAGCTGAG--AG-GAGGTGCATGGC---------CG +CCGTCAGCTCGTACCGTGAGGCGT--CCTGTTAAGTCAGGC-------AACGAGCGAGAC +-CCACGCCCTT-AGTTACCAGCGGATCCTT-T--GGGAT-G-CCGGGCACACTAAGGGGA +CCGCCAGTGATAA---ACTGGAGGAAGGAGTGGACGACGGTAGGTCCGTATGCCCCGAAT +C---CCCTGGGCTACACGCGGGCTACAATGGCTAGGACA---ATGG---------G-TTC +CGACACTGAA-AAGTGAAGGTAATCTCCTAAACCTAGCCTT-A--GTTCGGATTGAGGGC +TGTAACTCGCCCTCATGA-AGCTGGAATGCGTAGTAATCGCGTGTCATA-ACCG------ +----------------------------CGCGGTGAATACGTCCCTGCTCCTTGCACACA +CCGCCCGTCACGCCACCCAAAAAGGGTTTGGATGAGGCCATAGTCTTT------------ +--G--------------TTGGTTATGGTCGAATCTGGGTTCTTTGAGGAGGGCGAAGTCG +TAACAAGGTAGCCGTAG---GGGAACCTGCGGCTGGATCACCTCCTT------------- +------------------------------------------------------------ +------------------- +>RS_GCF_000993805.1~NZ_CP009961.1 +TCCGGTTGATCCTGCCGGACCCGAC-----TGCTATCAGGGTGGGGCTAACCCATGGAAG +TCTAGGAGCCGGG----------------------------------------------- +---------------------------------GC--TACGGCCGGCTCCGGCGGACGGC +TCAGTAGCACGTGGCTAACCTACCCTCGGGAGGGGGATAA-------------------- +CCCCGGGAAACTGGGGCTAAT---CCCCCATAGGCGCAGACTCCTGGAATGGGTCCGCGC +CGAAAAGGCTGCAACGCCAT-GCCCG---TTGCAGCCGCCCGAGGATGGGGCTGCGCCCC +AT-CAGG----TAGTTGGCGGGGTA---------ACGGCCCGCCAAGCCGATAACGGGTG +GGGG------CCGTGAGAG-CGGG-AGCCCCGAGATGGGCACTGAGACAAGGGCCCAGGC +C-CTACGGGGCGCACCAG--------GGGCGAAACTTCCGCAATG-----CGGGAAACCG +TGACGGAGCCACCCTGAGTGCCACCCGATGAGGG------TGGCTTTTGCCCGGTCTAA- +--------A-AAG-------CCGGGCGAATAAGC-GGGG--------GGCAAGCCTGGTG +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------TCAGCCGCCGCGGTAATACCAGC---------CCC-GCGA-- +-GTG--GTCGGGACGATTATTGGGCCTAAAGCGTCCGTAGCCGGCCCGGCAAGTCCCCCT +TT---AAAGCCCA--CGGCTCAACCG--TGGGAGCGGGGGGAT------A--CTGTCGGG +C-TAGGGGGC--GGGAGAGGCCGGGGGTACTCCTGGGGTAGGGGCGAAATCCTA------ +------------------------------------------TAATCCCAGGAGGACC-- +-ACCAGTGGCGAAGGCGCCCGGCTGGAACGCGCCCGACGGTGAGGG--------ACGAAA +GCTGGG-GGAG------------------CAAAGGGGATTAGATACCCCCGTAGTCCCAG +CTGTAAACGATGCGGG---CTAGGTGTTG---GGTGGG----------CCTCGAGCCCGC +CCAGTGTCGT---------------------AGGGAAGCCGTTAAGCCCGCCGC-CTGGG +GAGTACGGCCGCAAGGCTGAAA----------CTTAAAGGAATTG-GCGGGGGAGC---- +------------------------------------------------------------ +--------------------------ACCACAAGGGGTGAAGCTT-GCGGTTTAATTGGA +GTCAACGCCGGAAACC-TCACCGGGGGCGACAGCAGGATGAAGGCCAGG----------- +------------------------------------------------------------ +--------------------------------------CTA-------AC---------- +-------GACCTTGCCAGAC----GAGCTGAG--AG-GAGGTGCATGGC---------CG +TCGCCGGCTCGTGCCGTGAGGTGT--CCTGTTAAGTCAGGG-------AACGAGCGAGAC +-CCCCGCCCCT-AGTTGCAACCCAGCCTTT-CGGGGCTG-G-GG--CACTCTAGGGGGAC +TGCCGGCGA-TAA---GCCGGAGGAAGGTGGGGGCTACGGCAGGTCAGTATGCCCCGAAA +C---CCCCGGGCTACACGCGAGCTGCAATGGCGGGGACA---GCGG---------G-CTC +CG-ACCCCGAAAGGGGAAGGAAATCCCGTAAACCCCGCCTC-A--GTAGGAATCGAGGGC +TGCAACTCGCCCTCGTGA-ACGTGGAATCCCTAGTAACCGCGTGTCACC-AACG------ +----------------------------CGCGGTGAATACGTCCCTGCTCCTTGCACACA +CCGCCCGTCGCTCCACCCGAGGGAGGCCCAGGTGAGGCCTCTCGCCGAAAG--------- +-------------------GTGGGAGGTCGAATCTGGGCCTCCCAAGGGGGGAGAAGTCG +TAACAAGGTGGCCGTAG---GGGAACCTGCGGCCGGATCACCTCCTT------------- +------------------------------------------------------------ +------------------- diff --git a/recipes/sativa/taxonomy.tsv b/recipes/sativa/taxonomy.tsv new file mode 100644 index 0000000000000..349a7c83c9d8d --- /dev/null +++ b/recipes/sativa/taxonomy.tsv @@ -0,0 +1,5 @@ +RS_GCF_000019605.1~NC_010482.1 d__Archaea;p__Crenarchaeota;c__Korarchaeia;o__Korarchaeales;f__Korarchaeaceae;g__Korarchaeum;s__Korarchaeum +RS_GCF_000092465.1~NC_014205.1 d__Archaea;p__Crenarchaeota;c__Thermoprotei;o__Desulfurococcales;f__Desulfurococcaceae;g__Staphylothermus;s__Staphylothermus +RS_GCF_000970205.1~NZ_CP009512.1-#2 d__Archaea;p__Halobacterota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina;s__Methanosarcina +RS_GCF_000302455.1~NZ_AMPO01000020.1 d__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium;s__Methanobacterium +RS_GCF_000993805.1~NZ_CP009961.1 d__Archaea;p__Crenarchaeota;c__Thermoprotei;o__Thermofilales;f__Thermofilaceae;g__Thermofilum_A;s__Thermofilum_A From e3c687af7d2915990ed5e6a3d1b8a32756214195 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Wed, 27 Dec 2023 09:04:17 +0100 Subject: [PATCH 002/121] Update meta.yaml with new Sativa release --- recipes/sativa/meta.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/recipes/sativa/meta.yaml b/recipes/sativa/meta.yaml index 181e24c1630be..706277f3fbd73 100644 --- a/recipes/sativa/meta.yaml +++ b/recipes/sativa/meta.yaml @@ -1,14 +1,13 @@ {% set name = "sativa" %} -{% set version = "0.9.1" %} +{% set version = "0.9.2" %} package: name: {{ name|lower }} version: {{ version }} source: - #url: https://github.com/amkozlov/sativa/archive/refs/tags/v{{ version }}.zip - #sha256: 14b772c7e1bc242655e1876e7492fd8d50d363058236bdf513aa5afca7d94841 - git_url: https://github.com/amkozlov/sativa + url: https://github.com/amkozlov/sativa/archive/refs/tags/v{{ version }}.zip + sha256: e1ba4a89937dad23115575c0f6d185527ad1bb062b3fdd313a151492c21a6e2b build: number: 2 From 78eb08d216dfa845c5a9278147e4036659ef968d Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Wed, 27 Dec 2023 11:28:33 +0100 Subject: [PATCH 003/121] Linting --- recipes/sativa/gpl_license | 674 +++++++++++++++++++++++++++++++++++++ recipes/sativa/meta.yaml | 5 +- 2 files changed, 678 insertions(+), 1 deletion(-) create mode 100644 recipes/sativa/gpl_license diff --git a/recipes/sativa/gpl_license b/recipes/sativa/gpl_license new file mode 100644 index 0000000000000..818433ecc0e09 --- /dev/null +++ b/recipes/sativa/gpl_license @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/sativa/meta.yaml b/recipes/sativa/meta.yaml index 706277f3fbd73..45f3caa97d650 100644 --- a/recipes/sativa/meta.yaml +++ b/recipes/sativa/meta.yaml @@ -10,7 +10,9 @@ source: sha256: e1ba4a89937dad23115575c0f6d185527ad1bb062b3fdd313a151492c21a6e2b build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('sativa', max_pin="x.x") }} requirements: build: @@ -33,6 +35,7 @@ about: home: https://github.com/amkozlov/sativa license: GPL-3 license_family: GPL + license_file: gpl_license summary: "SATIVA Semi-Automatic Taxonomy Improvement and Validation Algorithm" extra: From afdc4c49ecf9d0b747c00b2299dd8fa1c375987c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 27 Dec 2023 05:46:14 -0500 Subject: [PATCH 004/121] Update keggcharter to 1.0.2 (#44992) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update keggcharter to 1.0.2 * Update meta.yaml Now put all TXTs and TSVs from "resources" folder into "share" folder. --------- Co-authored-by: João Sequeira --- recipes/keggcharter/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/keggcharter/meta.yaml b/recipes/keggcharter/meta.yaml index 939febdb892e0..b4284f829e7c1 100644 --- a/recipes/keggcharter/meta.yaml +++ b/recipes/keggcharter/meta.yaml @@ -1,6 +1,6 @@ {% set name = "keggcharter" %} -{% set version = "1.0.1" %} -{% set sha256 = "39e79c226a61ede80a1a95819293fde8fe69b1c2f0dc4713c6262db9b1fad4e2" %} +{% set version = "1.0.2" %} +{% set sha256 = "605795641af04a7045cc92b6f37ee0b0c0b8e508b85fb70bcc6c00234b9d5d89" %} package: name: {{ name|lower }} @@ -16,7 +16,7 @@ build: script: > mkdir -p $PREFIX/bin && mkdir -p $PREFIX/share && - cp *.py resources/KEGGCharter_prokaryotic_maps.txt $PREFIX/share && + cp *.py resources/*.txt resources/*.tsv $PREFIX/share && chmod +x $PREFIX/share/keggcharter.py && ln -s $PREFIX/share/keggcharter.py $PREFIX/bin/keggcharter run_exports: From 7c3d1d142d3d7919ff4d90ea89662f58e13f57a9 Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Wed, 27 Dec 2023 16:34:18 +0100 Subject: [PATCH 005/121] Update hictk to v0.0.5 (#44988) * Update conanfile.txt.patch * Bump version --- recipes/hictk/conanfile.txt.patch | 8 ++++---- recipes/hictk/meta.yaml | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/hictk/conanfile.txt.patch b/recipes/hictk/conanfile.txt.patch index 096e64e4b8187..05ea419f8ae85 100644 --- a/recipes/hictk/conanfile.txt.patch +++ b/recipes/hictk/conanfile.txt.patch @@ -1,5 +1,5 @@ diff --git a/conanfile.txt b/conanfile.txt -index 420c5b7..eb94f2c 100644 +index 0ea6184..eb94f2c 100644 --- a/conanfile.txt +++ b/conanfile.txt @@ -3,72 +3,11 @@ @@ -10,10 +10,10 @@ index 420c5b7..eb94f2c 100644 bshoshany-thread-pool/3.5.0#5aaea7ccf37107d3c1ba9ca9ab246e42 -cli11/2.3.2#1424b9b1d9e3682a7122f415b078b4d7 -eigen/3.4.0#2e192482a8acff96fe34766adca2b24c --fast_float/5.3.0#efd9bda97d5f77fa5a98981e014092a0 +-fast_float/6.0.0#6c8a953c57879453982a6ce69c0ba87c -fmt/10.1.1#cd63809a79574a2f9eb73ca35f16a243 --hdf5/1.14.2#1e12ccecd5ebc9b5191433862e196743 --highfive/2.8.0#19e1a6e78d9329851aa9da409f07d29a +-hdf5/1.14.3#31ccd8d4de83844f5db48471df1944a1 +-highfive/2.8.0#b1de99f678ff5699cce6fb5fcac44d2d -libdeflate/1.19#3ea74a4549efc14d4b1202dc4bfbf602 parallel-hashmap/1.3.11#1e67f4855a3f7cdeb977cc472113baf7 readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83 diff --git a/recipes/hictk/meta.yaml b/recipes/hictk/meta.yaml index 821f6aaed942b..02e7110847842 100644 --- a/recipes/hictk/meta.yaml +++ b/recipes/hictk/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hictk" %} -{% set version = "0.0.4" %} -{% set sha256 = "19f9b17f76e27603179abb946edbcf3447a813d08d143a9f42c46d99a309614b" %} +{% set version = "0.0.5" %} +{% set sha256 = "12a784bfb83e64c99c2fb36839bdcb2c4a579688dced1e342df8eb6da7c8506d" %} package: name: {{ name|lower }} From cd49b724f3a6464ce40723ccd9cbe948016a8461 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 27 Dec 2023 11:38:59 -0500 Subject: [PATCH 006/121] Update perl-minion to 10.28 (#44495) --- recipes/perl-minion/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/perl-minion/meta.yaml b/recipes/perl-minion/meta.yaml index bca6af67b1818..87a845511735d 100644 --- a/recipes/perl-minion/meta.yaml +++ b/recipes/perl-minion/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-minion" %} -{% set version = "10.27" %} -{% set sha256 = "c8c5c64d4b3ac8359ed78227b47992bd6ccc3496110849cef228191f895ceb54" %} +{% set version = "10.28" %} +{% set sha256 = "0bd774d2f42b36a5e1293cd3d5241ed35f45eb041599498e28d6f00f6ae910d5" %} package: name: {{ name }} From 8a45c4e1bd2736b67259bb2639e3f7223f51de2d Mon Sep 17 00:00:00 2001 From: DrYak Date: Wed, 27 Dec 2023 17:42:47 +0100 Subject: [PATCH 007/121] bugfix: strand deprecated and removed in BioPython 1.82 (#44987) - see: https://github.com/chapmanb/bcbb/issues/138 --- recipes/bcbio-gff/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/bcbio-gff/meta.yaml b/recipes/bcbio-gff/meta.yaml index 90f1c2105a763..ff55d1753cf3b 100644 --- a/recipes/bcbio-gff/meta.yaml +++ b/recipes/bcbio-gff/meta.yaml @@ -10,8 +10,10 @@ source: sha256: f7b3922ee274106f8716703f41f05a1795aa9d73e903f4e481995ed8f5f65d2d build: - number: 0 + number: 1 noarch: python + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x.x") }} script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" requirements: @@ -21,7 +23,8 @@ requirements: run: - python - six - - biopython + # see: https://github.com/chapmanb/bcbb/issues/138 + - biopython <=1.81 - bx-python test: From 22ed0a7f7928aa1a7f6c686bf9a3bf7bcf7a5ebc Mon Sep 17 00:00:00 2001 From: DrYak Date: Wed, 27 Dec 2023 17:47:26 +0100 Subject: [PATCH 008/121] bugfix: breaking API change between ruamel.yaml 0.17.x and 0.18 (#44989) --- recipes/lollipop/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/lollipop/meta.yaml b/recipes/lollipop/meta.yaml index 89f213a8aeaa8..5680df67393eb 100644 --- a/recipes/lollipop/meta.yaml +++ b/recipes/lollipop/meta.yaml @@ -12,7 +12,9 @@ source: build: noarch: python - number: 0 + number: 1 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x.x") }} script: - {{ PYTHON }} -m pip install '.[cli]' --ignore-installed --no-deps -v - mkdir -p ${PREFIX}/share/{{ name }}/presets @@ -30,7 +32,8 @@ requirements: - scipy - pandas - zstandard - - ruamel.yaml + # NOTE: change of API between ruamel.yaml 0.17.x and 0.18 + - ruamel.yaml <0.18 - strictyaml - tqdm - click From f93dc7b5223292c24af657742fbb16626ff96b9f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 27 Dec 2023 20:23:24 -0500 Subject: [PATCH 009/121] Update tsebra to 1.1.2.2 (#45000) --- recipes/tsebra/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tsebra/meta.yaml b/recipes/tsebra/meta.yaml index 35064ac4f90c6..d0c23407dc092 100644 --- a/recipes/tsebra/meta.yaml +++ b/recipes/tsebra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.1.2.1" %} +{% set version = "1.1.2.2" %} {% set name = "tsebra" %} -{% set sha256 = "66133f393bfe22ff5b113770175f358e8e4aa897fa865296707aee956b2ce560" %} +{% set sha256 = "e055efea29d3b73a6202c56fb9256bf6006005ef54c8a5de83b9aa0377fff27c" %} package: name: "{{ name }}" From 0eb5993ded4843411916af73ee2d0235386dc479 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 27 Dec 2023 20:23:46 -0500 Subject: [PATCH 010/121] Update sylph to 0.5.1 (#45001) --- recipes/sylph/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sylph/meta.yaml b/recipes/sylph/meta.yaml index c47e58e9a61e1..c83ec07b1e0fd 100644 --- a/recipes/sylph/meta.yaml +++ b/recipes/sylph/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.0" %} +{% set version = "0.5.1" %} package: name: sylph @@ -11,7 +11,7 @@ build: source: url: https://github.com/bluenote-1577/sylph/archive/v{{ version }}.tar.gz - sha256: dfa7859281aa0aabf01e0362c7016679024b8ab5f112bef12f7cffbb0b3dc1fc + sha256: 300b0f4ae77e25c28a05fd2f5323c112003a13111130f136d7d4bf4ded90e10c requirements: build: From 6d62909600750679877cf65f0cf315fbc8d4541a Mon Sep 17 00:00:00 2001 From: TPOB <19909103+TTTPOB@users.noreply.github.com> Date: Thu, 28 Dec 2023 09:25:10 +0800 Subject: [PATCH 011/121] add r-misha 3.7.0 (history version) (#44981) * add misha version 3.7.0 (history version) * fix hash * fix compiler settings * use template variable to specify name * add run_export to lock version --- recipes/r-misha/3.7.0/build.sh | 2 ++ recipes/r-misha/3.7.0/meta.yaml | 45 +++++++++++++++++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 recipes/r-misha/3.7.0/build.sh create mode 100644 recipes/r-misha/3.7.0/meta.yaml diff --git a/recipes/r-misha/3.7.0/build.sh b/recipes/r-misha/3.7.0/build.sh new file mode 100644 index 0000000000000..937ed18ca8d4d --- /dev/null +++ b/recipes/r-misha/3.7.0/build.sh @@ -0,0 +1,2 @@ +sed -i 's/CC=g++/CC=\$(CXX)/' src/Makefile +$R CMD INSTALL --build . diff --git a/recipes/r-misha/3.7.0/meta.yaml b/recipes/r-misha/3.7.0/meta.yaml new file mode 100644 index 0000000000000..29c2d9b973b1c --- /dev/null +++ b/recipes/r-misha/3.7.0/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "3.7.0" %} +{% set name = "r-misha" %} +{% set commit = "fb45473ac27833154724bac04136c601e7b2a6f0" %} + +package: + name: "{{ name|lower }}" + version: '{{ version }}' + +source: + url: 'https://github.com/tanaylab/misha/archive/{{ commit }}.zip' + sha256: a27885729422368972734cf7a657a0a4f8abada8aa5728cb9a4ac745f3184d5a + +build: + # https://github.com/tanaylab/misha/issues/9 + skip: True # [osx] + number: 0 + rpaths: + - lib/R/lib + - lib/ + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - sed + host: + - r-base + - r-devtools + run: + - r-base + +test: + commands: + - '$R -e "library(misha)"' + +about: + home: 'https://tanaylab.github.io/misha/index.html' + license: GPL-2 + summary: 'Toolkit for analysis of genomic data' + +extra: + maintainers: + - Misha Hoichman From 8398ee4a20614a535161a600e6931b2c49490f0a Mon Sep 17 00:00:00 2001 From: TPOB <19909103+TTTPOB@users.noreply.github.com> Date: Thu, 28 Dec 2023 09:56:44 +0800 Subject: [PATCH 012/121] add r-misha 3.7.1 (history version) (#44984) * add r-misha 3.7.1 (history version) * fix: incorrect commit and hash --- recipes/r-misha/3.7.1/build.sh | 2 ++ recipes/r-misha/3.7.1/meta.yaml | 45 +++++++++++++++++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 recipes/r-misha/3.7.1/build.sh create mode 100644 recipes/r-misha/3.7.1/meta.yaml diff --git a/recipes/r-misha/3.7.1/build.sh b/recipes/r-misha/3.7.1/build.sh new file mode 100644 index 0000000000000..937ed18ca8d4d --- /dev/null +++ b/recipes/r-misha/3.7.1/build.sh @@ -0,0 +1,2 @@ +sed -i 's/CC=g++/CC=\$(CXX)/' src/Makefile +$R CMD INSTALL --build . diff --git a/recipes/r-misha/3.7.1/meta.yaml b/recipes/r-misha/3.7.1/meta.yaml new file mode 100644 index 0000000000000..1a4b49c1cc2ec --- /dev/null +++ b/recipes/r-misha/3.7.1/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "3.7.1" %} +{% set name = "r-misha" %} +{% set commit = "eaf2e6122166f95b176c2c9746ef1505791683ef" %} + +package: + name: "{{ name|lower }}" + version: '{{ version }}' + +source: + url: 'https://github.com/tanaylab/misha/archive/{{ commit }}.zip' + sha256: 443b9ab461c36ff4da0f75868f7ac362ce3fff786574516d131ac6ddc671c4f1 + +build: + # https://github.com/tanaylab/misha/issues/9 + skip: True # [osx] + number: 0 + rpaths: + - lib/R/lib + - lib/ + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - sed + host: + - r-base + - r-devtools + run: + - r-base + +test: + commands: + - '$R -e "library(misha)"' + +about: + home: 'https://tanaylab.github.io/misha/index.html' + license: GPL-2 + summary: 'Toolkit for analysis of genomic data' + +extra: + maintainers: + - Misha Hoichman From 3601f8a92c185f44944cd68eb1d5c01d2a3306db Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Dec 2023 11:59:20 -0500 Subject: [PATCH 013/121] Update viguno to 0.2.0 (#44996) * Update viguno to 0.2.0 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/viguno/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/viguno/meta.yaml b/recipes/viguno/meta.yaml index 070e91018abd5..aee151869b737 100644 --- a/recipes/viguno/meta.yaml +++ b/recipes/viguno/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.1.6" %} -{% set sha256 = "c4696ba9dab271216b80c560f78cddf8e0010474b7d7b8b6c717e666fd13cebd" %} +{% set version = "0.2.0" %} +{% set sha256 = "a4217f7ba34d55cda76b392e774be8392c18d550e752eb9db81e6cc3afa53010" %} package: name: viguno @@ -8,6 +8,8 @@ package: build: skip: True # [osx] number: 0 + run_exports: + - {{ pin_subpackage("viguno", max_pin="x.x") }} source: url: https://github.com/bihealth/viguno/archive/v{{ version }}.tar.gz From af3c532f0079cb409710d74681c9727cd6824a17 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Dec 2023 12:59:59 -0500 Subject: [PATCH 014/121] Update annonars to 0.32.0 (#45013) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 6a78e3c350db0..7cd859e346249 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.31.2" %} +{% set version = "0.32.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: c7d953633d77c3c46cf3d9417e9b8e6d67afac2a529dea0e342da3d8bb0d6680 + sha256: 467ebd15737c4a6451f5993fa1e93f52c5ecb4a1cdf0b0cd754b414261730f37 requirements: build: From d54b085a409620dd605392c65d3bc61c2e31c693 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=A3o=20Sequeira?= Date: Fri, 29 Dec 2023 01:30:44 +0000 Subject: [PATCH 015/121] Fix recognizer (#45012) * Update recognizer to 1.10.0 * Update meta.yaml No more build.sh file * Update meta.yaml Forgot about the other TSV files * Removed build.sh --------- Co-authored-by: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> --- recipes/recognizer/build.sh | 7 ------- recipes/recognizer/meta.yaml | 10 ++++++++-- 2 files changed, 8 insertions(+), 9 deletions(-) delete mode 100644 recipes/recognizer/build.sh diff --git a/recipes/recognizer/build.sh b/recipes/recognizer/build.sh deleted file mode 100644 index 96dd646713b92..0000000000000 --- a/recipes/recognizer/build.sh +++ /dev/null @@ -1,7 +0,0 @@ -dir="${PREFIX}/share" -mkdir -p "${dir}" -mkdir -p "${PREFIX}/bin" -cp recognizer.py "${dir}" -cp -r resources/* "${dir}" -chmod +x "${dir}/recognizer.py" -ln -s "${dir}/recognizer.py" "${PREFIX}/bin/recognizer" diff --git a/recipes/recognizer/meta.yaml b/recipes/recognizer/meta.yaml index e894c66dab43d..c8acd63dc115b 100644 --- a/recipes/recognizer/meta.yaml +++ b/recipes/recognizer/meta.yaml @@ -1,6 +1,6 @@ {% set name = "recognizer" %} -{% set version = "1.9.4" %} -{% set sha256 = "36c3f08fff9c5eff6bf45491b3332eee44507d08f9839766b4fe81eeb8715630" %} +{% set version = "1.10.0" %} +{% set sha256 = "7f001a4fb888777a7b14707f76458f25fc98fe14299d1bdcbf2452eba7cab75f" %} package: name: {{ name|lower }} @@ -15,6 +15,12 @@ build: number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x") }} + script: > + mkdir -p $PREFIX/bin && + mkdir -p $PREFIX/share && + cp recognizer.py resources/*.tsv $PREFIX/share && + chmod +x $PREFIX/share/recognizer.py && + ln -s $PREFIX/share/recognizer.py $PREFIX/bin/recognizer requirements: run: From 0583b9828d498632d85d70bac0544ea2ca4a32e0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Dec 2023 20:31:52 -0500 Subject: [PATCH 016/121] Update last to 1522 (#45011) --- recipes/last/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index 2c8181378c734..673ba234ef336 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -1,5 +1,5 @@ {% set name = "LAST" %} -{% set version = "1521" %} +{% set version = "1522" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.zip - sha256: dcfe5339f048f635f02326d181e086469c16e54a0f674c5df814c4d54236fc26 + sha256: 0cc27dce53693c4d97864c012f9b9b34e4c02ebd0c38db23c5c5d978dbfd4d4e build: number: 0 From 4dc12ba8c03cdf92c3cf71972bfbdb64cf679b30 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Dec 2023 20:32:05 -0500 Subject: [PATCH 017/121] Update pcaone to 0.4.1 (#45009) --- recipes/pcaone/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pcaone/meta.yaml b/recipes/pcaone/meta.yaml index 636c605ed4401..3f67d9dbac7c4 100644 --- a/recipes/pcaone/meta.yaml +++ b/recipes/pcaone/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.4.0" %} -{% set sha256 = "b6bf45c20dddcc42811dcc902c7d92c5901d03fb4c69675ee8da39b3c92763a9" %} +{% set version = "0.4.1" %} +{% set sha256 = "03f8afa9870507e03aa90a349a00f70f56bbf202b05a4d3d648148f3c30b6518" %} package: From ba88f9e31018d29dd8004c59ede0090c7fedbf96 Mon Sep 17 00:00:00 2001 From: stuber Date: Thu, 28 Dec 2023 18:32:36 -0700 Subject: [PATCH 018/121] genoflu version 1.02 (#44995) * genoflu version 1.02 * Update meta.yaml * Update meta.yaml * https://spdx.org/licenses/GPL-3.0-or-later.html --------- Co-authored-by: Thanh Lee --- recipes/genoflu/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/genoflu/meta.yaml b/recipes/genoflu/meta.yaml index 9b8cdc7c00314..c7e66039d4536 100644 --- a/recipes/genoflu/meta.yaml +++ b/recipes/genoflu/meta.yaml @@ -1,8 +1,8 @@ {% set user = "USDA-VS" %} {% set name = "GenoFLU" %} -{% set version = "1.01" %} -{% set sha256 = "c97ad073c2cf14f1c14f1a705ddc3817189c30f03239ba97b068a1ddab90ceb8" %} +{% set version = "1.02" %} +{% set sha256 = "8cae43be805ee1822d6acc3d1d51a7c4445c5252b5004ab700b7f807fc78070d" %} package: name: {{ name|lower }} @@ -11,6 +11,8 @@ package: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('genoflu', max_pin="x") }} source: url: https://github.com/{{ user }}/{{ name }}/archive/{{ version }}.tar.gz @@ -30,7 +32,7 @@ test: about: home: https://github.com/{{ user }}/{{ name }} - license: GPL3 + license: GPL-3.0-or-later license_file: LICENSE summary: Influenza data pipeline to automate genotyping assignment. - dev_url: https://github.com/USDA-VS/GenoFLU \ No newline at end of file + dev_url: https://github.com/USDA-VS/GenoFLU From 3e747df44aec77e9d90a7201f77e471bc02678ee Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Dec 2023 05:58:17 -0500 Subject: [PATCH 019/121] Update chromhmm to 1.25 (#45016) * Update chromhmm to 1.25 * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/chromhmm/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/chromhmm/meta.yaml b/recipes/chromhmm/meta.yaml index 76da70b8016ab..22303f5fee131 100644 --- a/recipes/chromhmm/meta.yaml +++ b/recipes/chromhmm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ChromHMM" %} -{% set version = "1.24" %} +{% set version = "1.25" %} package: name: {{ name|lower }} @@ -8,10 +8,12 @@ package: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('chromhmm', max_pin=None) }} source: url: https://github.com/jernst98/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 84e14ebb78c197abe946007e72965296980339d4e3155604bf6c6734319af30c + sha256: 96b5773f7400835f16cc1d86d4e42e6dcc038e74569311cd73da2d5c5002a5d2 requirements: run: @@ -27,6 +29,7 @@ about: home: https://github.com/jernst98/ChromHMM license: GPLv3 summary: 'ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks.' + license_file: LICENSE extra: notes: 'ChromHMM comes with about 36MB of example data which is not included in the recipe. This recipe installs a script, "download_chromhmm_data.sh", which downloads the data in the proper location, and which can be run after ChromHMM has been installed.' From f5d6b554baf02a7f61b1e3e23d204d24f9ef6d6b Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Fri, 29 Dec 2023 23:42:46 +0900 Subject: [PATCH 020/121] Update ColabFold to 1.5.5 (#45008) * Update ColabFold to 1.5.4 * Use 1.5.5 instead, 1.5.4 had a bug * OpenMM 8.1 causes issues --- recipes/colabfold/fix-jax-04-nan.patch | 20 ------------------ recipes/colabfold/meta.yaml | 28 +++++++++++--------------- 2 files changed, 12 insertions(+), 36 deletions(-) delete mode 100644 recipes/colabfold/fix-jax-04-nan.patch diff --git a/recipes/colabfold/fix-jax-04-nan.patch b/recipes/colabfold/fix-jax-04-nan.patch deleted file mode 100644 index 9065fc61d3154..0000000000000 --- a/recipes/colabfold/fix-jax-04-nan.patch +++ /dev/null @@ -1,20 +0,0 @@ -diff --git a/alphafold/model/modules.py b/alphafold/model/modules.py -index 73f9cdd..4ca8827 100644 ---- a/alphafold/model/modules.py -+++ b/alphafold/model/modules.py -@@ -672,6 +672,7 @@ class Attention(hk.Module): - logits = jnp.einsum('bqhc,bkhc->bhqk', q, k) + bias - if nonbatched_bias is not None: - logits += jnp.expand_dims(nonbatched_bias, axis=0) -+ logits = jnp.clip(logits, -1e8, 1e8) - weights = jax.nn.softmax(logits) - weighted_avg = jnp.einsum('bhqk,bkhc->bqhc', weights, v) - -@@ -771,6 +772,7 @@ class GlobalAttention(hk.Module): - k = jnp.einsum('bka,ac->bkc', m_data, k_weights) - bias = (1e9 * (q_mask[:, None, :, 0] - 1.)) - logits = jnp.einsum('bhc,bkc->bhk', q, k) + bias -+ logits = jnp.clip(logits, -1e8, 1e8) - weights = jax.nn.softmax(logits) - weighted_avg = jnp.einsum('bhk,bkc->bhc', weights, v) - diff --git a/recipes/colabfold/meta.yaml b/recipes/colabfold/meta.yaml index 11697a3be4d8f..c8c5024145ad6 100644 --- a/recipes/colabfold/meta.yaml +++ b/recipes/colabfold/meta.yaml @@ -1,7 +1,7 @@ -{% set cf_version = "1.5.3" %} -{% set cf_hash = "1b2776f285981796559effbc3691ebbcfcde68514cc05559583ebab76c4c25e8" %} -{% set af_version = "2.3.5" %} -{% set af_hash = "6244c2143987dd4a6a87c1174c7a801c220034fbeb8d13f901b0f950b69d8543" %} +{% set cf_version = "1.5.5" %} +{% set cf_hash = "7fb0ad263c24ec00d46f2dff1611989234bc1351d71653dd06006f2c88f83dcb" %} +{% set af_version = "2.3.6" %} +{% set af_hash = "a5674257d92928511d70f94ec3261e275cb3442a7762b5210e01f445692d2182" %} package: name: colabfold @@ -14,7 +14,7 @@ build: python -m pip install --no-deps --ignore-installed alphafold/ run_exports: - {{ pin_subpackage('colabfold', max_pin="x") }} - number: 1 + number: 0 source: - url: https://github.com/sokrypton/ColabFold/archive/refs/tags/v{{ cf_version }}.tar.gz @@ -23,14 +23,12 @@ source: - url: https://github.com/steineggerlab/alphafold/archive/refs/tags/v{{ af_version }}.tar.gz sha256: {{ af_hash }} folder: alphafold - patches: - - fix-jax-04-nan.patch requirements: host: - pip - python - - poetry + - poetry-core >=1.0.0 run: - python - absl-py @@ -42,20 +40,18 @@ requirements: - pandas - appdirs - py3Dmol - - dm-haiku - dm-tree - ml-collections - - immutabledict - importlib-metadata - - biopython - - jax ==0.4.14 - - jaxlib ==0.4.14 - - chex ==0.1.8 - - tensorflow ==2.12.1=cpu* + - dm-haiku ==0.0.10 + - biopython <=1.82 + - jax >=0.4.14 + - jaxlib >=0.4.14 + - tensorflow >=2.12.1=cpu* - mmseqs2 >=15.6f452 - kalign2 >=2.04 - hhsuite >=3.3.0 - - openmm ==7.7.0 + - openmm >=7.7.0,<8.1.0 - pdbfixer test: From 005eb89ee7c931f84510f687702d098d36c201ea Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Dec 2023 10:32:41 -0500 Subject: [PATCH 021/121] Update expam to 1.2.2.4 (#45007) * Update expam to 1.2.2.4 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/expam/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/expam/meta.yaml b/recipes/expam/meta.yaml index a078e57679269..01df06215fcbd 100644 --- a/recipes/expam/meta.yaml +++ b/recipes/expam/meta.yaml @@ -1,5 +1,5 @@ {% set name = "expam" %} -{% set version = "1.2.2.3" %} +{% set version = "1.2.2.4" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 1a57cd160115ead399bd1b577dd071e0142d31e09df982c83c017e6ddfabcf96 + sha256: c33b249351c13fd3cfcbd0b2411a9d61e5e1e6239d5b841c2d980dcb9a88debc build: number: 0 skip: true # [py < 38] - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('expam', max_pin="x") }} requirements: build: From d73ebcc9107fe426e68b6bf94c67b4cd2b7bd656 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Dec 2023 10:35:33 -0500 Subject: [PATCH 022/121] Update upimapi to 1.13.1 (#45019) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: João Sequeira --- recipes/upimapi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/upimapi/meta.yaml b/recipes/upimapi/meta.yaml index 5ce94c96013c9..c146f7d09c704 100644 --- a/recipes/upimapi/meta.yaml +++ b/recipes/upimapi/meta.yaml @@ -1,6 +1,6 @@ {% set name = "upimapi" %} -{% set version = "1.13.0" %} -{% set sha256 = "0460d1f9485a05cab875521991feb43c4835b637e4955cba6e85abc9a01defe5" %} +{% set version = "1.13.1" %} +{% set sha256 = "72fd88f6c21b6982071c007e9ce9a92ffe2bbc75edff3f6eddcfb0653bced0d4" %} package: name: {{ name|lower }} From 08ddb43065f926d66d1a0530c9da0217c7a8aa87 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Fri, 29 Dec 2023 17:07:55 +0100 Subject: [PATCH 023/121] Update raptor (#44952) multiple binaries and a wrapper scripts depending on available instruction sets. --- recipes/raptor/build.sh | 47 +++++++++++++++++++++++++++++++++++----- recipes/raptor/meta.yaml | 2 +- recipes/raptor/raptor | 30 +++++++++++++++++++++++++ 3 files changed, 73 insertions(+), 6 deletions(-) create mode 100644 recipes/raptor/raptor diff --git a/recipes/raptor/build.sh b/recipes/raptor/build.sh index ae27ae77a6465..ea27c80c990bb 100644 --- a/recipes/raptor/build.sh +++ b/recipes/raptor/build.sh @@ -1,7 +1,44 @@ #!/bin/bash -mkdir -p build -cd build -cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="-mavx2 -D__STDC_FORMAT_MACROS" -DRAPTOR_NATIVE_BUILD=OFF -DCMAKE_INSTALL_PREFIX="${PREFIX}" -make -j"${CPU_COUNT}" -make install +set -eux + +get_instruction_set_flags() { + local instruction_set="$1" + case "${instruction_set}" in + none) + echo "" + ;; + sse2) + echo "-msse2" + ;; + sse4.2) + echo "-msse4.2" + ;; + avx2) + echo "-mavx2" + ;; + avx512) + echo "-mavx512f -mavx512bw" + ;; + *) + echo "Unknown instruction set: ${instruction_set}" >&2 + exit 1 + ;; + esac +} + +for INSTRUCTION_SET in "none" "sse2" "sse4.2" "avx2" "avx512"; do + mkdir -p build/${INSTRUCTION_SET} + cd build/${INSTRUCTION_SET} + cmake ../.. -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_CXX_FLAGS="$(get_instruction_set_flags ${INSTRUCTION_SET}) -Wno-interference-size -D__STDC_FORMAT_MACROS" \ + -DRAPTOR_NATIVE_BUILD=OFF \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" + make -j"${CPU_COUNT}" + make install + mv "${PREFIX}/bin/raptor" "${PREFIX}/bin/raptor_${INSTRUCTION_SET}" + cd ../.. +done + +cp "${RECIPE_DIR}/raptor" "${PREFIX}/bin/raptor" +chmod +x "${PREFIX}/bin/raptor" diff --git a/recipes/raptor/meta.yaml b/recipes/raptor/meta.yaml index 60599432442f1..0b38ef4ed151c 100644 --- a/recipes/raptor/meta.yaml +++ b/recipes/raptor/meta.yaml @@ -10,7 +10,7 @@ source: sha256: be44e7b2635e110c940cf40ff132956200551a2e25765d9f057e844f7a3ccebb build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin='x') }} diff --git a/recipes/raptor/raptor b/recipes/raptor/raptor new file mode 100644 index 0000000000000..180b5b084c99f --- /dev/null +++ b/recipes/raptor/raptor @@ -0,0 +1,30 @@ +#!/bin/bash + +set -eu + +# -c : return count +# -m 1 : stop after first match, i.e. count is either 0 or 1 +# -E : use extended regular expressions +# \b : matches any non alphanumeric character, i.e. space, tab, newline, etc. +HAS_SSE2=$(grep -c -m 1 -E '\bsse2\b' /proc/cpuinfo) +HAS_SSE4_2=$(grep -c -m 1 -E '\bsse4_2\b' /proc/cpuinfo) +HAS_AVX2=$(grep -c -m 1 -E '\bavx2\b' /proc/cpuinfo) +HAS_AVX512F=$(grep -c -m 1 -E '\bavx512f\b' /proc/cpuinfo) +HAS_AVX512BW=$(grep -c -m 1 -E '\bavx512bw\b' /proc/cpuinfo) +if [ ${HAS_AVX512F} -eq 1 ] && [ ${HAS_AVX512BW} -eq 1 ]; then + HAS_AVX512=1 +else + HAS_AVX512=0 +fi + +if [ ${HAS_AVX512} -eq 1 ]; then + raptor_avx512 "$@" +elif [ ${HAS_AVX2} -eq 1 ]; then + raptor_avx2 "$@" +elif [ ${HAS_SSE4_2} -eq 1 ]; then + raptor_sse4.2 "$@" +elif [ ${HAS_SSE2} -eq 1 ]; then + raptor_sse2 "$@" +else + raptor_none "$@" +fi From 578501e1597ff3bd8eddc8b2bad64549ad6447e7 Mon Sep 17 00:00:00 2001 From: Ray <851836818@qq.com> Date: Sat, 30 Dec 2023 00:58:06 +0800 Subject: [PATCH 024/121] add AnnoSINE2 recipes (#44980) * add strainscan recipes * add annosine2 recipes * Delete recipes/strainscan/meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/annosine2/meta.yaml | 59 +++++++++++++++++++++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 recipes/annosine2/meta.yaml diff --git a/recipes/annosine2/meta.yaml b/recipes/annosine2/meta.yaml new file mode 100644 index 0000000000000..9c474c8c73b80 --- /dev/null +++ b/recipes/annosine2/meta.yaml @@ -0,0 +1,59 @@ +{% set name = "annosine2" %} +{% set version = "1.0.4" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: c9d12adec9875c4a429c6e9da5b76d31c760ef7474635caf742d25592378f34c + +build: + number: 0 + entry_points: + - annosine2 = AnnoSINE.AnnoSINE_v2:main + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + run_exports: + - {{ pin_subpackage('annosine2', max_pin="x") }} + noarch: python + +requirements: + host: + - pip + - python + run: + - cycler ==0.10.0 + - kiwisolver + - matplotlib-base + - numpy + - pillow + - pyparsing + - python + - python-dateutil + - six + - hmmer ==3.3.1 + - minimap2 ==2.26 + - nodejs ==18.12.1 + - trf ==4.09 + - irf ==3.08 + - cd-hit ==4.8.1 + - repeatmasker ==4.1.2.p1 + - seqtk ==1.4 + + +test: + imports: + - AnnoSINE + commands: + - annosine2 --help + +about: + home: https://github.com/liaoherui/AnnoSINE + license: MIT + license_family: MIT + summary: AnnoSINE2 - SINE Annotation Tool for Plant and Animal Genomes + +extra: + recipe-maintainers: + - liaoherui From 4879db2464a1133b3e804422560c5a70bb63427f Mon Sep 17 00:00:00 2001 From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com> Date: Fri, 29 Dec 2023 12:38:56 -0500 Subject: [PATCH 025/121] Bulk (#45014) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * a round of fixes and build-skips * add some build failures * correct version for bioconductor-data-packages * add build failure for STdeconvolve * [ci run] trigger bulk run * run_exports on bioconductor-data-packages * [ci run] trigger bulk run * build failure for omnipathr * [ci run] trigger bulk run * Build important packages first * [ci run] trigger bulk run * revert to full build * [ci run] trigger bulk run * build failure files * skip iclusterplus * skip bioconductor-lpsymphony * bump bioconda-repodata-patches build number * [ci run] * build failures * next round of high priority packages * [ci run] trigger bulk run * [ci run] add dependency * [ci run] finish priority packages * re-enable full bulk * [ci run] trigger bulk run * build failures * [ci run] trigger bulk run * next round of high priority packages * [ci run] trigger bulk run * build more high priority packages * [ci run] test local channel fix * [ci run] increase workers * Try building bioconductor-geoquery (#44726) * Delete recipes/bioconductor-geoquery/build_failure.linux-64.yaml * Update meta.yaml * try fixing parsing error * [ci run] try rebuilding bioconductor-coregx (#44727) * try rebuilding bioconductor-coregx * Update meta.yaml * add opencl loading libraries - will this work * [ci run] remove a few build failure files * [ci run] Bioconductor graph (#44733) * remove build failure file * trigger build * Update meta.yaml * add patch back [ci run] * build failures * [ci run] high priority packages * bulk wiki page * [ci run] add missing packges * build failure for bioconductor-sictools * [ci run] missed one * [ci run] full run * Update build.sh * [ci run] fix dexseq * [ci run] next round of high priority packages * [ci run] missing packages * [ci run] high priority package * [ci run] build all bioconductor-bsgenome * [ci run] remove failures associated with bioconductor-bsgenome dependency * full build * use bioconda-common version * build failures: test dev version of utils * escape characters correctly * build failure for bioconductor-pics * use branch * build failure for bioconductor-inspect * try to fix build failure git range * build failure for bioconductor-distinct * use head branch * trigger build failure wf * [ci run] trigger bulk run * build failures fetch depth * build failure for biconductor-benchdamic * build failures * build failures with log * don't run build failures if last commit has ci skip * [ci skip] test build failure wiki * test build failure wiki job * [ci run] reenable record-build-failures * re-add token for build failure updates * build failures add category column * trigger wiki update * fix libsbml version for bioconductor-rsbml * build failure updates * fix bioconductor-glad * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-wppi * [ci skip] add build failure record for recipe recipes/bioconductor-gars * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-metascope * [ci skip] add build failure record for recipe recipes/bioconductor-biggr * [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank * [ci skip] add build failure record for recipe recipes/bioconductor-msbackendrawfilereader * [ci skip] add build failure record for recipe recipes/bioconductor-omicsviewer * [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr * [ci skip] add build failure record for recipe recipes/bioconductor-micsqtl * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-psygenet2r * [ci skip] add build failure record for recipe recipes/bioconductor-gesper * [ci skip] add build failure record for recipe recipes/bioconductor-sctensor * [ci skip] add build failure record for recipe recipes/bioconductor-seqcna * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-inpas * [ci skip] add build failure record for recipe recipes/bioconductor-factr * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-doubletrouble * [ci skip] add build failure record for recipe recipes/bioconductor-phyloprofile * [ci skip] add build failure record for recipe recipes/bioconductor-extrachips * [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank * [ci skip] add build failure record for recipe recipes/bioconductor-ularcirc * [ci skip] add build failure record for recipe 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recipes/bioconductor-otubase * [ci skip] add build failure record for recipe recipes/bioconductor-cocoa * [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes * retry http error * [ci run] full bulk build * [ci skip] add build failure record for recipe recipes/bioconductor-deepbluer * [ci skip] remove build failure record for recipe recipes/bioconductor-meb * [ci skip] add build failure record for recipe recipes/bioconductor-distinct * [ci run] categorize failures * add bioconductor-cdi * remove old failure files * update bioconductor-reusedata to 3.18 * remove failures for dependencies that have been built * [ci run] build certain packages * bulk: update bioconductor-ccfindr and bioconductor-rjmcmcnucleosomes with gsl (#44986) * update bioconductor-ccfindr with gsl * update bioconductor-rjmcmcnucleosomes with gsl * [ci run] build updated recipes * [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr * [ci skip] add build failure record for recipe recipes/bioconductor-reusedata * remove temporary changes from workflows * build got bumped in merge * remove temp files --------- Co-authored-by: Ryan Dale Co-authored-by: Björn Grüning Co-authored-by: Bjoern Gruening Co-authored-by: BiocondaBot --- .github/workflows/Bulk.yml | 14 +- .github/workflows/build-failures.yml | 2 +- build-fail-blacklist | 4 + recipes/bioconductor-a4/meta.yaml | 27 +-- recipes/bioconductor-a4base/meta.yaml | 35 ++-- recipes/bioconductor-a4classif/meta.yaml | 19 +- recipes/bioconductor-a4core/meta.yaml | 11 +- recipes/bioconductor-a4preproc/meta.yaml | 15 +- recipes/bioconductor-a4reporting/meta.yaml | 9 +- recipes/bioconductor-abarray/meta.yaml | 15 +- recipes/bioconductor-abseqr/meta.yaml | 15 +- recipes/bioconductor-absseq/meta.yaml | 11 +- recipes/bioconductor-acde/meta.yaml | 7 +- recipes/bioconductor-ace/meta.yaml | 19 +- recipes/bioconductor-acgh/meta.yaml | 15 +- recipes/bioconductor-acme/meta.yaml | 15 +- 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recipes/bioconductor-tweedeseqcountdata/build_failure.linux-64.yaml create mode 100644 recipes/pxblat/build_failure.linux-64.yaml create mode 100644 recipes/pxblat/build_failure.osx-64.yaml create mode 100644 recipes/r-interpretmsspectrum/meta.yaml diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 0ccdf6aa9c9d3..e8eeb8712145d 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -15,7 +15,10 @@ jobs: runner: [0, 1, 2, 3, 4, 5] steps: - uses: actions/checkout@v3 - + with: + # checkout as BiocondaBot in order to have the permission to push fail logs + token: ${{secrets.BIOCONDA_BOT_REPO_TOKEN}} + - name: set git user run: | git config user.name BiocondaBot @@ -68,7 +71,7 @@ jobs: bioconda-utils build recipes config.yml \ --worker-offset ${{ matrix.runner }} --n-workers 6 \ --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \ - --record-build-failures --skiplist-leafs + --lint --record-build-failures --skiplist-leafs conda clean -y --all build-osx: @@ -82,7 +85,10 @@ jobs: runner: [0, 1, 2, 3] steps: - uses: actions/checkout@v3 - + with: + # checkout as BiocondaBot in order to have the permission to push fail logs + token: ${{secrets.BIOCONDA_BOT_REPO_TOKEN}} + - name: set git user run: | git config user.name BiocondaBot @@ -139,5 +145,5 @@ jobs: echo '============' bioconda-utils build recipes config.yml \ --worker-offset ${{ matrix.runner }} --n-workers 4 \ - --anaconda-upload --record-build-failures --skiplist-leafs + --lint --anaconda-upload --record-build-failures --skiplist-leafs conda clean -y --all diff --git a/.github/workflows/build-failures.yml b/.github/workflows/build-failures.yml index 3fcdc275e6547..5037e91ec987e 100644 --- a/.github/workflows/build-failures.yml +++ b/.github/workflows/build-failures.yml @@ -64,4 +64,4 @@ jobs: OWNER: bioconda REPO_NAME: bioconda-recipes MD_FOLDER: build-failures - + \ No newline at end of file diff --git a/build-fail-blacklist b/build-fail-blacklist index e043d8ad3088c..31d92e56cbae9 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -1,3 +1,7 @@ +# ----- 2023-12-02 problematic on bulk ----- +r-ramclustr +# ------------------------------------------ + # Currently kills bulk, and dependants recipes/bioconductor-missmethyl recipes/bioconductor-conumee diff --git a/recipes/bioconductor-a4/meta.yaml b/recipes/bioconductor-a4/meta.yaml index 5b8e67556e076..5ce9102925ae3 100644 --- a/recipes/bioconductor-a4/meta.yaml +++ b/recipes/bioconductor-a4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "a4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5d945210d12e19d845e8949ef53b9d43 + md5: 54c9c4300db0c04edd9b531bb0f121a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-a4", max_pin="x.x") }}' noarch: generic # Suggests: MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats requirements: host: - - 'bioconductor-a4base >=1.48.0,<1.49.0' - - 'bioconductor-a4classif >=1.48.0,<1.49.0' - - 'bioconductor-a4core >=1.48.0,<1.49.0' - - 'bioconductor-a4preproc >=1.48.0,<1.49.0' - - 'bioconductor-a4reporting >=1.48.0,<1.49.0' + - 'bioconductor-a4base >=1.50.0,<1.51.0' + - 'bioconductor-a4classif >=1.50.0,<1.51.0' + - 'bioconductor-a4core >=1.50.0,<1.51.0' + - 'bioconductor-a4preproc >=1.50.0,<1.51.0' + - 'bioconductor-a4reporting >=1.50.0,<1.51.0' - r-base run: - - 'bioconductor-a4base >=1.48.0,<1.49.0' - - 'bioconductor-a4classif >=1.48.0,<1.49.0' - - 'bioconductor-a4core >=1.48.0,<1.49.0' - - 'bioconductor-a4preproc >=1.48.0,<1.49.0' - - 'bioconductor-a4reporting >=1.48.0,<1.49.0' + - 'bioconductor-a4base >=1.50.0,<1.51.0' + - 'bioconductor-a4classif >=1.50.0,<1.51.0' + - 'bioconductor-a4core >=1.50.0,<1.51.0' + - 'bioconductor-a4preproc >=1.50.0,<1.51.0' + - 'bioconductor-a4reporting >=1.50.0,<1.51.0' - r-base test: commands: diff --git a/recipes/bioconductor-a4base/meta.yaml b/recipes/bioconductor-a4base/meta.yaml index c3bc1ab6eee23..8d52ef862f80d 100644 --- a/recipes/bioconductor-a4base/meta.yaml +++ b/recipes/bioconductor-a4base/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "a4Base" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b4727840ebfa0c2fdb548b54320e4e39 + md5: 927ee5147653a1ee4df6380f52ad055a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-a4base", max_pin="x.x") }}' noarch: generic # Suggests: Cairo, ALL, hgu95av2.db, nlcv requirements: host: - - 'bioconductor-a4core >=1.48.0,<1.49.0' - - 'bioconductor-a4preproc >=1.48.0,<1.49.0' - - 'bioconductor-annaffy >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-a4core >=1.50.0,<1.51.0' + - 'bioconductor-a4preproc >=1.50.0,<1.51.0' + - 'bioconductor-annaffy >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-glmnet - r-gplots - r-mpm run: - - 'bioconductor-a4core >=1.48.0,<1.49.0' - - 'bioconductor-a4preproc >=1.48.0,<1.49.0' - - 'bioconductor-annaffy >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-a4core >=1.50.0,<1.51.0' + - 'bioconductor-a4preproc >=1.50.0,<1.51.0' + - 'bioconductor-annaffy >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-glmnet - r-gplots diff --git a/recipes/bioconductor-a4classif/meta.yaml b/recipes/bioconductor-a4classif/meta.yaml index 7690f421f98f1..c519e2749143a 100644 --- a/recipes/bioconductor-a4classif/meta.yaml +++ b/recipes/bioconductor-a4classif/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "a4Classif" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 44dc4f5d280303effaedb954307fb336 + md5: 2af82160c9909dd6fdec620de5710cfa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-a4classif", max_pin="x.x") }}' noarch: generic # Suggests: ALL, hgu95av2.db, knitr, rmarkdown requirements: host: - - 'bioconductor-a4core >=1.48.0,<1.49.0' - - 'bioconductor-a4preproc >=1.48.0,<1.49.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-a4core >=1.50.0,<1.51.0' + - 'bioconductor-a4preproc >=1.50.0,<1.51.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-glmnet - r-pamr - r-rocr - r-varselrf run: - - 'bioconductor-a4core >=1.48.0,<1.49.0' - - 'bioconductor-a4preproc >=1.48.0,<1.49.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-a4core >=1.50.0,<1.51.0' + - 'bioconductor-a4preproc >=1.50.0,<1.51.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-glmnet - r-pamr diff --git a/recipes/bioconductor-a4core/meta.yaml b/recipes/bioconductor-a4core/meta.yaml index b0135089b2ee1..581eed71adc05 100644 --- a/recipes/bioconductor-a4core/meta.yaml +++ b/recipes/bioconductor-a4core/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "a4Core" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f0cb8b9e0ac23f1cd176b17c4ef84aa + md5: fdca418afe3a74d9114d8d28afca2037 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-a4core", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-glmnet run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-glmnet test: diff --git a/recipes/bioconductor-a4preproc/meta.yaml b/recipes/bioconductor-a4preproc/meta.yaml index 3efdd56e61c2f..06b428d18d822 100644 --- a/recipes/bioconductor-a4preproc/meta.yaml +++ b/recipes/bioconductor-a4preproc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "a4Preproc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 268368ed5be41d5484b7b5967e2fa716 + md5: 5d9eea3d9957fc99156115052398f0cb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-a4preproc", max_pin="x.x") }}' noarch: generic # Suggests: ALL, hgu95av2.db, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-a4reporting/meta.yaml b/recipes/bioconductor-a4reporting/meta.yaml index 6c2d318ba1aa4..2da455e03ce4c 100644 --- a/recipes/bioconductor-a4reporting/meta.yaml +++ b/recipes/bioconductor-a4reporting/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "a4Reporting" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aace068e89a5238b844b694e81ef185b + md5: 3ba7f3c5606c2f898d84314ba63208fa build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-a4reporting", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-abarray/meta.yaml b/recipes/bioconductor-abarray/meta.yaml index cd518fd3629fd..7e528a9709f81 100644 --- a/recipes/bioconductor-abarray/meta.yaml +++ b/recipes/bioconductor-abarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.0" %} {% set name = "ABarray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c2ae9c221317ee561584dec59cd0ed37 + md5: 59e686f9daf6990fbe6e1594b8676197 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-abarray", max_pin="x.x") }}' noarch: generic # Suggests: limma, LPE requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-abseqr/meta.yaml b/recipes/bioconductor-abseqr/meta.yaml index 48cccf87678f5..da20a9a3cd15d 100644 --- a/recipes/bioconductor-abseqr/meta.yaml +++ b/recipes/bioconductor-abseqr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "abseqR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aef896b0c639d90e59a64148f07587c5 + md5: f35214f635511b611297a3730386b205 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-abseqr", max_pin="x.x") }}' noarch: generic # Suggests: testthat # SystemRequirements: pandoc (>= 1.19.2.1) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - r-base - r-circlize - r-flexdashboard @@ -43,8 +44,8 @@ requirements: - r-venndiagram - 'pandoc >=1.19.2.1' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - r-base - r-circlize - r-flexdashboard diff --git a/recipes/bioconductor-absseq/meta.yaml b/recipes/bioconductor-absseq/meta.yaml index bac5358be9274..7b51b8e054377 100644 --- a/recipes/bioconductor-absseq/meta.yaml +++ b/recipes/bioconductor-absseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "ABSSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e0e0790ae5c6424bf69ba5b2aa334204 + md5: d170bf2f9a37dcdffd2d91e233ce5132 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-absseq", max_pin="x.x") }}' noarch: generic # Suggests: edgeR requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-locfit run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-locfit test: diff --git a/recipes/bioconductor-acde/meta.yaml b/recipes/bioconductor-acde/meta.yaml index 8a7985595713d..2d4644f22d888 100644 --- a/recipes/bioconductor-acde/meta.yaml +++ b/recipes/bioconductor-acde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "acde" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7902aed44029d52dacbac22cba66509c + md5: 9a324caddfceb2aa977e0fc9e7e41615 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-acde", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, RUnit requirements: diff --git a/recipes/bioconductor-ace/meta.yaml b/recipes/bioconductor-ace/meta.yaml index bb78545967250..9befebeb13c7e 100644 --- a/recipes/bioconductor-ace/meta.yaml +++ b/recipes/bioconductor-ace/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "ACE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0403b6c89b9bcf3502feed89309e5922 + md5: dd177150c01a5547ca8edabf82ef85d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ace", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - r-base - r-ggplot2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-acgh/meta.yaml b/recipes/bioconductor-acgh/meta.yaml index c0be97797e3a6..ce96cf84127e5 100644 --- a/recipes/bioconductor-acgh/meta.yaml +++ b/recipes/bioconductor-acgh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "aCGH" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b4e5a21eaeab73202b57967602d0d19e + md5: 137af76dc5756a83094da18eb0bededa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-acgh", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-cluster - r-survival - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-cluster - r-survival diff --git a/recipes/bioconductor-acme/meta.yaml b/recipes/bioconductor-acme/meta.yaml index 701e468e22498..1a43fedf23501 100644 --- a/recipes/bioconductor-acme/meta.yaml +++ b/recipes/bioconductor-acme/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.56.0" %} +{% set version = "2.58.0" %} {% set name = "ACME" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ccefadaea2ecb53dcede052ddb6846b2 + md5: 6668a82e0a26ac03c9697e2cf22eb75e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-acme", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-adacgh2/meta.yaml b/recipes/bioconductor-adacgh2/meta.yaml index 5b1d78c12bba2..1c71ce07f7657 100644 --- a/recipes/bioconductor-adacgh2/meta.yaml +++ b/recipes/bioconductor-adacgh2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.40.0" %} +{% set version = "2.42.0" %} {% set name = "ADaCGH2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef58db06870d692ea9b0d7a065d0542d + md5: 0ce28a95b156205f60eeda851b36c958 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adacgh2", max_pin="x.x") }}' # Suggests: CGHregions, Cairo, limma requirements: host: - - 'bioconductor-acgh >=1.78.0,<1.79.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-glad >=2.64.0,<2.65.0' - - 'bioconductor-snapcgh >=1.70.0,<1.71.0' - - 'bioconductor-tilingarray >=1.78.0,<1.79.0' + - 'bioconductor-acgh >=1.80.0,<1.81.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' + - 'bioconductor-snapcgh >=1.72.0,<1.73.0' + - 'bioconductor-tilingarray >=1.80.0,<1.81.0' - r-base - r-bit - r-cluster @@ -33,11 +34,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-acgh >=1.78.0,<1.79.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-glad >=2.64.0,<2.65.0' - - 'bioconductor-snapcgh >=1.70.0,<1.71.0' - - 'bioconductor-tilingarray >=1.78.0,<1.79.0' + - 'bioconductor-acgh >=1.80.0,<1.81.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' + - 'bioconductor-snapcgh >=1.72.0,<1.73.0' + - 'bioconductor-tilingarray >=1.80.0,<1.81.0' - r-base - r-bit - r-cluster diff --git a/recipes/bioconductor-adam/meta.yaml b/recipes/bioconductor-adam/meta.yaml index 15009172ba8e2..ecee8bcc2ce80 100644 --- a/recipes/bioconductor-adam/meta.yaml +++ b/recipes/bioconductor-adam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "ADAM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d93cb7a12ab64f41db64cacdef965abe + md5: 7f051085afca603520dbb5cb010e58fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adam", max_pin="x.x") }}' # Suggests: testthat, rmarkdown, BiocStyle # SystemRequirements: C++11 requirements: host: - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-dplyr >=0.7.6' - 'r-dt >=0.4' @@ -34,9 +35,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-dplyr >=0.7.6' - 'r-dt >=0.4' diff --git a/recipes/bioconductor-adamgui/meta.yaml b/recipes/bioconductor-adamgui/meta.yaml index ebf62d0541668..d9cd81c8fabd7 100644 --- a/recipes/bioconductor-adamgui/meta.yaml +++ b/recipes/bioconductor-adamgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "ADAMgui" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c733676eecd9e6fe3acf3918534ee220 + md5: d6b76d93be7f193cd913f44f6ff41a64 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adamgui", max_pin="x.x") }}' noarch: generic # Suggests: markdown, BiocStyle requirements: host: - - 'bioconductor-adam >=1.16.0,<1.17.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-adam >=1.18.0,<1.19.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - 'r-colorramps >=2.3' - 'r-data.table >=1.11.4' @@ -43,8 +44,8 @@ requirements: - r-testthat - 'r-varhandle >=2.0.3' run: - - 'bioconductor-adam >=1.16.0,<1.17.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-adam >=1.18.0,<1.19.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - 'r-colorramps >=2.3' - 'r-data.table >=1.11.4' diff --git a/recipes/bioconductor-adductdata/meta.yaml b/recipes/bioconductor-adductdata/meta.yaml index 63ebe10e796a1..ad2a3978ce00b 100644 --- a/recipes/bioconductor-adductdata/meta.yaml +++ b/recipes/bioconductor-adductdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "adductData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: abd834104d02465a0f32a64be9974c64 + md5: bf0e3549ee672a31f32759f0535f360a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adductdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr (>= 1.15.1), rmarkdown (>= 1.5) requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-adductdata/post-link.sh b/recipes/bioconductor-adductdata/post-link.sh index 4f61cf8d1d91c..d3605c39b51d2 100644 --- a/recipes/bioconductor-adductdata/post-link.sh +++ b/recipes/bioconductor-adductdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "adductdata-1.16.0" +installBiocDataPackage.sh "adductdata-1.18.0" diff --git a/recipes/bioconductor-adductomicsr/meta.yaml b/recipes/bioconductor-adductomicsr/meta.yaml index 3e5bf8e9fdc27..0dae0b1138261 100644 --- a/recipes/bioconductor-adductomicsr/meta.yaml +++ b/recipes/bioconductor-adductomicsr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "adductomicsR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed852e0f573a83db85687be2f9fd6854 + md5: 82e24a09ba891b76e9497a6725b96fe0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adductomicsr", max_pin="x.x") }}' noarch: generic # Suggests: knitr (>= 1.15.1), rmarkdown (>= 1.5), Rdisop (>= 1.34.0), testthat requirements: host: - - 'bioconductor-adductdata >=1.16.0,<1.17.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-adductdata >=1.18.0,<1.19.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - 'r-ade4 >=1.7.6' - r-base - 'r-bootstrap >=2017.2' @@ -44,10 +45,10 @@ requirements: - 'r-smoother >=1.1' - 'r-zoo >=1.8' run: - - 'bioconductor-adductdata >=1.16.0,<1.17.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-adductdata >=1.18.0,<1.19.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - 'r-ade4 >=1.7.6' - r-base - 'r-bootstrap >=2017.2' diff --git a/recipes/bioconductor-adimpute/meta.yaml b/recipes/bioconductor-adimpute/meta.yaml index bca3ef416071c..dc9e7cde8ce66 100644 --- a/recipes/bioconductor-adimpute/meta.yaml +++ b/recipes/bioconductor-adimpute/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ADImpute" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c7d4917d6ba8a14b93e6ccb52e93b677 + md5: 488025707dc1ae48d36b1e936cd86e18 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adimpute", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-data.table @@ -35,10 +36,10 @@ requirements: - r-rsvd - r-saver run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-data.table diff --git a/recipes/bioconductor-adme16cod.db/meta.yaml b/recipes/bioconductor-adme16cod.db/meta.yaml index 6dd4d7e465201..e4dce7a0d51e4 100644 --- a/recipes/bioconductor-adme16cod.db/meta.yaml +++ b/recipes/bioconductor-adme16cod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "adme16cod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3902516a40a503302ef732143b2394b9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adme16cod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-adsplit/meta.yaml b/recipes/bioconductor-adsplit/meta.yaml index f3475e35dc258..63e85226e64ef 100644 --- a/recipes/bioconductor-adsplit/meta.yaml +++ b/recipes/bioconductor-adsplit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "adSplit" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c31606f8e4de1045362077ae9e7f0cc3 + md5: 4d50affb50e6f6a11d8c4e379b6116d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adsplit", max_pin="x.x") }}' # Suggests: golubEsets (>= 1.0), vsn (>= 1.5.0), hu6800.db (>= 1.8.1) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - 'r-cluster >=1.9.1' - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - 'r-cluster >=1.9.1' build: diff --git a/recipes/bioconductor-adverscarial/build.sh b/recipes/bioconductor-adverscarial/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-adverscarial/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-adverscarial/meta.yaml b/recipes/bioconductor-adverscarial/meta.yaml new file mode 100644 index 0000000000000..4a8c254b26e82 --- /dev/null +++ b/recipes/bioconductor-adverscarial/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.0.0" %} +{% set name = "adverSCarial" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 196840790cf7fd0a0cbfe6d1aeb60e07 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adverscarial", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, RUnit, BiocGenerics, TENxPBMCData, CHETAH, stringr, LoomExperiment +requirements: + host: + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-gtools + run: + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-gtools +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'adverSCarial, generate and analyze the vulnerability of scRNA-seq classifiers to adversarial attacks' + description: 'adverSCarial is an R Package designed for generating and analyzing the vulnerability of scRNA-seq classifiers to adversarial attacks. The package is versatile and provides a format for integrating any type of classifier. It offers functions for studying and generating two types of attacks, single gene attack and max change attack. The single gene attack involves making a small modification to the input to alter the classification. The max change attack involves making a large modification to the input without changing its classification. The package provides a comprehensive solution for evaluating the robustness of scRNA-seq classifiers against adversarial attacks.' + license_file: LICENSE + diff --git a/recipes/bioconductor-affixcan/meta.yaml b/recipes/bioconductor-affixcan/meta.yaml index e06e9f22978f5..239059a2abf23 100644 --- a/recipes/bioconductor-affixcan/meta.yaml +++ b/recipes/bioconductor-affixcan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "AffiXcan" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4372aaaf131ef8bced13fa847b0b09d0 + md5: 0fdb85714a4ee94e3c04117e56d35724 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affixcan", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-crayon run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-crayon test: diff --git a/recipes/bioconductor-affxparser/meta.yaml b/recipes/bioconductor-affxparser/meta.yaml index 874264d669dce..98a8b2a7afec4 100644 --- a/recipes/bioconductor-affxparser/meta.yaml +++ b/recipes/bioconductor-affxparser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "affxparser" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 532d0815920747092ca64f439fc2677a + md5: 2b6b9373d749a0ccbf930f834df90b92 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affxparser", max_pin="x.x") }}' # Suggests: R.oo (>= 1.22.0), R.utils (>= 2.7.0), AffymetrixDataTestFiles requirements: host: diff --git a/recipes/bioconductor-affy/meta.yaml b/recipes/bioconductor-affy/meta.yaml index b282b1628b862..b6cfed74b149d 100644 --- a/recipes/bioconductor-affy/meta.yaml +++ b/recipes/bioconductor-affy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "affy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1b3ca024b5fc6804d66023f11c058955 + md5: 09376016b32f86f707ff9b8f8cb8a1a5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools + run_exports: '{{ pin_subpackage("bioconductor-affy", max_pin="x.x") }}' +# Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools, hgu95av2cdf requirements: host: - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - bioconductor-annotationdbi - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-biocmanager - - r-curl - - r-plogr - - r-rsqlite - libblas - liblapack run: - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - bioconductor-annotationdbi - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-biocmanager - - r-curl - - r-plogr - - r-rsqlite build: - {{ compiler('c') }} - automake diff --git a/recipes/bioconductor-affycomp/meta.yaml b/recipes/bioconductor-affycomp/meta.yaml index 01d92610a5ec8..8637840fed6df 100644 --- a/recipes/bioconductor-affycomp/meta.yaml +++ b/recipes/bioconductor-affycomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "affycomp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 087b3614cc06dc45c424d3c9c8a2cafa + md5: f80b53dc57dcb88730eda3c0506b9df1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affycomp", max_pin="x.x") }}' noarch: generic # Suggests: splines, affycompData requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-affycompdata/meta.yaml b/recipes/bioconductor-affycompdata/meta.yaml index 0004ba77c7269..0095e5b77d597 100644 --- a/recipes/bioconductor-affycompdata/meta.yaml +++ b/recipes/bioconductor-affycompdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "affycompData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: adf2ee1552f1ee380e5ccbcf8246955d + md5: 205391e19fb160dcff1531892f28b006 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affycompdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affycomp >=1.76.0,<1.77.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affycomp >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-affycomp >=1.76.0,<1.77.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affycomp >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affycompdata/post-link.sh b/recipes/bioconductor-affycompdata/post-link.sh index 44727c3422456..8afa441ea7552 100644 --- a/recipes/bioconductor-affycompdata/post-link.sh +++ b/recipes/bioconductor-affycompdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affycompdata-1.38.0" +installBiocDataPackage.sh "affycompdata-1.40.0" diff --git a/recipes/bioconductor-affycontam/meta.yaml b/recipes/bioconductor-affycontam/meta.yaml index 2bfac5ee1f649..5b27747fc443e 100644 --- a/recipes/bioconductor-affycontam/meta.yaml +++ b/recipes/bioconductor-affycontam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "affyContam" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 033e0738e646d2f9ba5ba1b0b072b915 + md5: eb7e98d31e923d77d4e6197e5cf8b02d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affycontam", max_pin="x.x") }}' noarch: generic # Suggests: hgu95av2cdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affydata >=1.48.0,<1.49.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affydata >=1.50.0,<1.51.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affydata >=1.48.0,<1.49.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affydata >=1.50.0,<1.51.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-affycoretools/meta.yaml b/recipes/bioconductor-affycoretools/meta.yaml index bd9a73302edd7..a986df1b11158 100644 --- a/recipes/bioconductor-affycoretools/meta.yaml +++ b/recipes/bioconductor-affycoretools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "affycoretools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4235bb5e8547acf64c3c6a7d11c98c56 + md5: 0e35c33fb3f3a4cdc7778efacbc45441 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affycoretools", max_pin="x.x") }}' noarch: generic # Suggests: affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl, rmarkdown requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' - - 'bioconductor-glimma >=2.10.0,<2.11.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-reportingtools >=2.39.0,<2.40.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' + - 'bioconductor-glimma >=2.12.0,<2.13.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-reportingtools >=2.42.0,<2.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-ggplot2 @@ -42,18 +43,18 @@ requirements: - r-rsqlite - r-xtable run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' - - 'bioconductor-glimma >=2.10.0,<2.11.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-reportingtools >=2.39.0,<2.40.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' + - 'bioconductor-glimma >=2.12.0,<2.13.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-reportingtools >=2.42.0,<2.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-ggplot2 diff --git a/recipes/bioconductor-affydata/meta.yaml b/recipes/bioconductor-affydata/meta.yaml index 38fb326487ba1..2f929ae9839ca 100644 --- a/recipes/bioconductor-affydata/meta.yaml +++ b/recipes/bioconductor-affydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.1" %} +{% set version = "1.50.0" %} {% set name = "affydata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1c03aa529e4854f6680fcf4702d2bea7 + md5: 29caf389ca94d4c0c0b27d993f33354c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affydata", max_pin="x.x") }}' noarch: generic # Suggests: hgu95av2cdf, hgu133acdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230718 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affydata/post-link.sh b/recipes/bioconductor-affydata/post-link.sh index 998d4b687d633..d1076767bb073 100644 --- a/recipes/bioconductor-affydata/post-link.sh +++ b/recipes/bioconductor-affydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affydata-1.48.1" +installBiocDataPackage.sh "affydata-1.50.0" diff --git a/recipes/bioconductor-affyhgu133a2expr/meta.yaml b/recipes/bioconductor-affyhgu133a2expr/meta.yaml index 8833f245300de..c8a6b90c26c8e 100644 --- a/recipes/bioconductor-affyhgu133a2expr/meta.yaml +++ b/recipes/bioconductor-affyhgu133a2expr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "Affyhgu133A2Expr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09a1e306ad46f08b9508343050ffa756 + md5: 56296960e5539a4fd84724344f30aaaa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affyhgu133a2expr", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affyhgu133a2expr/post-link.sh b/recipes/bioconductor-affyhgu133a2expr/post-link.sh index 3489adaf54942..51c44933e7561 100644 --- a/recipes/bioconductor-affyhgu133a2expr/post-link.sh +++ b/recipes/bioconductor-affyhgu133a2expr/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affyhgu133a2expr-1.36.0" +installBiocDataPackage.sh "affyhgu133a2expr-1.38.0" diff --git a/recipes/bioconductor-affyhgu133aexpr/meta.yaml b/recipes/bioconductor-affyhgu133aexpr/meta.yaml index 23dee4fe8b1a9..cb49ec76a1c59 100644 --- a/recipes/bioconductor-affyhgu133aexpr/meta.yaml +++ b/recipes/bioconductor-affyhgu133aexpr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "Affyhgu133aExpr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e745cf07453b1f7151f28ddddced6be1 + md5: 2cf458278c574450a3a5ffe64a2aa72b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affyhgu133aexpr", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affyhgu133aexpr/post-link.sh b/recipes/bioconductor-affyhgu133aexpr/post-link.sh index c621da65bd9da..340a6ec306e19 100644 --- a/recipes/bioconductor-affyhgu133aexpr/post-link.sh +++ b/recipes/bioconductor-affyhgu133aexpr/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affyhgu133aexpr-1.38.0" +installBiocDataPackage.sh "affyhgu133aexpr-1.40.0" diff --git a/recipes/bioconductor-affyhgu133plus2expr/meta.yaml b/recipes/bioconductor-affyhgu133plus2expr/meta.yaml index 22f780b7b0273..34d5b6c564a12 100644 --- a/recipes/bioconductor-affyhgu133plus2expr/meta.yaml +++ b/recipes/bioconductor-affyhgu133plus2expr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "Affyhgu133Plus2Expr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 210b20595daf5314b8d5b90b5497eab4 + md5: f8baac83db4de07f941552d7b62c8d62 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affyhgu133plus2expr", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affyhgu133plus2expr/post-link.sh b/recipes/bioconductor-affyhgu133plus2expr/post-link.sh index e4d6cb7fb5882..61b0c8692f259 100644 --- a/recipes/bioconductor-affyhgu133plus2expr/post-link.sh +++ b/recipes/bioconductor-affyhgu133plus2expr/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affyhgu133plus2expr-1.34.0" +installBiocDataPackage.sh "affyhgu133plus2expr-1.36.0" diff --git a/recipes/bioconductor-affyilm/meta.yaml b/recipes/bioconductor-affyilm/meta.yaml index 575b77bd63e71..6433bba0da600 100644 --- a/recipes/bioconductor-affyilm/meta.yaml +++ b/recipes/bioconductor-affyilm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "affyILM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1e65e974cee281a713155a14d5ecf6a6 + md5: 96d1989fb75742f6a9b0f9d8df1c3fc0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affyilm", max_pin="x.x") }}' noarch: generic # Suggests: AffymetrixDataTestFiles, hgfocusprobe requirements: host: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' - r-base run: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' - r-base test: commands: diff --git a/recipes/bioconductor-affyio/meta.yaml b/recipes/bioconductor-affyio/meta.yaml index e2614e93f4455..0338d5377855c 100644 --- a/recipes/bioconductor-affyio/meta.yaml +++ b/recipes/bioconductor-affyio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "affyio" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9fb97bfde087591251d7cda5c978e528 + md5: 9bd1e4acedbf756386f96d4c1ebb21f3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affyio", max_pin="x.x") }}' requirements: host: - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-affylmgui/meta.yaml b/recipes/bioconductor-affylmgui/meta.yaml index 9ef33694a62a1..a22190a4e1974 100644 --- a/recipes/bioconductor-affylmgui/meta.yaml +++ b/recipes/bioconductor-affylmgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "affylmGUI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ae4622fe7a135671ded4e68d2e857760 + md5: 22d9ba796444840fc24cf9b7384f81c9 build: - number: 0 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affylmgui", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-affyplm >=1.76.0,<1.77.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-affyplm >=1.78.0,<1.79.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-biocmanager - r-r2html - r-tkrplot - r-xtable run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-affyplm >=1.76.0,<1.77.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-affyplm >=1.78.0,<1.79.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-biocmanager - r-r2html diff --git a/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml b/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml index 4d5d904bd46aa..66437faa2f9b4 100644 --- a/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml +++ b/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "AffymetrixDataTestFiles" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3aa3891584be3bcdab25e2b72b092edc + md5: 57ecb8e4d3f0d7a9cdcedb2a9648dd1e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affymetrixdatatestfiles", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,14 +25,14 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: LGPL-2.1 - summary: 'Affymetrix data files (CEL, CDF, CHP, EXP, PGF, PSI) for testing' + summary: 'Affymetrix Data Files (CEL, CDF, CHP, EXP, PGF, PSI) for Testing' description: 'This package contains annotation data files and sample data files of Affymetrix file formats. The files originate from the Affymetrix'' Fusion SDK distribution and other official sources.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2.1' diff --git a/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh b/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh index 3f6f79b4c0d41..e2ba7cf5c205a 100644 --- a/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh +++ b/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affymetrixdatatestfiles-0.38.0" +installBiocDataPackage.sh "affymetrixdatatestfiles-0.40.0" diff --git a/recipes/bioconductor-affymoe4302expr/meta.yaml b/recipes/bioconductor-affymoe4302expr/meta.yaml index d7d15bc46a474..2c17903299ff0 100644 --- a/recipes/bioconductor-affymoe4302expr/meta.yaml +++ b/recipes/bioconductor-affymoe4302expr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "Affymoe4302Expr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 277537172df894a0e7384d3e48d059b1 + md5: 4dcd432d350cf2f8000f67774d95481c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affymoe4302expr", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affymoe4302expr/post-link.sh b/recipes/bioconductor-affymoe4302expr/post-link.sh index 5c867c283a151..1c18e0a13e6be 100644 --- a/recipes/bioconductor-affymoe4302expr/post-link.sh +++ b/recipes/bioconductor-affymoe4302expr/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affymoe4302expr-1.38.0" +installBiocDataPackage.sh "affymoe4302expr-1.40.0" diff --git a/recipes/bioconductor-affyplm/meta.yaml b/recipes/bioconductor-affyplm/meta.yaml index 1b6dfa0e06c33..6f6f1faaf8e41 100644 --- a/recipes/bioconductor-affyplm/meta.yaml +++ b/recipes/bioconductor-affyplm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.1" %} +{% set version = "1.78.0" %} {% set name = "affyPLM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9aae2ea1fdeafc1e540428a6d9d988d2 + md5: cdfd69bc9c54f3c03b52b3fd6e9f86b7 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: affydata, MASS + run_exports: '{{ pin_subpackage("bioconductor-affyplm", max_pin="x.x") }}' +# Suggests: affydata, MASS, hgu95av2cdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-affyrnadegradation/meta.yaml b/recipes/bioconductor-affyrnadegradation/meta.yaml index e7d30099c638b..0cc0bd45177a2 100644 --- a/recipes/bioconductor-affyrnadegradation/meta.yaml +++ b/recipes/bioconductor-affyrnadegradation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "AffyRNADegradation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 81aaa5c79893376798c726d114779512 + md5: 4affd7f48b178750311671c1f2ac8c4f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affyrnadegradation", max_pin="x.x") }}' noarch: generic -# Suggests: AmpAffyExample +# Suggests: AmpAffyExample, hgu133acdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base test: commands: diff --git a/recipes/bioconductor-ag.db/meta.yaml b/recipes/bioconductor-ag.db/meta.yaml index 93456c5bae844..7b597e80ef24d 100644 --- a/recipes/bioconductor-ag.db/meta.yaml +++ b/recipes/bioconductor-ag.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "ag.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 925e808d2c9b21a11ed131d483e75ab6 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ag.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.at.tair.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.at.tair.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.at.tair.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.at.tair.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-agcdf/meta.yaml b/recipes/bioconductor-agcdf/meta.yaml index 5a63ca629b14e..312952757082a 100644 --- a/recipes/bioconductor-agcdf/meta.yaml +++ b/recipes/bioconductor-agcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "agcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5dd14bc6a6d2729f5e7b170105c78e48 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-agcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-agdex/meta.yaml b/recipes/bioconductor-agdex/meta.yaml index 3720941870845..4304a5d0cccc5 100644 --- a/recipes/bioconductor-agdex/meta.yaml +++ b/recipes/bioconductor-agdex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "AGDEX" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73f6cbece97c53821c785468dabca2e8 + md5: 9e74a7202bdc2e422e2213f1fb7a23f1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-agdex", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base test: commands: diff --git a/recipes/bioconductor-aggregatebiovar/meta.yaml b/recipes/bioconductor-aggregatebiovar/meta.yaml index 90ddcba32e1fb..a32ad85909c4c 100644 --- a/recipes/bioconductor-aggregatebiovar/meta.yaml +++ b/recipes/bioconductor-aggregatebiovar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "aggregateBioVar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 480e81b8e909d164fa86ce05b7d412a1 + md5: f389a909fab4bbc4cb526505c68f22e1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aggregatebiovar", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, magick, knitr, rmarkdown, testthat, BiocGenerics, DESeq2, magrittr, dplyr, ggplot2, cowplot, ggtext, RColorBrewer, pheatmap, viridis requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rlang - r-tibble run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rlang diff --git a/recipes/bioconductor-agilp/meta.yaml b/recipes/bioconductor-agilp/meta.yaml index 6d77d5bf3c196..e3c5bbb5a3261 100644 --- a/recipes/bioconductor-agilp/meta.yaml +++ b/recipes/bioconductor-agilp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.32.0" %} +{% set version = "3.34.0" %} {% set name = "agilp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 573fbba741e2d0b2a99db971555f598d + md5: 21b54a703747520483657dd63288f403 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-agilp", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-agimicrorna/meta.yaml b/recipes/bioconductor-agimicrorna/meta.yaml index ab7e912ca8bf9..5030fc363a442 100644 --- a/recipes/bioconductor-agimicrorna/meta.yaml +++ b/recipes/bioconductor-agimicrorna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.50.0" %} +{% set version = "2.52.0" %} {% set name = "AgiMicroRna" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d971cfaddf49f4b7296a833a4a818dd + md5: 1c1046ab29a7766af0c602c974b4ec21 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-agimicrorna", max_pin="x.x") }}' noarch: generic # Suggests: geneplotter,marray,gplots,gtools,gdata,codelink requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affycoretools >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affycoretools >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affycoretools >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affycoretools >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base test: commands: diff --git a/recipes/bioconductor-agprobe/meta.yaml b/recipes/bioconductor-agprobe/meta.yaml index 4740b9dcb4668..c2ba8fe20c5c7 100644 --- a/recipes/bioconductor-agprobe/meta.yaml +++ b/recipes/bioconductor-agprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "agprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 08f7527d4c8a30d8b2f86016a53f075a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-agprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ahcytobands/meta.yaml b/recipes/bioconductor-ahcytobands/meta.yaml index 1ee85ebf82f04..1fd99874310a1 100644 --- a/recipes/bioconductor-ahcytobands/meta.yaml +++ b/recipes/bioconductor-ahcytobands/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.1" %} {% set name = "AHCytoBands" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3dd85d02e7ed3fca4c7898b5e395edeb build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ahcytobands", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ahensdbs/meta.yaml b/recipes/bioconductor-ahensdbs/meta.yaml index e28373c8ea6a6..117aeb2c7ff6a 100644 --- a/recipes/bioconductor-ahensdbs/meta.yaml +++ b/recipes/bioconductor-ahensdbs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.1.8" %} +{% set version = "1.1.10" %} {% set name = "AHEnsDbs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f2c8c9338f09f480a46e1155d985d08f + md5: 63aa3efc1c85d5a26e4d69d50f781a2a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ahensdbs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, AnnotationHub (>= 2.7.13), rmarkdown requirements: host: - - 'bioconductor-annotationhubdata >=1.30.0,<1.31.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-annotationhubdata >=1.30.0,<1.31.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ahensdbs/post-link.sh b/recipes/bioconductor-ahensdbs/post-link.sh index fa692e021139b..e004d994abd34 100644 --- a/recipes/bioconductor-ahensdbs/post-link.sh +++ b/recipes/bioconductor-ahensdbs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ahensdbs-1.1.8" +installBiocDataPackage.sh "ahensdbs-1.1.10" diff --git a/recipes/bioconductor-ahlrbasedbs/meta.yaml b/recipes/bioconductor-ahlrbasedbs/meta.yaml index bd2c3c2f62e9d..29db9f49d2eb6 100644 --- a/recipes/bioconductor-ahlrbasedbs/meta.yaml +++ b/recipes/bioconductor-ahlrbasedbs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.7.0" %} {% set name = "AHLRBaseDbs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1427836afe85a5b580f7277e7d2c08ca + md5: 5df6ef84988477d6262e54abd07c82da build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ahlrbasedbs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ahlrbasedbs/post-link.sh b/recipes/bioconductor-ahlrbasedbs/post-link.sh index cfac5d956723a..b59c08f98bc83 100644 --- a/recipes/bioconductor-ahlrbasedbs/post-link.sh +++ b/recipes/bioconductor-ahlrbasedbs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ahlrbasedbs-1.6.0" +installBiocDataPackage.sh "ahlrbasedbs-1.7.0" diff --git a/recipes/bioconductor-ahmassbank/meta.yaml b/recipes/bioconductor-ahmassbank/meta.yaml index 7fea5ede930f7..6db48bd579837 100644 --- a/recipes/bioconductor-ahmassbank/meta.yaml +++ b/recipes/bioconductor-ahmassbank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "AHMassBank" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 05f8f3c29029047132ee58b4e2a1f4b0 + md5: b9ddc7dff0cabd4b170bc750cc3c47d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ahmassbank", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, AnnotationHub (>= 2.7.13), rmarkdown, methods, CompoundDb (>= 1.1.4) requirements: host: - - 'bioconductor-annotationhubdata >=1.30.0,<1.31.0' + - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-annotationhubdata >=1.30.0,<1.31.0' + - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-ahmeshdbs/meta.yaml b/recipes/bioconductor-ahmeshdbs/meta.yaml index b0c0131347691..f7efca97a5554 100644 --- a/recipes/bioconductor-ahmeshdbs/meta.yaml +++ b/recipes/bioconductor-ahmeshdbs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.7.0" %} {% set name = "AHMeSHDbs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7fe9c77aaff9175d842cb4f4b9313360 + md5: 9bbcae25794d2f854a122ba36a4e4c5c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ahmeshdbs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ahmeshdbs/post-link.sh b/recipes/bioconductor-ahmeshdbs/post-link.sh index 36a8a0bf2cf59..4b406789a1680 100644 --- a/recipes/bioconductor-ahmeshdbs/post-link.sh +++ b/recipes/bioconductor-ahmeshdbs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ahmeshdbs-1.6.0" +installBiocDataPackage.sh "ahmeshdbs-1.7.0" diff --git a/recipes/bioconductor-ahpathbankdbs/meta.yaml b/recipes/bioconductor-ahpathbankdbs/meta.yaml index 5caa56ea627f4..aa5554f14038d 100644 --- a/recipes/bioconductor-ahpathbankdbs/meta.yaml +++ b/recipes/bioconductor-ahpathbankdbs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.5" %} {% set name = "AHPathbankDbs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 70339eae8c03c47248b612b365bda4ff build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ahpathbankdbs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, magrittr, dplyr, tibble, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ahpubmeddbs/meta.yaml b/recipes/bioconductor-ahpubmeddbs/meta.yaml index e15a881301fbb..8692df0e1a8d1 100644 --- a/recipes/bioconductor-ahpubmeddbs/meta.yaml +++ b/recipes/bioconductor-ahpubmeddbs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.7.0" %} {% set name = "AHPubMedDbs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91815a0aa91e19d171fad3b116d02eed + md5: b2db2eda6009bc9cdec579c4ab579f25 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ahpubmeddbs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ahpubmeddbs/post-link.sh b/recipes/bioconductor-ahpubmeddbs/post-link.sh index c24116e69908e..42e051ec75f48 100644 --- a/recipes/bioconductor-ahpubmeddbs/post-link.sh +++ b/recipes/bioconductor-ahpubmeddbs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ahpubmeddbs-1.6.0" +installBiocDataPackage.sh "ahpubmeddbs-1.7.0" diff --git a/recipes/bioconductor-ahwikipathwaysdbs/meta.yaml b/recipes/bioconductor-ahwikipathwaysdbs/meta.yaml index 02f5241e55a69..73c928b6ecca4 100644 --- a/recipes/bioconductor-ahwikipathwaysdbs/meta.yaml +++ b/recipes/bioconductor-ahwikipathwaysdbs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.4" %} {% set name = "AHWikipathwaysDbs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ffa90f6d6e8832ae6f4b5bf8b151cd46 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ahwikipathwaysdbs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, magrittr, dplyr, tibble, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-aims/meta.yaml b/recipes/bioconductor-aims/meta.yaml index cd75109310927..4e9667789a111 100644 --- a/recipes/bioconductor-aims/meta.yaml +++ b/recipes/bioconductor-aims/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "AIMS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37736eda0cf70c07064ae8930a25b930 + md5: 23ef11145babcac9430b2c94db4dfae3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aims", max_pin="x.x") }}' noarch: generic # Suggests: breastCancerVDX, hgu133a.db, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-e1071 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-e1071 test: diff --git a/recipes/bioconductor-airpart/meta.yaml b/recipes/bioconductor-airpart/meta.yaml index 21438ee070670..c343eeefb76a6 100644 --- a/recipes/bioconductor-airpart/meta.yaml +++ b/recipes/bioconductor-airpart/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "airpart" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5c42ac799c2fa8c3364cb7cc965161a1 + md5: 59977674a0dc5eb9f4bd03ef89a73630 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-airpart", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, roxygen2 (>= 6.0.0), testthat (>= 3.0.0), gplots, tidyr requirements: host: - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-clue - r-dplyr @@ -43,12 +44,12 @@ requirements: - r-rlang - r-smurf run: - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-clue - r-dplyr diff --git a/recipes/bioconductor-airway/meta.yaml b/recipes/bioconductor-airway/meta.yaml index 9c721d737617c..ba924b9263df0 100644 --- a/recipes/bioconductor-airway/meta.yaml +++ b/recipes/bioconductor-airway/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "airway" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9c79ded2f4d44b3a865a1e489c6d151d + md5: ffed4ae3349ebeeeabff9f1456b8ba1d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-airway", max_pin="x.x") }}' noarch: generic # Suggests: knitr, GEOquery, markdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-airway/post-link.sh b/recipes/bioconductor-airway/post-link.sh index b21924a129852..a8e50bfc60ff3 100644 --- a/recipes/bioconductor-airway/post-link.sh +++ b/recipes/bioconductor-airway/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "airway-1.20.0" +installBiocDataPackage.sh "airway-1.22.0" diff --git a/recipes/bioconductor-alabaster.base/meta.yaml b/recipes/bioconductor-alabaster.base/meta.yaml index 7e76be0f452d4..22787eb448ec7 100644 --- a/recipes/bioconductor-alabaster.base/meta.yaml +++ b/recipes/bioconductor-alabaster.base/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.1" %} {% set name = "alabaster.base" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4bfa805d3a2b3c8a6c9ee45807ff68c5 + md5: 2d6215dfe9b8412438f9b05b54be2331 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.base", max_pin="x.x") }}' # Suggests: BiocStyle, rmarkdown, knitr, testthat, digest, Matrix # SystemRequirements: C++17, GNU make requirements: host: - - 'bioconductor-alabaster.schemas >=1.0.0,<1.1.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-alabaster.schemas >=1.2.0,<1.3.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-jsonlite - r-jsonvalidate @@ -32,10 +33,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-alabaster.schemas >=1.0.0,<1.1.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-alabaster.schemas >=1.2.0,<1.3.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-jsonlite - r-jsonvalidate diff --git a/recipes/bioconductor-alabaster.bumpy/meta.yaml b/recipes/bioconductor-alabaster.bumpy/meta.yaml index f35a409108fe7..ab61aee778ded 100644 --- a/recipes/bioconductor-alabaster.bumpy/meta.yaml +++ b/recipes/bioconductor-alabaster.bumpy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "alabaster.bumpy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7c4104e604cc3b9d6f7b3d8d9a81bfb1 + md5: 0d5111cd74d5b72fc88eb66ac5b670c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.bumpy", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown, knitr, testthat, jsonlite requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bumpymatrix >=1.8.0,<1.9.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bumpymatrix >=1.8.0,<1.9.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-alabaster.files/build.sh b/recipes/bioconductor-alabaster.files/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-alabaster.files/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-alabaster.files/meta.yaml b/recipes/bioconductor-alabaster.files/meta.yaml new file mode 100644 index 0000000000000..a91a9a98a4880 --- /dev/null +++ b/recipes/bioconductor-alabaster.files/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.0.0" %} +{% set name = "alabaster.files" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ea12d81dadbad7340c5f2d6be276a697 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.files", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, rmarkdown, knitr, testthat, VariantAnnotation +requirements: + host: + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + run: + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Wrappers to Save Common File Formats' + description: 'Save common bioinformatics file formats within the alabaster framework. This includes BAM, BED, VCF, bigWig, bigBed, FASTQ, FASTA and so on. We save and load additional metadata for each file, and we support linkage between each file and its corresponding index.' + license_file: LICENSE + diff --git a/recipes/bioconductor-alabaster.mae/meta.yaml b/recipes/bioconductor-alabaster.mae/meta.yaml index 7625f9251190e..15bed2c113976 100644 --- a/recipes/bioconductor-alabaster.mae/meta.yaml +++ b/recipes/bioconductor-alabaster.mae/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "alabaster.mae" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f6eceed081467ce7d72c747bb1a0d11a + md5: 43abcdda61fc9d69dbc24dbd1c91664d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.mae", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, SummarizedExperiment, BiocParallel, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.se >=1.0.0,<1.1.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.se >=1.0.0,<1.1.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-alabaster.matrix/meta.yaml b/recipes/bioconductor-alabaster.matrix/meta.yaml index ff390004bf852..73ee0d6404f07 100644 --- a/recipes/bioconductor-alabaster.matrix/meta.yaml +++ b/recipes/bioconductor-alabaster.matrix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "alabaster.matrix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4b93a993b0f4a9b3333da48a8f49ad36 + md5: 099a01bbb4a95bdaf0f91ffd2b89653d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.matrix", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, knitr, BiocGenerics, BiocStyle, S4Vectors, chihaya +# Suggests: testthat, knitr, BiocStyle, chihaya requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sparsearray >=1.2.0,<1.3.0' - r-base - r-matrix run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sparsearray >=1.2.0,<1.3.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-alabaster.ranges/meta.yaml b/recipes/bioconductor-alabaster.ranges/meta.yaml index 27bdfbd3ca23a..d912501aceef5 100644 --- a/recipes/bioconductor-alabaster.ranges/meta.yaml +++ b/recipes/bioconductor-alabaster.ranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "alabaster.ranges" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 846f2604ddc36ae98f28443f4b12d305 + md5: af5d849080999b0167cc39fc182721e9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.ranges", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle, jsonlite requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-alabaster.sce/meta.yaml b/recipes/bioconductor-alabaster.sce/meta.yaml index 0c99a764670fb..dbb5845379eba 100644 --- a/recipes/bioconductor-alabaster.sce/meta.yaml +++ b/recipes/bioconductor-alabaster.sce/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "alabaster.sce" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9a732c09296222711d8296d5b896ac62 + md5: e508f30fb84947c7246b093b63a5aea3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.sce", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.se >=1.0.0,<1.1.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.se >=1.0.0,<1.1.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base test: commands: diff --git a/recipes/bioconductor-alabaster.schemas/meta.yaml b/recipes/bioconductor-alabaster.schemas/meta.yaml index b54d01a99b1e8..6a45f9d6cc290 100644 --- a/recipes/bioconductor-alabaster.schemas/meta.yaml +++ b/recipes/bioconductor-alabaster.schemas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.2" %} +{% set version = "1.2.0" %} {% set name = "alabaster.schemas" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 07cb1f4f931f7fcde891ab11857ad443 + md5: 308883d85ab416d45eaa55428463d308 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.schemas", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: diff --git a/recipes/bioconductor-alabaster.se/meta.yaml b/recipes/bioconductor-alabaster.se/meta.yaml index a60bca1f22d7a..6a54ef0e020fa 100644 --- a/recipes/bioconductor-alabaster.se/meta.yaml +++ b/recipes/bioconductor-alabaster.se/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "alabaster.se" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e93f0f6699394a9fbb4b8048567a5538 + md5: 25133d88cc71ec6029229772a1eee0e8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.se", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat, BiocStyle, jsonlite requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.matrix >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.ranges >=1.0.0,<1.1.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.matrix >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.ranges >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.matrix >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.ranges >=1.0.0,<1.1.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.matrix >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.ranges >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-alabaster.spatial/meta.yaml b/recipes/bioconductor-alabaster.spatial/meta.yaml index 8981659d9e157..fa129e7aa9045 100644 --- a/recipes/bioconductor-alabaster.spatial/meta.yaml +++ b/recipes/bioconductor-alabaster.spatial/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "alabaster.spatial" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b8804e5e38ef912c8d1a04343f03f748 + md5: 906d73c492ba97e8eda563055c51bbfc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.spatial", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, knitr, rmarkdown, BiocStyle, magick, png, digest +# Suggests: testthat, knitr, rmarkdown, BiocStyle, DropletUtils, magick, png, digest requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.sce >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.sce >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-jsonlite run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.sce >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.sce >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-jsonlite test: diff --git a/recipes/bioconductor-alabaster.string/meta.yaml b/recipes/bioconductor-alabaster.string/meta.yaml index 332effb707a9e..3ab554683fc97 100644 --- a/recipes/bioconductor-alabaster.string/meta.yaml +++ b/recipes/bioconductor-alabaster.string/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "alabaster.string" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0ca363e28ab6a9dd4cba70484a090f13 + md5: b7add7aa52b8835471b04038842da095 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.string", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown, knitr, testthat requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base test: commands: diff --git a/recipes/bioconductor-alabaster.vcf/meta.yaml b/recipes/bioconductor-alabaster.vcf/meta.yaml index b21377382c639..191429828c512 100644 --- a/recipes/bioconductor-alabaster.vcf/meta.yaml +++ b/recipes/bioconductor-alabaster.vcf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "alabaster.vcf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a512241aa940a4dd220d86da0b94aea4 + md5: e0873ba68051843f6a35b01fef673423 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.vcf", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.se >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.string >=1.0.0,<1.1.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.string >=1.2.0,<1.3.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.se >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.string >=1.0.0,<1.1.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.string >=1.2.0,<1.3.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-alabaster/meta.yaml b/recipes/bioconductor-alabaster/meta.yaml index 89cfcdd85a328..2189836f4b577 100644 --- a/recipes/bioconductor-alabaster/meta.yaml +++ b/recipes/bioconductor-alabaster/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "alabaster" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8755db5053974ae9995e52dc59ac6dd1 + md5: 359d26d34b8867dd418d0d277b0228c9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.bumpy >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.mae >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.matrix >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.ranges >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.sce >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.se >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.spatial >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.string >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.vcf >=1.0.0,<1.1.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.bumpy >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.mae >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.matrix >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.ranges >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.sce >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.spatial >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.string >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.vcf >=1.2.0,<1.3.0' - r-base run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.bumpy >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.mae >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.matrix >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.ranges >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.sce >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.se >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.spatial >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.string >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.vcf >=1.0.0,<1.1.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.bumpy >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.mae >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.matrix >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.ranges >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.sce >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.spatial >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.string >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.vcf >=1.2.0,<1.3.0' - r-base test: commands: diff --git a/recipes/bioconductor-aldex2/meta.yaml b/recipes/bioconductor-aldex2/meta.yaml index 700bf9e091a1a..70392f9f4f9ec 100644 --- a/recipes/bioconductor-aldex2/meta.yaml +++ b/recipes/bioconductor-aldex2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "ALDEx2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 345d5814c97ec89e886d3cea6de71fc2 + md5: 359e47382b7cac1093aa1a5c24307cec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aldex2", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, BiocStyle, knitr, rmarkdown +# Suggests: testthat, BiocStyle, knitr, rmarkdown, purrr, ggpattern, ggplot2, cowplot, tidyverse, magick requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base + - r-directlabels + - r-lattice + - r-latticeextra - r-rfast - r-zcompositions run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base + - r-directlabels + - r-lattice + - r-latticeextra - r-rfast - r-zcompositions test: @@ -45,9 +52,9 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Analysis Of Differential Abundance Taking Sample Variation Into Account' - description: 'A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcoxon Rank Sum test and Welch''s t-test (via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear model (via aldex.glm), or a correlation test (via aldex.corr). All tests report p-values and Benjamini-Hochberg corrected p-values. ALDEx2 also calculates expected standardized effect sizes for paired or unpaired study designs.' + license: 'GPL (>=3)' + summary: 'Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account' + description: 'A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcoxon Rank Sum test and Welch''s t-test (via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear model (via aldex.glm), or a correlation test (via aldex.corr). All tests report predicted p-values and posterior Benjamini-Hochberg corrected p-values. ALDEx2 also calculates expected standardized effect sizes for paired or unpaired study designs. ALDEx2 can now be used to estimate the effect of scale on the results and report on the scale-dependent robustness of results.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: identifiers: diff --git a/recipes/bioconductor-alevinqc/meta.yaml b/recipes/bioconductor-alevinqc/meta.yaml index ac2601164b7a3..619d9e458faed 100644 --- a/recipes/bioconductor-alevinqc/meta.yaml +++ b/recipes/bioconductor-alevinqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "alevinQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bced99162e87f3f524220f1609769e5a + md5: fa79ac8ac72e4d6d16c096886e9f759d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alevinqc", max_pin="x.x") }}' # Suggests: knitr, BiocStyle, testthat (>= 3.0.0), BiocManager # SystemRequirements: C++11 requirements: host: - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-base - r-cowplot - r-dplyr - r-dt - r-ggally - - r-ggplot2 + - 'r-ggplot2 >=3.4.0' - r-rcpp - r-rjson - r-rlang @@ -37,13 +38,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-base - r-cowplot - r-dplyr - r-dt - r-ggally - - r-ggplot2 + - 'r-ggplot2 >=3.4.0' - r-rcpp - r-rjson - r-rlang @@ -61,6 +62,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Generate QC Reports For Alevin Output' - description: 'Generate QC reports summarizing the output from an alevin run. Reports can be generated as html or pdf files, or as shiny applications.' + description: 'Generate QC reports summarizing the output from an alevin, alevin-fry, or simpleaf run. Reports can be generated as html or pdf files, or as shiny applications.' license_file: LICENSE diff --git a/recipes/bioconductor-all/meta.yaml b/recipes/bioconductor-all/meta.yaml index db938a4bcb525..21dff1b6d6ed1 100644 --- a/recipes/bioconductor-all/meta.yaml +++ b/recipes/bioconductor-all/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "ALL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_{{ name|lower }}.tar.gz' - md5: 11b7809ea96d31a9f1bc3eb56a2650c1 + md5: b80eb482b4937ef4eac01027ac95a61a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-all", max_pin="x.x") }}' noarch: generic # Suggests: rpart requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-all/post-link.sh b/recipes/bioconductor-all/post-link.sh index 447c44b75808a..2c5b04230e97b 100644 --- a/recipes/bioconductor-all/post-link.sh +++ b/recipes/bioconductor-all/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "all-1.42.0" +installBiocDataPackage.sh "all-1.44.0" diff --git a/recipes/bioconductor-allelicimbalance/meta.yaml b/recipes/bioconductor-allelicimbalance/meta.yaml index 9180922a1fa1d..bcbc7a1991cf6 100644 --- a/recipes/bioconductor-allelicimbalance/meta.yaml +++ b/recipes/bioconductor-allelicimbalance/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "AllelicImbalance" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c8e2b8b1555f07edd8140aaca21e530 + md5: 9eb6991f47f1337aef63f9ce750db08a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-allelicimbalance", max_pin="x.x") }}' noarch: generic # Suggests: testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-gridextra - r-lattice @@ -42,20 +43,20 @@ requirements: - r-nlme - r-seqinr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-gridextra - r-lattice diff --git a/recipes/bioconductor-allmll/meta.yaml b/recipes/bioconductor-allmll/meta.yaml index 693c6f690c605..e181a78da8504 100644 --- a/recipes/bioconductor-allmll/meta.yaml +++ b/recipes/bioconductor-allmll/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "ALLMLL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4c0642007ed854280b06339d989d94f + md5: 669e7ff030b6fea51c8013816bd6fae7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-allmll", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-allmll/post-link.sh b/recipes/bioconductor-allmll/post-link.sh index 9fdf373467321..f9958cf78ac2a 100644 --- a/recipes/bioconductor-allmll/post-link.sh +++ b/recipes/bioconductor-allmll/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "allmll-1.40.0" +installBiocDataPackage.sh "allmll-1.42.0" diff --git a/recipes/bioconductor-alphabeta/meta.yaml b/recipes/bioconductor-alphabeta/meta.yaml index 7b455fcd87496..a5240ce1ab0a6 100644 --- a/recipes/bioconductor-alphabeta/meta.yaml +++ b/recipes/bioconductor-alphabeta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "AlphaBeta" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3daff3508c604ad2d2bea4d51bfd3e9b + md5: b03e94ae649db2b4141f97a7859e0683 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alphabeta", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - 'r-data.table >=1.10' - 'r-dplyr >=0.7' @@ -33,7 +34,7 @@ requirements: - 'r-plotly >=4.9' - 'r-stringr >=1.3' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - 'r-data.table >=1.10' - 'r-dplyr >=0.7' diff --git a/recipes/bioconductor-alphamissense.v2023.hg19/meta.yaml b/recipes/bioconductor-alphamissense.v2023.hg19/meta.yaml new file mode 100644 index 0000000000000..c4e4b98feb206 --- /dev/null +++ b/recipes/bioconductor-alphamissense.v2023.hg19/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "3.18.2" %} +{% set name = "AlphaMissense.v2023.hg19" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e8784ad000be637321f432188a5a3f45 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alphamissense.v2023.hg19", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle +requirements: + host: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - r-base + run: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'AlphaMissense v2023 Pathogenicity Scores AnnotationHub Resource Metadata for hg19' + description: 'Store Google DeepMind AlphaMissense v2023 hg19 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for Google DeepMind AlphaMissense v2023 hg19 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.' + diff --git a/recipes/bioconductor-alphamissense.v2023.hg19/post-link.sh b/recipes/bioconductor-alphamissense.v2023.hg19/post-link.sh new file mode 100644 index 0000000000000..ed7e4efe56562 --- /dev/null +++ b/recipes/bioconductor-alphamissense.v2023.hg19/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "alphamissense.v2023.hg19-3.18.2" diff --git a/recipes/bioconductor-alphamissense.v2023.hg19/pre-unlink.sh b/recipes/bioconductor-alphamissense.v2023.hg19/pre-unlink.sh new file mode 100644 index 0000000000000..410f375b8c15b --- /dev/null +++ b/recipes/bioconductor-alphamissense.v2023.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ AlphaMissense.v2023.hg19 diff --git a/recipes/bioconductor-alphamissense.v2023.hg38/meta.yaml b/recipes/bioconductor-alphamissense.v2023.hg38/meta.yaml new file mode 100644 index 0000000000000..5974912274231 --- /dev/null +++ b/recipes/bioconductor-alphamissense.v2023.hg38/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "3.18.2" %} +{% set name = "AlphaMissense.v2023.hg38" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bedac9523e18829c5067dec1ebf801d4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alphamissense.v2023.hg38", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle +requirements: + host: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - r-base + run: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'AlphaMissense v2023 Pathogenicity Scores AnnotationHub Resource Metadata for hg38' + description: 'Store Google DeepMind AlphaMissense v2023 hg38 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for Google DeepMind AlphaMissense v2023 hg38 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.' + diff --git a/recipes/bioconductor-alphamissense.v2023.hg38/post-link.sh b/recipes/bioconductor-alphamissense.v2023.hg38/post-link.sh new file mode 100644 index 0000000000000..7709b6ee909c5 --- /dev/null +++ b/recipes/bioconductor-alphamissense.v2023.hg38/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "alphamissense.v2023.hg38-3.18.2" diff --git a/recipes/bioconductor-alphamissense.v2023.hg38/pre-unlink.sh b/recipes/bioconductor-alphamissense.v2023.hg38/pre-unlink.sh new file mode 100644 index 0000000000000..40728685a22f9 --- /dev/null +++ b/recipes/bioconductor-alphamissense.v2023.hg38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ AlphaMissense.v2023.hg38 diff --git a/recipes/bioconductor-alpinedata/meta.yaml b/recipes/bioconductor-alpinedata/meta.yaml index 513dca99acc28..d1b1d2ca09aad 100644 --- a/recipes/bioconductor-alpinedata/meta.yaml +++ b/recipes/bioconductor-alpinedata/meta.yaml @@ -31,7 +31,7 @@ requirements: - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20230706 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-alpsnmr/meta.yaml b/recipes/bioconductor-alpsnmr/meta.yaml index cf21c958eebb1..6ae5496aa23be 100644 --- a/recipes/bioconductor-alpsnmr/meta.yaml +++ b/recipes/bioconductor-alpsnmr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.2.0" %} +{% set version = "4.4.0" %} {% set name = "AlpsNMR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8238f13c688c0a53bf17b60b321ca80f + md5: 938d77895e6337a35d98b6a57fa90303 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alpsnmr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, ChemoSpec, cowplot, curl, DT (>= 0.5), GGally (>= 1.4.0), ggrepel (>= 0.8.0), gridExtra, knitr, plotly (>= 4.7.1), progressr, SummarizedExperiment, S4Vectors, testthat (>= 2.0.0), writexl (>= 1.0), zip (>= 2.0.4) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-mixomics >=6.24.0,<6.25.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' - r-base - 'r-baseline >=1.2-1' - r-cli @@ -50,8 +51,8 @@ requirements: - r-tidyselect - 'r-vctrs >=0.3.0' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-mixomics >=6.24.0,<6.25.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' - r-base - 'r-baseline >=1.2-1' - r-cli diff --git a/recipes/bioconductor-altcdfenvs/meta.yaml b/recipes/bioconductor-altcdfenvs/meta.yaml index e5dc218de4db5..2f56521289f0e 100644 --- a/recipes/bioconductor-altcdfenvs/meta.yaml +++ b/recipes/bioconductor-altcdfenvs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.62.0" %} +{% set version = "2.64.0" %} {% set name = "altcdfenvs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8a3985abeef481d9886b0f0f566bf5e5 + md5: 8bd83d29c11857ae73a4046289748f90 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-altcdfenvs", max_pin="x.x") }}' noarch: generic # Suggests: plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db, hgu133acdf, Rgraphviz, RColorBrewer requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-hypergraph >=1.72.0,<1.73.0' - - 'bioconductor-makecdfenv >=1.76.0,<1.77.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-hypergraph >=1.74.0,<1.75.0' + - 'bioconductor-makecdfenv >=1.78.0,<1.79.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-hypergraph >=1.72.0,<1.73.0' - - 'bioconductor-makecdfenv >=1.76.0,<1.77.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-hypergraph >=1.74.0,<1.75.0' + - 'bioconductor-makecdfenv >=1.78.0,<1.79.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml b/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml index 35216c97bee60..7d1ab3e0251b4 100644 --- a/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml +++ b/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "alternativeSplicingEvents.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b1acae776c9e9c5d961cf4884cadc58f build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alternativesplicingevents.hg19", max_pin="x.x") }}' noarch: generic # Suggests: data.frame, dplyr, GenomicRanges, S4Vectors requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml b/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml index d722f96d8bb48..30e73e4117234 100644 --- a/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml +++ b/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "alternativeSplicingEvents.hg38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8d49710eebd62fb15a48cab252ff3eca build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alternativesplicingevents.hg38", max_pin="x.x") }}' noarch: generic # Suggests: dplyr, GenomicRanges, S4Vectors requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-amaretto/meta.yaml b/recipes/bioconductor-amaretto/meta.yaml index e6ac5fa2df802..687714cb9991a 100644 --- a/recipes/bioconductor-amaretto/meta.yaml +++ b/recipes/bioconductor-amaretto/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "AMARETTO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 221ee4ff61c9784ce231a2632ff9d860 + md5: d6b16e06e3eb15ba4cac645265a43db1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-amaretto", max_pin="x.x") }}' # Suggests: testthat, MASS, knitr, BiocStyle requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-curatedtcgadata >=1.22.0,<1.23.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-curatedtcgadata >=1.24.0,<1.25.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - r-base - 'r-callr >=3.0.0.9001' - r-circlize @@ -48,12 +49,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-curatedtcgadata >=1.22.0,<1.23.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-curatedtcgadata >=1.24.0,<1.25.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - r-base - 'r-callr >=3.0.0.9001' - r-circlize diff --git a/recipes/bioconductor-amountain/meta.yaml b/recipes/bioconductor-amountain/meta.yaml index 16cb11a74a7a2..e8e64af069238 100644 --- a/recipes/bioconductor-amountain/meta.yaml +++ b/recipes/bioconductor-amountain/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "AMOUNTAIN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d999f893262716e598b8816f9d585b7 + md5: acf007b4bceaa196843cbcf221b762ba build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-amountain", max_pin="x.x") }}' # Suggests: BiocStyle, qgraph, knitr, rmarkdown # SystemRequirements: gsl requirements: diff --git a/recipes/bioconductor-ampaffyexample/meta.yaml b/recipes/bioconductor-ampaffyexample/meta.yaml index ca79fef896674..a4124743b758b 100644 --- a/recipes/bioconductor-ampaffyexample/meta.yaml +++ b/recipes/bioconductor-ampaffyexample/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "AmpAffyExample" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8863d31491bb756d0f630d09c012904 + md5: 3277d6d26f145ddbb45c3808273cd150 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ampaffyexample", max_pin="x.x") }}' noarch: generic # Suggests: hgu133acdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ampaffyexample/post-link.sh b/recipes/bioconductor-ampaffyexample/post-link.sh index 9c4b6ba62ddf7..2d12c440e0cea 100644 --- a/recipes/bioconductor-ampaffyexample/post-link.sh +++ b/recipes/bioconductor-ampaffyexample/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ampaffyexample-1.40.0" +installBiocDataPackage.sh "ampaffyexample-1.42.0" diff --git a/recipes/bioconductor-amplican/meta.yaml b/recipes/bioconductor-amplican/meta.yaml index 1cf3fc17c68a4..d57bcd680d241 100644 --- a/recipes/bioconductor-amplican/meta.yaml +++ b/recipes/bioconductor-amplican/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "amplican" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7cc66936261be4fa00c6cee261cce6ab + md5: 73fd9acdf5066ee76b1157068151f1f4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-amplican", max_pin="x.x") }}' # Suggests: testthat, BiocStyle, GenomicAlignments requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - 'r-cluster >=2.1.4' - 'r-data.table >=1.10.4-3' @@ -46,14 +47,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - 'r-cluster >=2.1.4' - 'r-data.table >=1.10.4-3' diff --git a/recipes/bioconductor-anaquin/meta.yaml b/recipes/bioconductor-anaquin/meta.yaml index 0510b163517c6..aa5132a62ebf8 100644 --- a/recipes/bioconductor-anaquin/meta.yaml +++ b/recipes/bioconductor-anaquin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "Anaquin" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7dbfecc409b693298ad398782947d682 + md5: a0b480fdac1e56d9b308c2c23518b4a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anaquin", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, rmarkdown requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - 'r-ggplot2 >=2.2.0' - r-knitr @@ -30,8 +31,8 @@ requirements: - r-plyr - r-rocr run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - 'r-ggplot2 >=2.2.0' - r-knitr diff --git a/recipes/bioconductor-ancombc/meta.yaml b/recipes/bioconductor-ancombc/meta.yaml index bf379d0df9d84..25c2d9638dbc9 100644 --- a/recipes/bioconductor-ancombc/meta.yaml +++ b/recipes/bioconductor-ancombc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "ANCOMBC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,67 +11,60 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 877867a31ab16c43bbb1eab0b4a92bf1 + md5: 42059f62faa03e818d0cd15b7bcf0094 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ancombc", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, testthat, DT, caret, microbiome, tidyverse +# Suggests: dplyr, knitr, rmarkdown, testthat, DT, tidyr, tidyverse, microbiome, magrittr requirements: host: - - 'bioconductor-mia >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-mia >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-cvxr - r-desctools - r-doparallel - r-dorng - - r-dplyr - - r-emmeans - r-energy - r-foreach + - r-gtools - r-hmisc - r-lme4 - r-lmertest - - r-magrittr - r-mass + - r-matrix + - r-multcomp - r-nloptr - r-rdpack - - r-rlang - - r-rngtools - - r-tibble - - r-tidyr run: - - 'bioconductor-mia >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-mia >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-cvxr - r-desctools - r-doparallel - r-dorng - - r-dplyr - - r-emmeans - r-energy - r-foreach + - r-gtools - r-hmisc - r-lme4 - r-lmertest - - r-magrittr - r-mass + - r-matrix + - r-multcomp - r-nloptr - r-rdpack - - r-rlang - - r-rngtools - - r-tibble - - r-tidyr test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-aneufinder/meta.yaml b/recipes/bioconductor-aneufinder/meta.yaml index ac862ee49cfa2..c0989067c743b 100644 --- a/recipes/bioconductor-aneufinder/meta.yaml +++ b/recipes/bioconductor-aneufinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "AneuFinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a38ae17997909fe55521eeeb7927f47b + md5: 421efa90a617606c8db2c947d302c6b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aneufinder", max_pin="x.x") }}' # Suggests: knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 requirements: host: - - 'bioconductor-aneufinderdata >=1.28.0,<1.29.0' - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-aneufinderdata >=1.30.0,<1.31.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-doparallel @@ -44,17 +45,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-aneufinderdata >=1.28.0,<1.29.0' - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-aneufinderdata >=1.30.0,<1.31.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-doparallel diff --git a/recipes/bioconductor-aneufinderdata/meta.yaml b/recipes/bioconductor-aneufinderdata/meta.yaml index 7d2ecb6161957..7556ff6e34b2c 100644 --- a/recipes/bioconductor-aneufinderdata/meta.yaml +++ b/recipes/bioconductor-aneufinderdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "AneuFinderData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 703ac91ee510ae00274632026f14a065 + md5: 895230cd9b780dbb286a012f3c8777eb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aneufinderdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-aneufinderdata/post-link.sh b/recipes/bioconductor-aneufinderdata/post-link.sh index 2b407d94f6c62..25c0a75eda265 100644 --- a/recipes/bioconductor-aneufinderdata/post-link.sh +++ b/recipes/bioconductor-aneufinderdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "aneufinderdata-1.28.0" +installBiocDataPackage.sh "aneufinderdata-1.30.0" diff --git a/recipes/bioconductor-annaffy/meta.yaml b/recipes/bioconductor-annaffy/meta.yaml index 677262a02d32d..843f2adced6d4 100644 --- a/recipes/bioconductor-annaffy/meta.yaml +++ b/recipes/bioconductor-annaffy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "annaffy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 007b32dfee6b9d9584ba4d723fb523f6 + md5: a590578d3e87dbab236a5531f0a5bce0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annaffy", max_pin="x.x") }}' noarch: generic # Suggests: hgu95av2.db, multtest, tcltk requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-biocmanager - r-dbi run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-biocmanager - r-dbi diff --git a/recipes/bioconductor-annmap/meta.yaml b/recipes/bioconductor-annmap/meta.yaml index 68d79ae0b90f4..54d7f473f442b 100644 --- a/recipes/bioconductor-annmap/meta.yaml +++ b/recipes/bioconductor-annmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "annmap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 414b7e6fe75e48d8e3a612a51cb29d38 + md5: 4e793a7c30de8248f566e7c14bf3fa90 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annmap", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, rjson, Gviz requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-dbi - r-digest - r-lattice - 'r-rmysql >=0.6-0' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-dbi - r-digest diff --git a/recipes/bioconductor-annotate/meta.yaml b/recipes/bioconductor-annotate/meta.yaml index ceefbf3fa9dae..0e27f09050df3 100644 --- a/recipes/bioconductor-annotate/meta.yaml +++ b/recipes/bioconductor-annotate/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "annotate" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fb5187ca7fdd4e1be47a470d528397df + md5: 04d25cadc03401556364f8ca9c3b2a61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annotate", max_pin="x.x") }}' noarch: generic # Suggests: hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit, requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dbi - r-httr - r-xml - r-xtable run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dbi - r-httr diff --git a/recipes/bioconductor-annotationdbi/meta.yaml b/recipes/bioconductor-annotationdbi/meta.yaml index df46ea4a23f46..092d59455da59 100644 --- a/recipes/bioconductor-annotationdbi/meta.yaml +++ b/recipes/bioconductor-annotationdbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.2" %} +{% set version = "1.64.1" %} {% set name = "AnnotationDbi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e12679a9cb4533c5f24fc27458b8d8e6 + md5: 965300db0b7a8b527ed3eb00fdd6d10f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annotationdbi", max_pin="x.x") }}' noarch: generic # Suggests: utils, hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-rsqlite diff --git a/recipes/bioconductor-annotationfilter/meta.yaml b/recipes/bioconductor-annotationfilter/meta.yaml index 3d6de9ccd9af2..72a8de6d1d3e4 100644 --- a/recipes/bioconductor-annotationfilter/meta.yaml +++ b/recipes/bioconductor-annotationfilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "AnnotationFilter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2838a3b75e2f41d27325908586729c4f + md5: 512eececc247990236fd09aa1fc46966 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annotationfilter", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-lazyeval run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-lazyeval test: diff --git a/recipes/bioconductor-annotationforge/meta.yaml b/recipes/bioconductor-annotationforge/meta.yaml index 4aedb25498143..0ff1070736cfa 100644 --- a/recipes/bioconductor-annotationforge/meta.yaml +++ b/recipes/bioconductor-annotationforge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.2" %} +{% set version = "1.44.0" %} {% set name = "AnnotationForge" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ed5d42ecb97e5ab9123d078ff766c66 + md5: 4aa011cdbdc464bbfe1542ec418e7749 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annotationforge", max_pin="x.x") }}' noarch: generic # Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db, markdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-rcurl - r-rsqlite - r-xml run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-rcurl diff --git a/recipes/bioconductor-annotationhub/meta.yaml b/recipes/bioconductor-annotationhub/meta.yaml index 98ee765be3f0b..06f8f353cee10 100644 --- a/recipes/bioconductor-annotationhub/meta.yaml +++ b/recipes/bioconductor-annotationhub/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.8.0" %} +{% set version = "3.10.0" %} {% set name = "AnnotationHub" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 458bb90d5680afe0b2e6b7c75ce37f16 + md5: 9dcc8ea705c0e7f8ac8e9af262de876f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annotationhub", max_pin="x.x") }}' noarch: generic -# Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub +# Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocversion >=3.17.0,<3.18.0' - - 'bioconductor-interactivedisplaybase >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocversion >=3.18.0,<3.19.0' + - 'bioconductor-interactivedisplaybase >=1.40.0,<1.41.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-curl @@ -36,12 +37,12 @@ requirements: - r-rsqlite - r-yaml run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocversion >=3.17.0,<3.18.0' - - 'bioconductor-interactivedisplaybase >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocversion >=3.18.0,<3.19.0' + - 'bioconductor-interactivedisplaybase >=1.40.0,<1.41.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-curl diff --git a/recipes/bioconductor-annotationhubdata/meta.yaml b/recipes/bioconductor-annotationhubdata/meta.yaml index 6ab68144f4d88..712e0387d8f7f 100644 --- a/recipes/bioconductor-annotationhubdata/meta.yaml +++ b/recipes/bioconductor-annotationhubdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "AnnotationHubData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d924856924548dfcd2814cb0247c60a7 + md5: 0c08db64bda6298ca0d673b190a90dee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annotationhubdata", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData, rmarkdown, HubPub requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationforge >=1.42.0,<1.43.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-bioccheck >=1.36.0,<1.37.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationforge >=1.44.0,<1.45.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-bioccheck >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-dbi @@ -47,23 +48,23 @@ requirements: - r-rsqlite - r-xml run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationforge >=1.42.0,<1.43.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-bioccheck >=1.36.0,<1.37.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationforge >=1.44.0,<1.45.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-bioccheck >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-dbi diff --git a/recipes/bioconductor-annotationtools/meta.yaml b/recipes/bioconductor-annotationtools/meta.yaml index a4fadf6af1516..e72898bc9a532 100644 --- a/recipes/bioconductor-annotationtools/meta.yaml +++ b/recipes/bioconductor-annotationtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "annotationTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c04239bb8a757f32c045586db12761c + md5: 3b0a795d7898c0b6112ed596f9d2de27 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annotationtools", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-annotatr/meta.yaml b/recipes/bioconductor-annotatr/meta.yaml index 8165e5c27a448..a2faf6e30caba 100644 --- a/recipes/bioconductor-annotatr/meta.yaml +++ b/recipes/bioconductor-annotatr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "annotatr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 24fa1da45dd9a0e0af22f4d358970ec6 + md5: 433372717ce78a1ae23a91a80601f2b6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annotatr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2, testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Ggallus.UCSC.galGal5.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ggplot2 - r-readr - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-anopheles.db0/meta.yaml b/recipes/bioconductor-anopheles.db0/meta.yaml index 9b13d37a1e2aa..df8ab3def33f1 100644 --- a/recipes/bioconductor-anopheles.db0/meta.yaml +++ b/recipes/bioconductor-anopheles.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "anopheles.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d26110289d806c4d1bd6e039c5873100 + md5: cd7b03fffb4ffd0cf0877a55a3636d93 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anopheles.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-anopheles.db0/post-link.sh b/recipes/bioconductor-anopheles.db0/post-link.sh index fb5a134da283e..9febec5c61f5f 100644 --- a/recipes/bioconductor-anopheles.db0/post-link.sh +++ b/recipes/bioconductor-anopheles.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "anopheles.db0-3.17.0" +installBiocDataPackage.sh "anopheles.db0-3.18.0" diff --git a/recipes/bioconductor-anota/meta.yaml b/recipes/bioconductor-anota/meta.yaml index 51d07f713c147..eabf4ab9ea756 100644 --- a/recipes/bioconductor-anota/meta.yaml +++ b/recipes/bioconductor-anota/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "anota" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 043ed2d07c85599feb160ff62e65369a + md5: dc1461d1c43ffdfedc8e0f49a2b4ac6b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anota", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base run: - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base test: commands: diff --git a/recipes/bioconductor-anota2seq/meta.yaml b/recipes/bioconductor-anota2seq/meta.yaml index dccb1f285651f..295afda5304e6 100644 --- a/recipes/bioconductor-anota2seq/meta.yaml +++ b/recipes/bioconductor-anota2seq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "anota2seq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 67cf3d06cd925a69936cf6b784da0a7a + md5: c14a5f4c2cd7c51fbc9c7ecd844ad0be build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anota2seq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle,knitr requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-rcolorbrewer test: diff --git a/recipes/bioconductor-antiprofiles/meta.yaml b/recipes/bioconductor-antiprofiles/meta.yaml index c65773a4a3397..b885a849653a4 100644 --- a/recipes/bioconductor-antiprofiles/meta.yaml +++ b/recipes/bioconductor-antiprofiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "antiProfiles" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 62ed7ee12254e32c8cb6c5820b53b230 + md5: 80b3c1174d02d3b00b3ebf5d14a75b90 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-antiprofiles", max_pin="x.x") }}' noarch: generic # Suggests: antiProfilesData, RColorBrewer requirements: diff --git a/recipes/bioconductor-antiprofilesdata/meta.yaml b/recipes/bioconductor-antiprofilesdata/meta.yaml index a2787e87c261b..4803d0b345804 100644 --- a/recipes/bioconductor-antiprofilesdata/meta.yaml +++ b/recipes/bioconductor-antiprofilesdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "antiProfilesData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d5eab300113940ec702cdd00de617761 + md5: dc40c00fb296b31cf65369e801d6f2f8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-antiprofilesdata", max_pin="x.x") }}' noarch: generic # Suggests: frma, GEOquery, GEOmetadb requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-antiprofilesdata/post-link.sh b/recipes/bioconductor-antiprofilesdata/post-link.sh index cf588366537b0..7de926d0707ed 100644 --- a/recipes/bioconductor-antiprofilesdata/post-link.sh +++ b/recipes/bioconductor-antiprofilesdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "antiprofilesdata-1.36.0" +installBiocDataPackage.sh "antiprofilesdata-1.38.0" diff --git a/recipes/bioconductor-anvil/meta.yaml b/recipes/bioconductor-anvil/meta.yaml index b7d5c34b2696c..27898e91b994e 100644 --- a/recipes/bioconductor-anvil/meta.yaml +++ b/recipes/bioconductor-anvil/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.3" %} +{% set version = "1.14.0" %} {% set name = "AnVIL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c773fdc6581ece77262038390b7ffba0 + md5: 960614983c195ba60dca0a63a0fbf352 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anvil", max_pin="x.x") }}' noarch: generic # Suggests: parallel, knitr, rmarkdown, testthat, withr, readr, BiocStyle, devtools requirements: diff --git a/recipes/bioconductor-anvilbilling/meta.yaml b/recipes/bioconductor-anvilbilling/meta.yaml index 86334e0faaadd..a68235d62783f 100644 --- a/recipes/bioconductor-anvilbilling/meta.yaml +++ b/recipes/bioconductor-anvilbilling/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "AnVILBilling" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad02ff4c8be1fdf4e48b493b55fa4c8b + md5: 9e6cd90c2e4e31067dfab860b5130cf8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anvilbilling", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle, rmarkdown requirements: diff --git a/recipes/bioconductor-anvilpublish/meta.yaml b/recipes/bioconductor-anvilpublish/meta.yaml index a74f9837912ea..60a805d1f9759 100644 --- a/recipes/bioconductor-anvilpublish/meta.yaml +++ b/recipes/bioconductor-anvilpublish/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "AnVILPublish" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ce3d510992dfb125c6fac3adfc84a42 + md5: bbd5bd8ab36e2563e7b4b01e2b11295d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anvilpublish", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, BiocManager, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-anvil >=1.12.0,<1.13.0' + - 'bioconductor-anvil >=1.14.0,<1.15.0' - r-base - r-httr - r-jsonlite @@ -30,7 +31,7 @@ requirements: - r-whisker - r-yaml run: - - 'bioconductor-anvil >=1.12.0,<1.13.0' + - 'bioconductor-anvil >=1.14.0,<1.15.0' - r-base - r-httr - r-jsonlite diff --git a/recipes/bioconductor-anvilworkflow/meta.yaml b/recipes/bioconductor-anvilworkflow/meta.yaml index 39e81f1c3b85e..de05da6b61a56 100644 --- a/recipes/bioconductor-anvilworkflow/meta.yaml +++ b/recipes/bioconductor-anvilworkflow/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "AnVILWorkflow" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 351e6afcc0568d82cb69f4fa6efb67ee + md5: af890e3cea3c42346ec887603ba12e40 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anvilworkflow", max_pin="x.x") }}' noarch: generic # Suggests: knitr, tibble, BiocStyle requirements: host: - - 'bioconductor-anvil >=1.12.0,<1.13.0' + - 'bioconductor-anvil >=1.14.0,<1.15.0' - r-base - r-httr - r-jsonlite run: - - 'bioconductor-anvil >=1.12.0,<1.13.0' + - 'bioconductor-anvil >=1.14.0,<1.15.0' - r-base - r-httr - r-jsonlite diff --git a/recipes/bioconductor-apalyzer/meta.yaml b/recipes/bioconductor-apalyzer/meta.yaml index 04317074d9d00..744b59ec3073e 100644 --- a/recipes/bioconductor-apalyzer/meta.yaml +++ b/recipes/bioconductor-apalyzer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "APAlyzer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90cb4679a0915479395a3955c7c75cbb + md5: 88aebb2681d07ad9bc8b7e3499339d51 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-apalyzer", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, testthat, pasillaBamSubset requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hybridmtest >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hybridmtest >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-dplyr - r-ggplot2 @@ -38,16 +39,16 @@ requirements: - r-repmis - r-tidyr run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hybridmtest >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hybridmtest >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-apcomplex/meta.yaml b/recipes/bioconductor-apcomplex/meta.yaml index 53e5b265bec60..78e15d595cd68 100644 --- a/recipes/bioconductor-apcomplex/meta.yaml +++ b/recipes/bioconductor-apcomplex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.66.0" %} +{% set version = "2.68.0" %} {% set name = "apComplex" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 51e69711964aab117703064718f5fbf5 + md5: 03418539dfa5904bf05f430718789fde build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-apcomplex", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.sc.sgd.db >=3.17.0,<3.18.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.sc.sgd.db >=3.17.0,<3.18.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-apeglm/meta.yaml b/recipes/bioconductor-apeglm/meta.yaml index 938a77dfbe3cb..3d750a1756a2b 100644 --- a/recipes/bioconductor-apeglm/meta.yaml +++ b/recipes/bioconductor-apeglm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "apeglm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 79070e75b8ea4968e63f8e17afa73d38 + md5: 0f8e64bdd8eec2566238fdc487afabb8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-apeglm", max_pin="x.x") }}' # Suggests: DESeq2, airway, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-emdbook - r-rcpp @@ -30,8 +31,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-emdbook - r-rcpp diff --git a/recipes/bioconductor-apl/meta.yaml b/recipes/bioconductor-apl/meta.yaml index cc417acd554cd..3cefe27602f15 100644 --- a/recipes/bioconductor-apl/meta.yaml +++ b/recipes/bioconductor-apl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "APL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 41f52a6b448fbb963f3ef02f3e9f319b + md5: 725b38bc042e6b6fd349aac0ff3d471c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-apl", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, testthat # SystemRequirements: python, pytorch, numpy requirements: host: - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-ggplot2 - r-ggrepel @@ -37,11 +38,11 @@ requirements: - r-seurat - r-viridislite run: - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-appreci8r/meta.yaml b/recipes/bioconductor-appreci8r/meta.yaml index b3a99c97d31a0..fdbd9dac892ba 100644 --- a/recipes/bioconductor-appreci8r/meta.yaml +++ b/recipes/bioconductor-appreci8r/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.1" %} {% set name = "appreci8R" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,73 +11,72 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 47501e7afbbe98a31b837ea71d094727 + md5: 9165459dd4a98c9645928c87b934c081 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-appreci8r", max_pin="x.x") }}' noarch: generic -# Suggests: GO.db, org.Hs.eg.db +# Suggests: GO.db, org.Hs.eg.db, utils requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-cosmic.67 >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' + - 'bioconductor-cosmic.67 >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-mafdb.1kgenomes.phase3.hs37d5 >=3.10.0,<3.11.0' - 'bioconductor-mafdb.exac.r1.0.hs37d5 >=3.10.0,<3.11.0' - 'bioconductor-mafdb.gnomadex.r2.1.hs37d5 >=3.10.0,<3.11.0' - 'bioconductor-polyphen.hsapiens.dbsnp131 >=1.0.0,<1.1.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-sift.hsapiens.dbsnp137 >=1.0.0,<1.1.0' - 'bioconductor-snplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - 'bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' - r-base - r-dt - r-openxlsx - r-rentrez - - r-rsnps - r-seqinr - r-shiny - r-shinyjs - r-stringr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-cosmic.67 >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' + - 'bioconductor-cosmic.67 >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-mafdb.1kgenomes.phase3.hs37d5 >=3.10.0,<3.11.0' - 'bioconductor-mafdb.exac.r1.0.hs37d5 >=3.10.0,<3.11.0' - 'bioconductor-mafdb.gnomadex.r2.1.hs37d5 >=3.10.0,<3.11.0' - 'bioconductor-polyphen.hsapiens.dbsnp131 >=1.0.0,<1.1.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-sift.hsapiens.dbsnp137 >=1.0.0,<1.1.0' - 'bioconductor-snplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - 'bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' - r-base - r-dt - r-openxlsx - r-rentrez - - r-rsnps - r-seqinr - r-shiny - r-shinyjs diff --git a/recipes/bioconductor-arabidopsis.db0/meta.yaml b/recipes/bioconductor-arabidopsis.db0/meta.yaml index 59d8ccdd4d9fd..a353a6fe036e9 100644 --- a/recipes/bioconductor-arabidopsis.db0/meta.yaml +++ b/recipes/bioconductor-arabidopsis.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "arabidopsis.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 773844428cd90716c8e32f942328618d + md5: 5896dbae0f9f8fdc87712dba0bb6cbd1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-arabidopsis.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-arabidopsis.db0/post-link.sh b/recipes/bioconductor-arabidopsis.db0/post-link.sh index ff530db18e421..45f1d087e4fb9 100644 --- a/recipes/bioconductor-arabidopsis.db0/post-link.sh +++ b/recipes/bioconductor-arabidopsis.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "arabidopsis.db0-3.17.0" +installBiocDataPackage.sh "arabidopsis.db0-3.18.0" diff --git a/recipes/bioconductor-aracne.networks/meta.yaml b/recipes/bioconductor-aracne.networks/meta.yaml index 4de189b8200a4..a1725ffbcf2bf 100644 --- a/recipes/bioconductor-aracne.networks/meta.yaml +++ b/recipes/bioconductor-aracne.networks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "aracne.networks" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 766b50311db15b7c36dffbb945277382 + md5: 42657d0acf4c1ba54aa2057fa4525d51 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aracne.networks", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-aracne.networks/post-link.sh b/recipes/bioconductor-aracne.networks/post-link.sh index 62f03eb5bec12..a25ee53fa9383 100644 --- a/recipes/bioconductor-aracne.networks/post-link.sh +++ b/recipes/bioconductor-aracne.networks/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "aracne.networks-1.26.0" +installBiocDataPackage.sh "aracne.networks-1.28.0" diff --git a/recipes/bioconductor-aroma.light/meta.yaml b/recipes/bioconductor-aroma.light/meta.yaml index cbb3a8373f6eb..30e404c5a01cf 100644 --- a/recipes/bioconductor-aroma.light/meta.yaml +++ b/recipes/bioconductor-aroma.light/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.30.0" %} +{% set version = "3.32.0" %} {% set name = "aroma.light" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 479f763a3001b487d9b3111d6505eece + md5: 07d98bcf8be950a16c1d6aaae375f17d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aroma.light", max_pin="x.x") }}' noarch: generic # Suggests: princurve (>= 2.1.4) requirements: diff --git a/recipes/bioconductor-arrayexpress/meta.yaml b/recipes/bioconductor-arrayexpress/meta.yaml index eca4847f54ffb..6efa3dbf50684 100644 --- a/recipes/bioconductor-arrayexpress/meta.yaml +++ b/recipes/bioconductor-arrayexpress/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "ArrayExpress" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9dc6f2a3298a96b6416d7b6cbacf59de + md5: 6232db8158e5ba9cde38da322b0c5163 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-arrayexpress", max_pin="x.x") }}' noarch: generic # Suggests: affy requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' - r-base - r-httr - r-jsonlite - r-rlang run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' - r-base - r-httr - r-jsonlite diff --git a/recipes/bioconductor-arraymvout/meta.yaml b/recipes/bioconductor-arraymvout/meta.yaml index 765e9efcc5abb..612d3124a7a6b 100644 --- a/recipes/bioconductor-arraymvout/meta.yaml +++ b/recipes/bioconductor-arraymvout/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "arrayMvout" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 496faed8293a47944fe26efa75276598 + md5: 7aa46c496dbe47218ea774cb02108800 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-arraymvout", max_pin="x.x") }}' noarch: generic # Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affycontam >=1.58.0,<1.59.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' - - 'bioconductor-mdqc >=1.62.0,<1.63.0' - - 'bioconductor-parody >=1.58.0,<1.59.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affycontam >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' + - 'bioconductor-mdqc >=1.64.0,<1.65.0' + - 'bioconductor-parody >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affycontam >=1.58.0,<1.59.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' - - 'bioconductor-mdqc >=1.62.0,<1.63.0' - - 'bioconductor-parody >=1.58.0,<1.59.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affycontam >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' + - 'bioconductor-mdqc >=1.64.0,<1.65.0' + - 'bioconductor-parody >=1.60.0,<1.61.0' - r-base test: commands: diff --git a/recipes/bioconductor-arrayquality/meta.yaml b/recipes/bioconductor-arrayquality/meta.yaml index 0429256522126..c3c33beb6b5c6 100644 --- a/recipes/bioconductor-arrayquality/meta.yaml +++ b/recipes/bioconductor-arrayquality/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "arrayQuality" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 05fac545dc5122c38913b83e9788c06e + md5: 9d875e31dc2f51e4c476d1a13330ad18 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-arrayquality", max_pin="x.x") }}' noarch: generic # Suggests: mclust, MEEBOdata, HEEBOdata requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-gridbase - r-hexbin - r-rcolorbrewer run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-gridbase - r-hexbin diff --git a/recipes/bioconductor-arrayqualitymetrics/meta.yaml b/recipes/bioconductor-arrayqualitymetrics/meta.yaml index 4b809dc9ebc2a..46f59c2bc01a2 100644 --- a/recipes/bioconductor-arrayqualitymetrics/meta.yaml +++ b/recipes/bioconductor-arrayqualitymetrics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.56.0" %} +{% set version = "3.58.0" %} {% set name = "arrayQualityMetrics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d6e27fd09971235379b22a11ec9a0e8 + md5: 65128c55b6181bdadb73d256e399091e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-arrayqualitymetrics", max_pin="x.x") }}' noarch: generic # Suggests: ALLMLL, CCl4, BiocStyle, knitr requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyplm >=1.76.0,<1.77.0' - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyplm >=1.78.0,<1.79.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - 'r-gridsvg >=1.4-3' - r-hmisc @@ -39,13 +40,13 @@ requirements: - r-svglite - r-xml run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyplm >=1.76.0,<1.77.0' - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyplm >=1.78.0,<1.79.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - 'r-gridsvg >=1.4-3' - r-hmisc diff --git a/recipes/bioconductor-arrmdata/meta.yaml b/recipes/bioconductor-arrmdata/meta.yaml index 3360d61788513..a7fe1357a1d0d 100644 --- a/recipes/bioconductor-arrmdata/meta.yaml +++ b/recipes/bioconductor-arrmdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "ARRmData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d1a4ecc042b17945f8a02625fbfa97b5 + md5: 95475f869b8ff3d6344c0f45f2e616c9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-arrmdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-arrmdata/post-link.sh b/recipes/bioconductor-arrmdata/post-link.sh index ca315f09c39d6..92579cc4ac064 100644 --- a/recipes/bioconductor-arrmdata/post-link.sh +++ b/recipes/bioconductor-arrmdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "arrmdata-1.36.0" +installBiocDataPackage.sh "arrmdata-1.38.0" diff --git a/recipes/bioconductor-arrmnormalization/meta.yaml b/recipes/bioconductor-arrmnormalization/meta.yaml index 225d1b87b01ad..437968da022a4 100644 --- a/recipes/bioconductor-arrmnormalization/meta.yaml +++ b/recipes/bioconductor-arrmnormalization/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "ARRmNormalization" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1331a6d43b42563841b7712441e0d14d + md5: a6223cb64b7077670d38fb437638e0fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-arrmnormalization", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-arrmdata >=1.36.0,<1.37.0' + - 'bioconductor-arrmdata >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-arrmdata >=1.36.0,<1.37.0' + - 'bioconductor-arrmdata >=1.38.0,<1.39.0' - r-base test: commands: diff --git a/recipes/bioconductor-artms/meta.yaml b/recipes/bioconductor-artms/meta.yaml index 0f79e21cd6bd9..25f17daed6675 100644 --- a/recipes/bioconductor-artms/meta.yaml +++ b/recipes/bioconductor-artms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "artMS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de4a453a5d57a20ee95302254d866981 + md5: d52a9405bcf6f4a3920ecb70be49c1d9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-artms", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR, knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-bit64 - r-circlize @@ -50,10 +51,10 @@ requirements: - r-venndiagram - r-yaml run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-bit64 - r-circlize diff --git a/recipes/bioconductor-asafe/meta.yaml b/recipes/bioconductor-asafe/meta.yaml index 74c736c362256..46bae4e0a4f2d 100644 --- a/recipes/bioconductor-asafe/meta.yaml +++ b/recipes/bioconductor-asafe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "ASAFE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02ac2aeccd6067529507ff1b46c0fdaf + md5: e054d986c3b6f2574c26498eaf6e4f7c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-asafe", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat requirements: diff --git a/recipes/bioconductor-aseb/meta.yaml b/recipes/bioconductor-aseb/meta.yaml index 0efab8d563af3..185e0ab4c1db4 100644 --- a/recipes/bioconductor-aseb/meta.yaml +++ b/recipes/bioconductor-aseb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.3" %} {% set name = "ASEB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 205d8716d05f9046395de90b9d48cdc2 + md5: 7e9312371523d44d7f1cb759af2d150e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aseb", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-asgsca/meta.yaml b/recipes/bioconductor-asgsca/meta.yaml index 740cffa843961..2fd57fbdec08e 100644 --- a/recipes/bioconductor-asgsca/meta.yaml +++ b/recipes/bioconductor-asgsca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "ASGSCA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: db2fb611216db58fd5fa05720151ab2e + md5: c0e60b4fa228444ab7863044881fa8bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-asgsca", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: diff --git a/recipes/bioconductor-ashkenazimsonchr21/meta.yaml b/recipes/bioconductor-ashkenazimsonchr21/meta.yaml index b4e1289ce168f..e111494e14c2a 100644 --- a/recipes/bioconductor-ashkenazimsonchr21/meta.yaml +++ b/recipes/bioconductor-ashkenazimsonchr21/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "AshkenazimSonChr21" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6180e43108e29d9194ed93bc0f208124 + md5: a4455fab1d47dcf8dc2411fec1066a2c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ashkenazimsonchr21", max_pin="x.x") }}' noarch: generic # Suggests: knitr, VariantAnnotation requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ashkenazimsonchr21/post-link.sh b/recipes/bioconductor-ashkenazimsonchr21/post-link.sh index 27d6400da0ce0..20f8d2ad38a7e 100644 --- a/recipes/bioconductor-ashkenazimsonchr21/post-link.sh +++ b/recipes/bioconductor-ashkenazimsonchr21/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ashkenazimsonchr21-1.30.0" +installBiocDataPackage.sh "ashkenazimsonchr21-1.32.0" diff --git a/recipes/bioconductor-asics/meta.yaml b/recipes/bioconductor-asics/meta.yaml index 52580c3dcf753..49a962cda7e85 100644 --- a/recipes/bioconductor-asics/meta.yaml +++ b/recipes/bioconductor-asics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "ASICS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7e6efa85c8bc0444a5cac2114338cff + md5: 526bfb1ebf38574a4914a434cd159769 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-asics", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat, ASICSdata requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-pepsnmr >=1.18.0,<1.19.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-pepsnmr >=1.20.0,<1.21.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-glmnet @@ -35,10 +36,10 @@ requirements: - r-quadprog - r-zoo run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-pepsnmr >=1.18.0,<1.19.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-pepsnmr >=1.20.0,<1.21.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-glmnet diff --git a/recipes/bioconductor-asicsdata/meta.yaml b/recipes/bioconductor-asicsdata/meta.yaml index 47f0f44eabcb9..6863b79647e76 100644 --- a/recipes/bioconductor-asicsdata/meta.yaml +++ b/recipes/bioconductor-asicsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ASICSdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46a4e15b37bd49b3cd5693c1a900b581 + md5: afb117c0db733e23239bf2cf4e18d364 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-asicsdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-asicsdata/post-link.sh b/recipes/bioconductor-asicsdata/post-link.sh index 5e413191611a5..cacabdb1a734e 100644 --- a/recipes/bioconductor-asicsdata/post-link.sh +++ b/recipes/bioconductor-asicsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "asicsdata-1.20.0" +installBiocDataPackage.sh "asicsdata-1.22.0" diff --git a/recipes/bioconductor-aspli/meta.yaml b/recipes/bioconductor-aspli/meta.yaml index 9008a0e8a4d46..7b9d0fd06dfdf 100644 --- a/recipes/bioconductor-aspli/meta.yaml +++ b/recipes/bioconductor-aspli/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "ASpli" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 718667b9b158c89ef2f05649516aa3aa + md5: abf86e5478e3191f21892ba2eb35e442 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aspli", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dt @@ -42,18 +43,18 @@ requirements: - r-tidyr - r-upsetr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dt diff --git a/recipes/bioconductor-assessorf/meta.yaml b/recipes/bioconductor-assessorf/meta.yaml index dc05bd73c91d6..b03bbb0dcf99d 100644 --- a/recipes/bioconductor-assessorf/meta.yaml +++ b/recipes/bioconductor-assessorf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "AssessORF" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4f5157d6177c7915fc9776c5b4d8b214 + md5: b11ca260fff21c6afe98ee471d79b3ec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-assessorf", max_pin="x.x") }}' noarch: generic # Suggests: AssessORFData, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base test: commands: diff --git a/recipes/bioconductor-assessorfdata/meta.yaml b/recipes/bioconductor-assessorfdata/meta.yaml index e2efc67f2625b..59253cef5e2df 100644 --- a/recipes/bioconductor-assessorfdata/meta.yaml +++ b/recipes/bioconductor-assessorfdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "AssessORFData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d7c0f6953391e3f1f610467f14384774 + md5: 0dd44e672021a9179762efe4959e8608 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-assessorfdata", max_pin="x.x") }}' noarch: generic # Suggests: AssessORF, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-decipher >=2.28.0,<2.29.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' - r-base run: - - 'bioconductor-decipher >=2.28.0,<2.29.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-assessorfdata/post-link.sh b/recipes/bioconductor-assessorfdata/post-link.sh index 6728e501cc5c3..dc7f9d707e3cd 100644 --- a/recipes/bioconductor-assessorfdata/post-link.sh +++ b/recipes/bioconductor-assessorfdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "assessorfdata-1.18.0" +installBiocDataPackage.sh "assessorfdata-1.20.0" diff --git a/recipes/bioconductor-asset/meta.yaml b/recipes/bioconductor-asset/meta.yaml index 96c79973b49fa..fe7f5b9cdda56 100644 --- a/recipes/bioconductor-asset/meta.yaml +++ b/recipes/bioconductor-asset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "ASSET" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c92854756cfbc064a6843c69dfefbfd5 + md5: 395bcc1b0256acc248c5d3440bf5dfeb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-asset", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr requirements: diff --git a/recipes/bioconductor-assign/meta.yaml b/recipes/bioconductor-assign/meta.yaml index f13680a216ae7..ce78d053d88c9 100644 --- a/recipes/bioconductor-assign/meta.yaml +++ b/recipes/bioconductor-assign/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "ASSIGN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95d9e71f088aa3369298e6889fe82a2c + md5: c03c8eedec6379aa0fac65d11377fdf8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-assign", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, lintr, knitr, rmarkdown requirements: host: - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-ggplot2 - r-gplots @@ -29,7 +30,7 @@ requirements: - r-rlab - r-yaml run: - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-ggplot2 - r-gplots diff --git a/recipes/bioconductor-asurat/meta.yaml b/recipes/bioconductor-asurat/meta.yaml index 77d1a41e21d31..79307284cafc7 100644 --- a/recipes/bioconductor-asurat/meta.yaml +++ b/recipes/bioconductor-asurat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "ASURAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f7bc663de993eed55f2a14aaa4946385 + md5: a1cb615f6ddab8cb8b9ccb1a73ba39de build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-asurat", max_pin="x.x") }}' # Suggests: ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi, BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-cluster @@ -32,10 +33,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-cluster diff --git a/recipes/bioconductor-ataccogaps/meta.yaml b/recipes/bioconductor-ataccogaps/meta.yaml index 9a6e32fe9f3cb..3988a44053f03 100644 --- a/recipes/bioconductor-ataccogaps/meta.yaml +++ b/recipes/bioconductor-ataccogaps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ATACCoGAPS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 266f86c0e01ae75b62a42f9ff65d69e1 + md5: f8cf8dd559b05caf23934090510297de build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ataccogaps", max_pin="x.x") }}' noarch: generic # Suggests: knitr, viridis requirements: host: - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - - 'bioconductor-chromvar >=1.22.0,<1.23.0' - - 'bioconductor-cogaps >=3.19.0,<3.20.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-geneoverlap >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-chromvar >=1.24.0,<1.25.0' + - 'bioconductor-cogaps >=3.22.0,<3.23.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-geneoverlap >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-jaspar2016 >=1.28.0,<1.29.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-jaspar2016 >=1.30.0,<1.31.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' - 'bioconductor-mus.musculus >=1.3.0,<1.4.0' - - 'bioconductor-projectr >=1.16.0,<1.17.0' - - 'bioconductor-rgreat >=2.2.0,<2.3.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-projectr >=1.18.0,<1.19.0' + - 'bioconductor-rgreat >=2.4.0,<2.5.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-dplyr - r-gplots @@ -47,20 +48,20 @@ requirements: run: - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - - 'bioconductor-chromvar >=1.22.0,<1.23.0' - - 'bioconductor-cogaps >=3.19.0,<3.20.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-geneoverlap >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-chromvar >=1.24.0,<1.25.0' + - 'bioconductor-cogaps >=3.22.0,<3.23.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-geneoverlap >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-jaspar2016 >=1.28.0,<1.29.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-jaspar2016 >=1.30.0,<1.31.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' - 'bioconductor-mus.musculus >=1.3.0,<1.4.0' - - 'bioconductor-projectr >=1.16.0,<1.17.0' - - 'bioconductor-rgreat >=2.2.0,<2.3.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-projectr >=1.18.0,<1.19.0' + - 'bioconductor-rgreat >=2.4.0,<2.5.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-dplyr - r-gplots diff --git a/recipes/bioconductor-atacseqqc/meta.yaml b/recipes/bioconductor-atacseqqc/meta.yaml index 0ee2956e6770a..46ba87f49caf2 100644 --- a/recipes/bioconductor-atacseqqc/meta.yaml +++ b/recipes/bioconductor-atacseqqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "ATACseqQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,51 +11,52 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43463f55028e1db0b7f94d6014507700 + md5: 6742da3bbb4073be7aa5f2544b65df23 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-atacseqqc", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-kernsmooth - r-preseqr - r-randomforest run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-kernsmooth - r-preseqr diff --git a/recipes/bioconductor-atacseqtfea/meta.yaml b/recipes/bioconductor-atacseqtfea/meta.yaml index f00ef0af0ce58..e11f613d103a9 100644 --- a/recipes/bioconductor-atacseqtfea/meta.yaml +++ b/recipes/bioconductor-atacseqtfea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ATACseqTFEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de251ce1a7cb6b4e6a670db088bb0c23 + md5: 30284cc31687d97f23d2a7c023e8561d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-atacseqtfea", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-dplyr - r-ggplot2 @@ -39,17 +40,17 @@ requirements: - r-matrix - r-pracma run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-atena/meta.yaml b/recipes/bioconductor-atena/meta.yaml index f3faff83b15d8..f34d851d4bc20 100644 --- a/recipes/bioconductor-atena/meta.yaml +++ b/recipes/bioconductor-atena/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "atena" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,43 +11,44 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7522b8df9e9bb705d981a2f10adf1b39 + md5: c7ae11b12240ed1d848301b4c40b019e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-atena", max_pin="x.x") }}' noarch: generic # Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit, TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-matrixstats - r-squarem run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-matrixstats diff --git a/recipes/bioconductor-ath1121501.db/meta.yaml b/recipes/bioconductor-ath1121501.db/meta.yaml index 1df20035f550b..ad07150ccead6 100644 --- a/recipes/bioconductor-ath1121501.db/meta.yaml +++ b/recipes/bioconductor-ath1121501.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "ath1121501.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c5d937ca9c6bcbb4385fb37a3b14ad15 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ath1121501.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.at.tair.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.at.tair.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.at.tair.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.at.tair.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ath1121501cdf/meta.yaml b/recipes/bioconductor-ath1121501cdf/meta.yaml index 288550799f467..24a018cde9f47 100644 --- a/recipes/bioconductor-ath1121501cdf/meta.yaml +++ b/recipes/bioconductor-ath1121501cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ath1121501cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8b63798143219b7c1c2666a91a1a2440 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ath1121501cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ath1121501probe/meta.yaml b/recipes/bioconductor-ath1121501probe/meta.yaml index e976c42b63525..b5f881e5be459 100644 --- a/recipes/bioconductor-ath1121501probe/meta.yaml +++ b/recipes/bioconductor-ath1121501probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ath1121501probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: eeeae5e6550bb472ba3419d71bbd7dfb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ath1121501probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-atsnp/meta.yaml b/recipes/bioconductor-atsnp/meta.yaml index ee86773b673f5..22b2497f49120 100644 --- a/recipes/bioconductor-atsnp/meta.yaml +++ b/recipes/bioconductor-atsnp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "atSNP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d73cffb926671ee83a72e6f5cf34428 + md5: e7de15cd417026f8449b14841ff89bd2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-atsnp", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' - r-base - r-data.table - r-ggplot2 @@ -34,10 +35,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-attract/meta.yaml b/recipes/bioconductor-attract/meta.yaml index d15a94a2d8b3c..8bf0a00a35862 100644 --- a/recipes/bioconductor-attract/meta.yaml +++ b/recipes/bioconductor-attract/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "attract" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bc7912564093f9fbc689a27829012832 + md5: e7d563026d5d00b5dd3bd906268af221 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-attract", max_pin="x.x") }}' noarch: generic # Suggests: illuminaHumanv1.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - r-base - r-cluster run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - r-base - r-cluster test: diff --git a/recipes/bioconductor-aucell/meta.yaml b/recipes/bioconductor-aucell/meta.yaml index 5d91c15ceb337..806723573eb1a 100644 --- a/recipes/bioconductor-aucell/meta.yaml +++ b/recipes/bioconductor-aucell/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "AUCell" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20e4725a450ea1ef9ae1de7b6e0b2a4c + md5: 4d095823da2fd13bf83c831c037564ff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aucell", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, rbokeh, Rtsne, testthat, zoo requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-matrix @@ -33,11 +34,11 @@ requirements: - r-r.utils - r-shiny run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-matrix diff --git a/recipes/bioconductor-autonomics/meta.yaml b/recipes/bioconductor-autonomics/meta.yaml index 10078e09c11a3..506a4b040c9ad 100644 --- a/recipes/bioconductor-autonomics/meta.yaml +++ b/recipes/bioconductor-autonomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.2" %} {% set name = "autonomics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 79d945c34c8797df2eb8140818e05b57 + md5: 9034c755764d54d8bf0eb0e330f4e54f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-autonomics", max_pin="x.x") }}' noarch: generic # Suggests: affy, AnnotationDbi, BiocManager, BiocStyle, diagram, GenomicRanges, GEOquery, hgu95av2.db, ICSNP, knitr, lme4, lmerTest, MASS, mixOmics, mpm, nlme, org.Hs.eg.db, org.Mm.eg.db, RCurl, remotes, rmarkdown, ropls, Rsubread, rtracklayer, seqinr, statmod, testthat requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - - r-assertive + - r-assertive.base + - r-assertive.files + - r-assertive.numbers + - r-assertive.sets - r-base - r-bit64 - r-colorspace @@ -49,16 +53,19 @@ requirements: - r-stringi - r-tidyr run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - - r-assertive + - r-assertive.base + - r-assertive.files + - r-assertive.numbers + - r-assertive.sets - r-base - r-bit64 - r-colorspace diff --git a/recipes/bioconductor-awfisher/meta.yaml b/recipes/bioconductor-awfisher/meta.yaml index 3d0ec3cad3dd0..cc019247c8442 100644 --- a/recipes/bioconductor-awfisher/meta.yaml +++ b/recipes/bioconductor-awfisher/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "AWFisher" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a52828e4fdc882bcc16a7a4de22af840 + md5: ba9b2824782018cc7626ebc72b6bb81e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-awfisher", max_pin="x.x") }}' # Suggests: knitr, tightClust requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - libblas - liblapack run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-awst/meta.yaml b/recipes/bioconductor-awst/meta.yaml index 4e3ebced198fc..c735340e61235 100644 --- a/recipes/bioconductor-awst/meta.yaml +++ b/recipes/bioconductor-awst/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "awst" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 88c6bfd36a182af8d3107bcb8cacba4a + md5: a7ca0636a8f728b63d6cf56729b856eb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-awst", max_pin="x.x") }}' noarch: generic # Suggests: airway, ggplot2, testthat, EDASeq, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-baalchip/meta.yaml b/recipes/bioconductor-baalchip/meta.yaml index 95ce06a3db06a..4596a55c8a87c 100644 --- a/recipes/bioconductor-baalchip/meta.yaml +++ b/recipes/bioconductor-baalchip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "BaalChIP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d5b38867245ae1ce58e3d6e1f50f6e5f + md5: 5f2cf6dd86b26982d4d7ed693f961246 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-baalchip", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-coda - r-doby @@ -35,11 +36,11 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-coda - r-doby diff --git a/recipes/bioconductor-bacon/meta.yaml b/recipes/bioconductor-bacon/meta.yaml index 988a288f5b586..350eb69311bf0 100644 --- a/recipes/bioconductor-bacon/meta.yaml +++ b/recipes/bioconductor-bacon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "bacon" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fdad543dfc946ebc8aa940e9f5a9da4e + md5: 3757e896d5a8253845a21e37e555044a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bacon", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-ellipse - r-ggplot2 - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-ellipse - r-ggplot2 diff --git a/recipes/bioconductor-bader/meta.yaml b/recipes/bioconductor-bader/meta.yaml index c86c6dd83e7e6..346caafa84021 100644 --- a/recipes/bioconductor-bader/meta.yaml +++ b/recipes/bioconductor-bader/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "BADER" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec42e5966b46992505dacfb8880b24b0 + md5: 10d4e5e231ff178df7922078024f9d89 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bader", max_pin="x.x") }}' # Suggests: pasilla (>= 0.2.10) requirements: host: diff --git a/recipes/bioconductor-badregionfinder/meta.yaml b/recipes/bioconductor-badregionfinder/meta.yaml index e4d5277acfd58..18612ea8cae65 100644 --- a/recipes/bioconductor-badregionfinder/meta.yaml +++ b/recipes/bioconductor-badregionfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "BadRegionFinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3fe981fffe29fd21bcc16672c1d46205 + md5: c492af1d6b1297cd322a79355e3d3664 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-badregionfinder", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-bags/meta.yaml b/recipes/bioconductor-bags/meta.yaml index 8e523dd945fc8..9aa67ffe4f606 100644 --- a/recipes/bioconductor-bags/meta.yaml +++ b/recipes/bioconductor-bags/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.40.0" %} +{% set version = "2.42.0" %} {% set name = "BAGS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 206c6b841ff841017f5a6af951bcbbef + md5: 42c7a57422ddbb5c2d5263703a7e22d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bags", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-breastcancervdx >=1.38.0,<1.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-breastcancervdx >=1.40.0,<1.41.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-breastcancervdx >=1.38.0,<1.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-breastcancervdx >=1.40.0,<1.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-ballgown/meta.yaml b/recipes/bioconductor-ballgown/meta.yaml index e927ffedbda31..a9d3e0017fa92 100644 --- a/recipes/bioconductor-ballgown/meta.yaml +++ b/recipes/bioconductor-ballgown/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "ballgown" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8bf7da5968f9f4cc1aa14d8f0693d8e2 + md5: 805a1514b4080a8b00b4bdfce051dcda build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ballgown", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, markdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-rcolorbrewer test: diff --git a/recipes/bioconductor-bambu/meta.yaml b/recipes/bioconductor-bambu/meta.yaml index bb14fbe4730d8..0a5192523653c 100644 --- a/recipes/bioconductor-bambu/meta.yaml +++ b/recipes/bioconductor-bambu/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.2.4" %} +{% set version = "3.4.0" %} {% set name = "bambu" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d9a12cd1329e08735800e7928b98fb97 + md5: 900e0e67c251f12989154113c54d2b32 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bambu", max_pin="x.x") }}' # Suggests: AnnotationDbi, Biostrings, rmarkdown, BiocFileCache, ggplot2, ComplexHeatmap, circlize, ggbio, gridExtra, knitr, testthat, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3), DESeq2, NanoporeRNASeq, purrr, apeglm, utils, DEXSeq requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr @@ -41,17 +42,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-bamsignals/meta.yaml b/recipes/bioconductor-bamsignals/meta.yaml index 6e7abbf45ed04..fe49237768045 100644 --- a/recipes/bioconductor-bamsignals/meta.yaml +++ b/recipes/bioconductor-bamsignals/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "bamsignals" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ee29481c743d792e65ebff380d4fdf1e + md5: e7b42351aa9651bdf7d429a6377143f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bamsignals", max_pin="x.x") }}' # Suggests: testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - 'r-rcpp >=0.10.6' - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - 'r-rcpp >=0.10.6' build: diff --git a/recipes/bioconductor-bandits/meta.yaml b/recipes/bioconductor-bandits/meta.yaml index de9b008f4a75a..7ad9f0390a7b8 100644 --- a/recipes/bioconductor-bandits/meta.yaml +++ b/recipes/bioconductor-bandits/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.1" %} {% set name = "BANDITS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c6ef9178205f8a59be55faea48e08b90 + md5: 2a65b9a4669d4075f5882047445491eb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bandits", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings -# SystemRequirements: C++11 +# SystemRequirements: C++17 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-drimseq >=1.28.0,<1.29.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-drimseq >=1.30.0,<1.31.0' - r-base - r-data.table - r-doparallel @@ -36,8 +37,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-drimseq >=1.28.0,<1.29.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-drimseq >=1.30.0,<1.31.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-bandle/meta.yaml b/recipes/bioconductor-bandle/meta.yaml index 41051d877b568..c2bea3dd5035c 100644 --- a/recipes/bioconductor-bandle/meta.yaml +++ b/recipes/bioconductor-bandle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "bandle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 18a4217c592ace34eccbb1b9ea46295d + md5: 9c8dd928dd2b7900ff453ddc590ad6e4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bandle", max_pin="x.x") }}' # Suggests: coda (>= 0.19-4), testthat, interp, fields, pheatmap, viridis, rmarkdown, spelling requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-proloc >=1.40.0,<1.41.0' - - 'bioconductor-prolocdata >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-proloc >=1.42.0,<1.43.0' + - 'bioconductor-prolocdata >=1.40.0,<1.41.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bh - r-circlize @@ -45,13 +46,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-proloc >=1.40.0,<1.41.0' - - 'bioconductor-prolocdata >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-proloc >=1.42.0,<1.43.0' + - 'bioconductor-prolocdata >=1.40.0,<1.41.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bh - r-circlize diff --git a/recipes/bioconductor-banocc/meta.yaml b/recipes/bioconductor-banocc/meta.yaml index 0aff09d41f5b8..6c42e52f10707 100644 --- a/recipes/bioconductor-banocc/meta.yaml +++ b/recipes/bioconductor-banocc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "banocc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f67213c67fb7ef2fa721d0c38dceb1b0 + md5: 5a73975945814e725991bd67552349e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-banocc", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, methods, testthat, BiocStyle requirements: diff --git a/recipes/bioconductor-barcodetrackr/meta.yaml b/recipes/bioconductor-barcodetrackr/meta.yaml index 56dad017f8320..c001ab2392527 100644 --- a/recipes/bioconductor-barcodetrackr/meta.yaml +++ b/recipes/bioconductor-barcodetrackr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "barcodetrackR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ef50b9baf6cb0f19e3ad67f6afb445e + md5: 34e3b62fbe85f743278fba96cfc8c618 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-barcodetrackr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, magick, rmarkdown, testthat requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-cowplot @@ -42,8 +43,8 @@ requirements: - r-vegan - r-viridis run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-cowplot diff --git a/recipes/bioconductor-barley1cdf/meta.yaml b/recipes/bioconductor-barley1cdf/meta.yaml index c86da8e98d869..462dda51f3f36 100644 --- a/recipes/bioconductor-barley1cdf/meta.yaml +++ b/recipes/bioconductor-barley1cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "barley1cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 16a2ca83f550518756d9fa3273672157 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-barley1cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-barley1probe/meta.yaml b/recipes/bioconductor-barley1probe/meta.yaml index a6bb73c10d152..851b639c63da9 100644 --- a/recipes/bioconductor-barley1probe/meta.yaml +++ b/recipes/bioconductor-barley1probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "barley1probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 80595d8ecf83ba83ea84a722a24ab474 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-barley1probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-basecallqc/meta.yaml b/recipes/bioconductor-basecallqc/meta.yaml index 20641673259f7..a9a2496602e83 100644 --- a/recipes/bioconductor-basecallqc/meta.yaml +++ b/recipes/bioconductor-basecallqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "basecallQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d01b22d917934112ec3feaad5268060 + md5: ad61b901f8e533f817dccfb4830b222a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-basecallqc", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle # SystemRequirements: bcl2Fastq (versions >= 2.1.7) requirements: host: - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-data.table - r-dplyr @@ -39,7 +40,7 @@ requirements: - r-xml - r-yaml run: - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-basespacer/meta.yaml b/recipes/bioconductor-basespacer/meta.yaml index 0f6a9d240c07b..d19b37977de6b 100644 --- a/recipes/bioconductor-basespacer/meta.yaml +++ b/recipes/bioconductor-basespacer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "BaseSpaceR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 940b776f826fff5208c944e26a4fa538 + md5: b141511c6e978d4f26c8ec4c42c078c2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-basespacer", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, IRanges, Rsamtools requirements: diff --git a/recipes/bioconductor-basic4cseq/meta.yaml b/recipes/bioconductor-basic4cseq/meta.yaml index 05f70073532b7..1a5adc44f4e62 100644 --- a/recipes/bioconductor-basic4cseq/meta.yaml +++ b/recipes/bioconductor-basic4cseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "Basic4Cseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c3471249017f78eda382aba54e760ea + md5: b6e8e624b34a0626cfa015e9814d017b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-basic4cseq", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.ecoli.ncbi.20080805 >=1.3.0,<1.4.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-catools - r-rcircos run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.ecoli.ncbi.20080805 >=1.3.0,<1.4.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-catools - r-rcircos diff --git a/recipes/bioconductor-basics/meta.yaml b/recipes/bioconductor-basics/meta.yaml index b2c87423a85e7..71548c210ade6 100644 --- a/recipes/bioconductor-basics/meta.yaml +++ b/recipes/bioconductor-basics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.3" %} +{% set version = "2.14.0" %} {% set name = "BASiCS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 148355fc63bab3ac6c9b742f6613286f + md5: 1252fa180b0da21a4a22e3400550ab93 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-basics", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, magick # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-coda @@ -47,14 +48,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-coda diff --git a/recipes/bioconductor-basicstan/meta.yaml b/recipes/bioconductor-basicstan/meta.yaml index 3f917708d53b6..5e7eecf766f1d 100644 --- a/recipes/bioconductor-basicstan/meta.yaml +++ b/recipes/bioconductor-basicstan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "BASiCStan" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 130a35d534f52c5361f97c16bb7af5c2 + md5: b7179ffcf510240c0c3cc6e8e31b60d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-basicstan", max_pin="x.x") }}' # Suggests: testthat (>= 3.0.0), knitr, rmarkdown # SystemRequirements: GNU make requirements: host: - - 'bioconductor-basics >=2.12.0,<2.13.0' - - 'bioconductor-glmgampoi >=1.12.0,<1.13.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basics >=2.14.0,<2.15.0' + - 'bioconductor-glmgampoi >=1.14.0,<1.15.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-bh >=1.66.0' - 'r-rcpp >=0.12.0' @@ -38,12 +39,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-basics >=2.12.0,<2.13.0' - - 'bioconductor-glmgampoi >=1.12.0,<1.13.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basics >=2.14.0,<2.15.0' + - 'bioconductor-glmgampoi >=1.14.0,<1.15.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-bh >=1.66.0' - 'r-rcpp >=0.12.0' diff --git a/recipes/bioconductor-basicstarrseq/meta.yaml b/recipes/bioconductor-basicstarrseq/meta.yaml index 603ee18b85d63..0962d27074600 100644 --- a/recipes/bioconductor-basicstarrseq/meta.yaml +++ b/recipes/bioconductor-basicstarrseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "BasicSTARRseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5309450baf05eaa4b75962a1c51a42d2 + md5: 45c21fe93b28467ae466fd4017792494 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-basicstarrseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-basilisk.utils/meta.yaml b/recipes/bioconductor-basilisk.utils/meta.yaml index bbf7fae14022c..50279f87793f9 100644 --- a/recipes/bioconductor-basilisk.utils/meta.yaml +++ b/recipes/bioconductor-basilisk.utils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.1" %} {% set name = "basilisk.utils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4c999a6536d2c0b080b9f2ee83f3bd47 + md5: d5e61359283886e8653f772e65b0a898 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-basilisk.utils", max_pin="x.x") }}' noarch: generic # Suggests: reticulate, knitr, rmarkdown, BiocStyle, testthat, basilisk requirements: host: - - 'bioconductor-dir.expiry >=1.8.0,<1.9.0' + - 'bioconductor-dir.expiry >=1.10.0,<1.11.0' - r-base run: - - 'bioconductor-dir.expiry >=1.8.0,<1.9.0' + - 'bioconductor-dir.expiry >=1.10.0,<1.11.0' - r-base test: commands: diff --git a/recipes/bioconductor-basilisk/meta.yaml b/recipes/bioconductor-basilisk/meta.yaml index 1537a740c3827..8e6089e3f742c 100644 --- a/recipes/bioconductor-basilisk/meta.yaml +++ b/recipes/bioconductor-basilisk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.1" %} {% set name = "basilisk" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5335a9b864bad01710c0e326dabc29e3 + md5: b47dde22cc3bb45ec9c785fe025241a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-basilisk", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat, callr requirements: host: - - 'bioconductor-basilisk.utils >=1.12.0,<1.13.0' - - 'bioconductor-dir.expiry >=1.8.0,<1.9.0' + - 'bioconductor-basilisk.utils >=1.14.0,<1.15.0' + - 'bioconductor-dir.expiry >=1.10.0,<1.11.0' - r-base - r-reticulate run: - - 'bioconductor-basilisk.utils >=1.12.0,<1.13.0' - - 'bioconductor-dir.expiry >=1.8.0,<1.9.0' + - 'bioconductor-basilisk.utils >=1.14.0,<1.15.0' + - 'bioconductor-dir.expiry >=1.10.0,<1.11.0' - r-base - r-reticulate test: diff --git a/recipes/bioconductor-batchelor/meta.yaml b/recipes/bioconductor-batchelor/meta.yaml index 9b702df1f403a..85f55bdbb422e 100644 --- a/recipes/bioconductor-batchelor/meta.yaml +++ b/recipes/bioconductor-batchelor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "batchelor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c513fab91211a116143880cf00fc0f60 + md5: e78aa00a2e343b79e7ad7aeb0fde1196 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-batchelor", max_pin="x.x") }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown, scran, scater, bluster, scRNAseq # SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-residualmatrix >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scaledmatrix >=1.8.0,<1.9.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-residualmatrix >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-matrix @@ -41,19 +42,19 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-residualmatrix >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scaledmatrix >=1.8.0,<1.9.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-residualmatrix >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-matrix diff --git a/recipes/bioconductor-batchqc/meta.yaml b/recipes/bioconductor-batchqc/meta.yaml index 499d4b9ec9822..b8c5d00be9898 100644 --- a/recipes/bioconductor-batchqc/meta.yaml +++ b/recipes/bioconductor-batchqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "BatchQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9b92d0d1fb1c172b3558a5c0505b32df + md5: c8940666878af6ea1981e6d90095bc98 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-batchqc", max_pin="x.x") }}' noarch: generic # Suggests: testthat # SystemRequirements: pandoc (http://pandoc.org/installing.html) for generating reports from markdown files. requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-corpcor - r-ggvis @@ -40,8 +41,8 @@ requirements: - r-shiny - pandoc run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-corpcor - r-ggvis diff --git a/recipes/bioconductor-bayesknockdown/meta.yaml b/recipes/bioconductor-bayesknockdown/meta.yaml index dffb36eda212c..34fc090aa009a 100644 --- a/recipes/bioconductor-bayesknockdown/meta.yaml +++ b/recipes/bioconductor-bayesknockdown/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "BayesKnockdown" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ba8a6b2608364a8b8cecee2d4ef1ba6 + md5: 6efc97e1bf0448a97ca0b3d595096a3d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bayesknockdown", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-bayesspace/meta.yaml b/recipes/bioconductor-bayesspace/meta.yaml index bd630d27942de..8c53962e97f47 100644 --- a/recipes/bioconductor-bayesspace/meta.yaml +++ b/recipes/bioconductor-bayesspace/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "BayesSpace" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 674dcaf64d6130d014c2c1fbdf7d15a1 + md5: 5505178450768dc45884632e3e0a3baf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bayesspace", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, igraph, spatialLIBD, dplyr, viridis, patchwork, RColorBrewer, Seurat # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-coda @@ -47,14 +48,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-coda diff --git a/recipes/bioconductor-baynorm/meta.yaml b/recipes/bioconductor-baynorm/meta.yaml index 62993041a0030..32927dab2124f 100644 --- a/recipes/bioconductor-baynorm/meta.yaml +++ b/recipes/bioconductor-baynorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "bayNorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a17fbe6ef50d0b03b97ab29c7fa085c + md5: fda25f54086787e9a038cc59f0660a58 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-baynorm", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bb - r-dosnow @@ -38,9 +39,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bb - r-dosnow diff --git a/recipes/bioconductor-bayseq/build.sh b/recipes/bioconductor-bayseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bayseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bayseq/meta.yaml b/recipes/bioconductor-bayseq/meta.yaml new file mode 100644 index 0000000000000..1060cb2108ad2 --- /dev/null +++ b/recipes/bioconductor-bayseq/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "2.36.0" %} +{% set name = "baySeq" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f46b63ebca2bda7c124133149aa7e552 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bayseq", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, BiocGenerics +requirements: + host: + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - r-abind + - r-base + run: + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - r-abind + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Empirical Bayesian analysis of patterns of differential expression in count data' + description: 'This package identifies differential expression in high-throughput ''count'' data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-bbcanalyzer/meta.yaml b/recipes/bioconductor-bbcanalyzer/meta.yaml index 8f40477b642e7..953c2118d4578 100644 --- a/recipes/bioconductor-bbcanalyzer/meta.yaml +++ b/recipes/bioconductor-bbcanalyzer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "BBCAnalyzer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b6171b730ca7bc3859dd0964e928afd0 + md5: 33b123d417f53ee03c547220dfdb1612 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bbcanalyzer", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-bcellviper/meta.yaml b/recipes/bioconductor-bcellviper/meta.yaml index 33168059ab5e1..62edc4c0af227 100644 --- a/recipes/bioconductor-bcellviper/meta.yaml +++ b/recipes/bioconductor-bcellviper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "bcellViper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c35a1f30610cc929acc8bfdc79af1d13 + md5: 7e93bbaa204826358c77282e2a370074 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bcellviper", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bcellviper/post-link.sh b/recipes/bioconductor-bcellviper/post-link.sh index e892ee98f5a1b..00b243486be7d 100644 --- a/recipes/bioconductor-bcellviper/post-link.sh +++ b/recipes/bioconductor-bcellviper/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bcellviper-1.36.0" +installBiocDataPackage.sh "bcellviper-1.38.0" diff --git a/recipes/bioconductor-bcrank/meta.yaml b/recipes/bioconductor-bcrank/meta.yaml index 04a571ea243c0..e76407cf7cf0a 100644 --- a/recipes/bioconductor-bcrank/meta.yaml +++ b/recipes/bioconductor-bcrank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "BCRANK" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 36cb7441c4c60585348d43c0a6b08692 + md5: 6c551ab389af456ab76449642c01881a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bcrank", max_pin="x.x") }}' # Suggests: seqLogo requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-bcseq/meta.yaml b/recipes/bioconductor-bcseq/meta.yaml index 8b0acc15f7949..272410c1503a5 100644 --- a/recipes/bioconductor-bcseq/meta.yaml +++ b/recipes/bioconductor-bcseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "bcSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 210e968615481f3c2a8671d9bf1f7a84 + md5: e582b114bc4743a328b6ada2953a74da build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bcseq", max_pin="x.x") }}' # Suggests: knitr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-matrix - 'r-rcpp >=0.12.12' - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-matrix - 'r-rcpp >=0.12.12' diff --git a/recipes/bioconductor-beachmat.hdf5/build.sh b/recipes/bioconductor-beachmat.hdf5/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-beachmat.hdf5/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-beachmat.hdf5/meta.yaml b/recipes/bioconductor-beachmat.hdf5/meta.yaml new file mode 100644 index 0000000000000..d26114501a536 --- /dev/null +++ b/recipes/bioconductor-beachmat.hdf5/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.0.0" %} +{% set name = "beachmat.hdf5" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b2ca9b6358fb05895101e6a911ca0e39 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beachmat.hdf5", max_pin="x.x") }}' +# Suggests: testthat, BiocStyle, knitr, rmarkdown, rhdf5, Matrix +# SystemRequirements: C++17, GNU make +requirements: + host: + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - r-base + - r-rcpp + - libblas + - liblapack + run: + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - r-base + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'beachmat bindings for HDF5-backed matrices' + description: 'Extends beachmat to support initialization of tatami matrices from HDF5-backed arrays. This allows C++ code in downstream packages to directly call the HDF5 C/C++ library to access array data, without the need for block processing via DelayedArray. Some utilities are also provided for direct creation of an in-memory tatami matrix from a HDF5 file.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-beachmat/meta.yaml b/recipes/bioconductor-beachmat/meta.yaml index 774c7927729ed..b7ae4f0aa3360 100644 --- a/recipes/bioconductor-beachmat/meta.yaml +++ b/recipes/bioconductor-beachmat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "beachmat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4401998e14a9c1cfc516bd3167b4c8cc + md5: ec47172a09aba997192731b4a5f2f284 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beachmat", max_pin="x.x") }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown, rcmdcheck, BiocParallel, HDF5Array -# SystemRequirements: C++11 +# SystemRequirements: C++17 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-sparsearray >=1.2.0,<1.3.0' - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-sparsearray >=1.2.0,<1.3.0' - r-base - r-matrix - r-rcpp @@ -45,7 +48,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Compiling Bioconductor to Handle Each Matrix Type' - description: 'Provides a consistent C++ class interface for reading from and writing data to a variety of commonly used matrix types. Ordinary matrices and several sparse/dense Matrix classes are directly supported, third-party S4 classes may be supported by external linkage, while all other matrices are handled by DelayedArray block processing.' + description: 'Provides a consistent C++ class interface for reading from a variety of commonly used matrix types. Ordinary matrices and several sparse/dense Matrix classes are directly supported, along with a subset of the delayed operations implemented in the DelayedArray package. All other matrix-like objects are supported by calling back into R.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: parent_recipe: diff --git a/recipes/bioconductor-beadarray/meta.yaml b/recipes/bioconductor-beadarray/meta.yaml index 0aa5898a78f0a..16d2467732896 100644 --- a/recipes/bioconductor-beadarray/meta.yaml +++ b/recipes/bioconductor-beadarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.50.0" %} +{% set version = "2.52.0" %} {% set name = "beadarray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e9d095d2a6a7bd24581de5f6c0435e48 + md5: ed1729be533d0731833e523174b9dbb4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beadarray", max_pin="x.x") }}' # Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-beaddatapackr >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-beaddatapackr >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-hexbin @@ -35,14 +36,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-beaddatapackr >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-beaddatapackr >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-hexbin diff --git a/recipes/bioconductor-beadarrayexampledata/meta.yaml b/recipes/bioconductor-beadarrayexampledata/meta.yaml index e1ac0a8c19463..8a5709c7d1053 100644 --- a/recipes/bioconductor-beadarrayexampledata/meta.yaml +++ b/recipes/bioconductor-beadarrayexampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "beadarrayExampleData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8607365b2ef3e8a20b33eac9ae52c51 + md5: d327e659adc868f1e3c7ae457c60087b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beadarrayexampledata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-beadarrayexampledata/post-link.sh b/recipes/bioconductor-beadarrayexampledata/post-link.sh index 422f2ab789574..42281c8dc3e00 100644 --- a/recipes/bioconductor-beadarrayexampledata/post-link.sh +++ b/recipes/bioconductor-beadarrayexampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "beadarrayexampledata-1.38.0" +installBiocDataPackage.sh "beadarrayexampledata-1.40.0" diff --git a/recipes/bioconductor-beadarraysnp/meta.yaml b/recipes/bioconductor-beadarraysnp/meta.yaml index 0a37329c07dab..4302ccd7cd7b4 100644 --- a/recipes/bioconductor-beadarraysnp/meta.yaml +++ b/recipes/bioconductor-beadarraysnp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "beadarraySNP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 65dff50fe83456771977aa02caaa90e5 + md5: 748ed20ee2b38f5eee765be8125e5aca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beadarraysnp", max_pin="x.x") }}' noarch: generic # Suggests: aCGH, affy, limma, snapCGH, beadarray, DNAcopy requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-quantsmooth >=1.66.0,<1.67.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-quantsmooth >=1.68.0,<1.69.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-quantsmooth >=1.66.0,<1.67.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-quantsmooth >=1.68.0,<1.69.0' - r-base test: commands: diff --git a/recipes/bioconductor-beadarrayusecases/meta.yaml b/recipes/bioconductor-beadarrayusecases/meta.yaml index 60801e1b3fd24..29e716cd61f24 100644 --- a/recipes/bioconductor-beadarrayusecases/meta.yaml +++ b/recipes/bioconductor-beadarrayusecases/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "BeadArrayUseCases" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f02d0ef2902c1223d8e240b55bf77b91 + md5: a939c03744773755b9a80de63a925c3e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beadarrayusecases", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db requirements: host: - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base run: - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-beadarrayusecases/post-link.sh b/recipes/bioconductor-beadarrayusecases/post-link.sh index 82f46270f399b..60fda081d37d8 100644 --- a/recipes/bioconductor-beadarrayusecases/post-link.sh +++ b/recipes/bioconductor-beadarrayusecases/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "beadarrayusecases-1.38.0" +installBiocDataPackage.sh "beadarrayusecases-1.40.0" diff --git a/recipes/bioconductor-beaddatapackr/meta.yaml b/recipes/bioconductor-beaddatapackr/meta.yaml index c18dfa1d34f87..6613cebb430b6 100644 --- a/recipes/bioconductor-beaddatapackr/meta.yaml +++ b/recipes/bioconductor-beaddatapackr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "BeadDataPackR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c17047b30d1353607cbbcce03c90c182 + md5: b1e73395e4f18af4b799a1f447487a87 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beaddatapackr", max_pin="x.x") }}' # Suggests: BiocStyle, knitr requirements: host: diff --git a/recipes/bioconductor-beadsorted.saliva.epic/meta.yaml b/recipes/bioconductor-beadsorted.saliva.epic/meta.yaml index 889e16cef92f4..c39f60e6e07de 100644 --- a/recipes/bioconductor-beadsorted.saliva.epic/meta.yaml +++ b/recipes/bioconductor-beadsorted.saliva.epic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "BeadSorted.Saliva.EPIC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c521cbcd30e56de9e00a659d9e349320 + md5: ca080a144452fad8ce1bdf8e86d88c74 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beadsorted.saliva.epic", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-beadsorted.saliva.epic/post-link.sh b/recipes/bioconductor-beadsorted.saliva.epic/post-link.sh index c8f7addca48d3..4ce7d05773879 100644 --- a/recipes/bioconductor-beadsorted.saliva.epic/post-link.sh +++ b/recipes/bioconductor-beadsorted.saliva.epic/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "beadsorted.saliva.epic-1.8.0" +installBiocDataPackage.sh "beadsorted.saliva.epic-1.10.0" diff --git a/recipes/bioconductor-bearscc/meta.yaml b/recipes/bioconductor-bearscc/meta.yaml index 2189683b26e73..7c4d24a0d7462 100644 --- a/recipes/bioconductor-bearscc/meta.yaml +++ b/recipes/bioconductor-bearscc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "BEARscc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 035ff6012c3c148dc0a38c75640a9f3b + md5: 44eee85006f40ec0a81fa5b6bf26f6c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bearscc", max_pin="x.x") }}' noarch: generic # Suggests: testthat, cowplot, knitr, rmarkdown, BiocStyle, NMF requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-data.table - r-ggplot2 run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-beat/meta.yaml b/recipes/bioconductor-beat/meta.yaml index 3c8ccf6974465..3305424e4dae2 100644 --- a/recipes/bioconductor-beat/meta.yaml +++ b/recipes/bioconductor-beat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "BEAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d41321849b8d11806159fbbe3ec9b636 + md5: 46e0caf216c816dbe7323a1b0117fbf6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beat", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base test: commands: diff --git a/recipes/bioconductor-beclear/meta.yaml b/recipes/bioconductor-beclear/meta.yaml index 7514638502fec..22a3733efe5e5 100644 --- a/recipes/bioconductor-beclear/meta.yaml +++ b/recipes/bioconductor-beclear/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "BEclear" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ce5326c16adef82ee0e2d563b10d9b9 + md5: bd34703e5a35dfc888f0029395df2c80 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beclear", max_pin="x.x") }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown, pander, seewave # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-abind - r-base - 'r-data.table >=1.11.8' @@ -34,7 +35,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-abind - r-base - 'r-data.table >=1.11.8' diff --git a/recipes/bioconductor-beer/meta.yaml b/recipes/bioconductor-beer/meta.yaml index 546117288f23e..db26d4c26e576 100644 --- a/recipes/bioconductor-beer/meta.yaml +++ b/recipes/bioconductor-beer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "beer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9af7a20cd4d9384bf123a7ef854572de + md5: c8e6192a3f9bd04b62ed564c8164ba00 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beer", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr, rmarkdown, dplyr, ggplot2, spelling # SystemRequirements: JAGS (4.3.0) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-phipdata >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-phipdata >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-progressr - r-rjags run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-phipdata >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-phipdata >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-progressr diff --git a/recipes/bioconductor-benchdamic/build.sh b/recipes/bioconductor-benchdamic/build.sh index c1d13421f5f1e..497f7b5bdb678 100644 --- a/recipes/bioconductor-benchdamic/build.sh +++ b/recipes/bioconductor-benchdamic/build.sh @@ -8,4 +8,5 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars +export LD_LIBRARY_PATH=${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-benchdamic/build_failure.linux-64.yaml b/recipes/bioconductor-benchdamic/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..19d91cac3dd0e --- /dev/null +++ b/recipes/bioconductor-benchdamic/build_failure.linux-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 7993ff7f131f07a197238e7749097371f8ba7a13db8b1848d3a153e2501e2ab8 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-mast[version='>=1.28.0,<1.29.0']"), MatchSpec("r-microbiomestat")} +category: |- + dependency issue diff --git a/recipes/bioconductor-benchdamic/meta.yaml b/recipes/bioconductor-benchdamic/meta.yaml index b450a23c7ce83..bfe0f5be96b33 100644 --- a/recipes/bioconductor-benchdamic/meta.yaml +++ b/recipes/bioconductor-benchdamic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.1" %} {% set name = "benchdamic" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,77 +11,94 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 60b5a20af2bcf5272457ab2427f7f702 + md5: ca158383ebf87138c91438c7946fe567 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-benchdamic", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, kableExtra, BiocStyle, SPsimSeq, testthat +# Suggests: knitr, rmarkdown, kableExtra, BiocStyle, magick, SPsimSeq, testthat requirements: host: - - 'bioconductor-aldex2 >=1.32.0,<1.33.0' - - 'bioconductor-ancombc >=2.2.0,<2.3.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-dearseq >=1.12.0,<1.13.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mast >=1.26.0,<1.27.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' - - 'bioconductor-noiseq >=2.44.0,<2.45.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' - - 'bioconductor-zinbwave >=1.22.0,<1.23.0' + - 'bioconductor-aldex2 >=1.34.0,<1.35.0' + - 'bioconductor-ancombc >=2.4.0,<2.5.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-dearseq >=1.14.0,<1.15.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-maaslin2 >=1.16.0,<1.17.0' + - 'bioconductor-mast >=1.28.0,<1.29.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' + - 'bioconductor-noiseq >=2.46.0,<2.47.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - 'bioconductor-zinbwave >=1.24.0,<1.25.0' - r-base - - r-corncob - r-cowplot - r-ggdendro - r-ggplot2 - r-ggridges + - r-gunifrac - r-lme4 - r-mglm + - r-microbiomestat - r-plyr - r-rcolorbrewer - r-reshape2 - r-seurat - r-tidytext run: - - 'bioconductor-aldex2 >=1.32.0,<1.33.0' - - 'bioconductor-ancombc >=2.2.0,<2.3.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-dearseq >=1.12.0,<1.13.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mast >=1.26.0,<1.27.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' - - 'bioconductor-noiseq >=2.44.0,<2.45.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' - - 'bioconductor-zinbwave >=1.22.0,<1.23.0' + - 'bioconductor-aldex2 >=1.34.0,<1.35.0' + - 'bioconductor-ancombc >=2.4.0,<2.5.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-dearseq >=1.14.0,<1.15.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-maaslin2 >=1.16.0,<1.17.0' + - 'bioconductor-mast >=1.28.0,<1.29.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' + - 'bioconductor-noiseq >=2.46.0,<2.47.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - 'bioconductor-zinbwave >=1.24.0,<1.25.0' - r-base - - r-corncob - r-cowplot - r-ggdendro - r-ggplot2 - r-ggridges + - r-gunifrac - r-lme4 - r-mglm + - r-microbiomestat - r-plyr - r-rcolorbrewer - r-reshape2 - r-seurat - r-tidytext + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] test: commands: - - '$R -e "library(''{{ name }}'')"' + - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Benchmark of differential abundance methods on microbiome data' description: 'Starting from a microbiome dataset (16S or WMS with absolute count values) it is possible to perform several analysis to assess the performances of many differential abundance detection methods. A basic and standardized version of the main differential abundance analysis methods is supplied but the user can also add his method to the benchmark. The analyses focus on 4 main aspects: i) the goodness of fit of each method''s distributional assumptions on the observed count data, ii) the ability to control the false discovery rate, iii) the within and between method concordances, iv) the truthfulness of the findings if any apriori knowledge is given. Several graphical functions are available for result visualization.' +extra: + container: + extended-base: true diff --git a/recipes/bioconductor-benchmarkfdrdata2019/meta.yaml b/recipes/bioconductor-benchmarkfdrdata2019/meta.yaml index c4165ebe13f2c..2b84b56cb70ce 100644 --- a/recipes/bioconductor-benchmarkfdrdata2019/meta.yaml +++ b/recipes/bioconductor-benchmarkfdrdata2019/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "benchmarkfdrData2019" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b50a599a3c8ca8b276400e6dc523b894 + md5: 50ce7eb4100da1909ddd6c71c31e7e0c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-benchmarkfdrdata2019", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, BiocStyle, testthat, SummarizedBenchmark, dplyr, ggplot2, rlang requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-benchmarkfdrdata2019/post-link.sh b/recipes/bioconductor-benchmarkfdrdata2019/post-link.sh index 3deac42f34a2e..1129bed5479d6 100644 --- a/recipes/bioconductor-benchmarkfdrdata2019/post-link.sh +++ b/recipes/bioconductor-benchmarkfdrdata2019/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "benchmarkfdrdata2019-1.14.0" +installBiocDataPackage.sh "benchmarkfdrdata2019-1.16.0" diff --git a/recipes/bioconductor-beta7/meta.yaml b/recipes/bioconductor-beta7/meta.yaml index 4c0bd96f335f4..47ad27c91e376 100644 --- a/recipes/bioconductor-beta7/meta.yaml +++ b/recipes/bioconductor-beta7/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "beta7" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0049331687b2d8ce06153507e09a4a03 + md5: 7beee3699282a97c765cf418036fc0ed build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beta7", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-beta7/post-link.sh b/recipes/bioconductor-beta7/post-link.sh index 4f0c62a57883d..8c038bab630b5 100644 --- a/recipes/bioconductor-beta7/post-link.sh +++ b/recipes/bioconductor-beta7/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "beta7-1.38.0" +installBiocDataPackage.sh "beta7-1.40.0" diff --git a/recipes/bioconductor-bg2/meta.yaml b/recipes/bioconductor-bg2/meta.yaml index 09813ceea2158..707795e15d457 100644 --- a/recipes/bioconductor-bg2/meta.yaml +++ b/recipes/bioconductor-bg2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "BG2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 261572229e90f2182464a60b7e938b5b + md5: da6ea59dda3c728bdce70a5b43e4541e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bg2", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP, testthat (>= 3.0.0) requirements: diff --git a/recipes/bioconductor-bgeecall/meta.yaml b/recipes/bioconductor-bgeecall/meta.yaml index 5f5b52d928a09..75110cb7b2571 100644 --- a/recipes/bioconductor-bgeecall/meta.yaml +++ b/recipes/bioconductor-bgeecall/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.1" %} {% set name = "BgeeCall" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4320d2ccfdaf2088c987b762dd3ce930 + md5: d6ffd11b71faf135832b99515c7ba4cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bgeecall", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown, AnnotationHub, httr # SystemRequirements: kallisto requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-base - r-data.table - r-dplyr @@ -35,12 +36,12 @@ requirements: - r-rslurm - r-sjmisc run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-bgeedb/meta.yaml b/recipes/bioconductor-bgeedb/meta.yaml index 04d135b56e86a..c84ee3e31ee05 100644 --- a/recipes/bioconductor-bgeedb/meta.yaml +++ b/recipes/bioconductor-bgeedb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "BgeeDB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e5d66ef5cae6f2ee50528e452ebbdb68 + md5: 9b8f5e9e829bd05d9a8322b3ff3408dd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bgeedb", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, testthat, rmarkdown, markdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-curl - r-data.table @@ -34,9 +35,9 @@ requirements: - r-rsqlite - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-curl - r-data.table diff --git a/recipes/bioconductor-bgx/meta.yaml b/recipes/bioconductor-bgx/meta.yaml index f2ea8223608db..a5f285e769368 100644 --- a/recipes/bioconductor-bgx/meta.yaml +++ b/recipes/bioconductor-bgx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "bgx" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: afab2c381aa1f363f242c26c13c23e14 + md5: f068c237db58f3d75d3fef9cd5645cf4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bgx", max_pin="x.x") }}' # Suggests: affydata, hgu95av2cdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' - r-base - 'r-rcpp >=0.11.0' - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' - r-base - 'r-rcpp >=0.11.0' build: diff --git a/recipes/bioconductor-bhc/meta.yaml b/recipes/bioconductor-bhc/meta.yaml index cd59cd3e4c9d7..0ee0b47bf9658 100644 --- a/recipes/bioconductor-bhc/meta.yaml +++ b/recipes/bioconductor-bhc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "BHC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b08d636ca1e237816a3c0ad4ddae86f + md5: 855087c8854bd3014111477e1c3cdcb9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bhc", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-bicare/meta.yaml b/recipes/bioconductor-bicare/meta.yaml index 5effab9942084..e703872a25ea2 100644 --- a/recipes/bioconductor-bicare/meta.yaml +++ b/recipes/bioconductor-bicare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "BicARE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7bdfe915b7a5fa05496b4dea685e3dc8 + md5: d2498da49d01723934f42b4bf235fa05 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bicare", max_pin="x.x") }}' # Suggests: hgu95av2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-bifet/meta.yaml b/recipes/bioconductor-bifet/meta.yaml index f1c53ba4c19bf..9355f41630d56 100644 --- a/recipes/bioconductor-bifet/meta.yaml +++ b/recipes/bioconductor-bifet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "BiFET" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df9b0e887f85ef2881e011ea1979ef57 + md5: 11fcc80fc0c2745e5a15524fd2279bed build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bifet", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, testthat, knitr requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-poibin run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-poibin test: diff --git a/recipes/bioconductor-biggr/build_failure.linux-64.yaml b/recipes/bioconductor-biggr/build_failure.linux-64.yaml index 8d80c1d161066..1f88c079d088c 100644 --- a/recipes/bioconductor-biggr/build_failure.linux-64.yaml +++ b/recipes/bioconductor-biggr/build_failure.linux-64.yaml @@ -1,34 +1,35 @@ -recipe_sha: 5e4fb5d121cf8aff07e93d0614aac6a517def277ef61149a3a34e4a932691581 # The commit at which this recipe failed to build. +recipe_sha: b7766d035130ae790cea751e3ffdd9b9db7a9ee165bdd6eac0deefe15615c9f1 # The commit at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + dependency issue log: |- - conda-forge/linux-64 100%[2K[1A[2K[0G[] 7.5s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 7.6s conda-forge/linux-64 100%[2K[1A[2K[0Gconda-forge/linux-64 [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m [?25l[2K[0G[] 0.0s [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 1.4MB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.2MB/s 0.0s [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m [?25l[2K[0G[] 0.0s [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 2.6MB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.2MB/s 0.0s [?25hMamba failed to solve: + - bioconductor-rsbml >=2.60.0,<2.61.0 + - r-stringr + - bioconductor-hyperdraw >=1.54.0,<1.55.0 - r-lim - r-base 4.3.* - - bioconductor-hypergraph >=1.72.0,<1.73.0 + - bioconductor-hypergraph >=1.74.0,<1.75.0 - r-limsolve - - r-stringr - - bioconductor-rsbml >=2.58.0,<2.59.0 - - bioconductor-hyperdraw >=1.52.0,<1.53.0 with channels: + - file:///opt/host-conda-bld - conda-forge - bioconda - defaults The reported errors are: - Encountered problems while solving: - - - package bioconductor-hyperdraw-1.52.0-r43hba55f59_0 requires graphviz >=8.1.0,<9.0a0, but none of the providers can be installed + - - package bioconductor-hyperdraw-1.54.0-r43hba55f59_0 requires graphviz >=8.1.0,<9.0a0, but none of the providers can be installed - Leaving build/test directories: @@ -51,22 +52,23 @@ log: |- File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve raise RuntimeError("Solver could not find solution." error_string) RuntimeError: Solver could not find solution.Mamba failed to solve: + - bioconductor-rsbml >=2.60.0,<2.61.0 + - r-stringr + - bioconductor-hyperdraw >=1.54.0,<1.55.0 - r-lim - r-base 4.3.* - - bioconductor-hypergraph >=1.72.0,<1.73.0 + - bioconductor-hypergraph >=1.74.0,<1.75.0 - r-limsolve - - r-stringr - - bioconductor-rsbml >=2.58.0,<2.59.0 - - bioconductor-hyperdraw >=1.52.0,<1.53.0 with channels: + - file:///opt/host-conda-bld - conda-forge - bioconda - defaults The reported errors are: - Encountered problems while solving: - - - package bioconductor-hyperdraw-1.52.0-r43hba55f59_0 requires graphviz >=8.1.0,<9.0a0, but none of the providers can be installed + - - package bioconductor-hyperdraw-1.54.0-r43hba55f59_0 requires graphviz >=8.1.0,<9.0a0, but none of the providers can be installed - During handling of the above exception, another exception occurred: @@ -100,5 +102,5 @@ log: |- actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-hyperdraw==1.52.0=r43hba55f59_0"), MatchSpec("graphviz[version='>=8.1.0,<9.0a0']")} + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-hyperdraw==1.54.0=r43hba55f59_0"), MatchSpec("graphviz[version='>=8.1.0,<9.0a0']")} # Last 100 lines of the build log. diff --git a/recipes/bioconductor-biggr/meta.yaml b/recipes/bioconductor-biggr/meta.yaml index 605e46d2f9f9f..4ea339b2a2ef1 100644 --- a/recipes/bioconductor-biggr/meta.yaml +++ b/recipes/bioconductor-biggr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "BiGGR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f95dbd34a7f3f8c0a918b6460b1bf3ef + md5: 16eeec0ca7502101425cbb568e6eef15 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biggr", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-hyperdraw >=1.52.0,<1.53.0' - - 'bioconductor-hypergraph >=1.72.0,<1.73.0' - - 'bioconductor-rsbml >=2.58.0,<2.59.0' + - 'bioconductor-hyperdraw >=1.54.0,<1.55.0' + - 'bioconductor-hypergraph >=1.74.0,<1.75.0' + - 'bioconductor-rsbml >=2.60.0,<2.61.0' - r-base - r-lim - r-limsolve - r-stringr run: - - 'bioconductor-hyperdraw >=1.52.0,<1.53.0' - - 'bioconductor-hypergraph >=1.72.0,<1.73.0' - - 'bioconductor-rsbml >=2.58.0,<2.59.0' + - 'bioconductor-hyperdraw >=1.54.0,<1.55.0' + - 'bioconductor-hypergraph >=1.74.0,<1.75.0' + - 'bioconductor-rsbml >=2.60.0,<2.61.0' - r-base - r-lim - r-limsolve diff --git a/recipes/bioconductor-bigmelon/meta.yaml b/recipes/bioconductor-bigmelon/meta.yaml index adc1e4a1657a3..0f7c8a2a7a8ee 100644 --- a/recipes/bioconductor-bigmelon/meta.yaml +++ b/recipes/bioconductor-bigmelon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "bigmelon" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2793b4b6a4b2d2239f731c0f6fb60a4f + md5: 1c6944989ec4f16b1903143a34296bf0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bigmelon", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, RUnit, BiocStyle, minfiData, parallel, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-watermelon >=2.6.0,<2.7.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-watermelon >=2.8.0,<2.9.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-watermelon >=2.6.0,<2.7.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-watermelon >=2.8.0,<2.9.0' - r-base test: commands: diff --git a/recipes/bioconductor-bindingsitefinder/meta.yaml b/recipes/bioconductor-bindingsitefinder/meta.yaml index 9a14cffb08f4d..0d45dbb551c79 100644 --- a/recipes/bioconductor-bindingsitefinder/meta.yaml +++ b/recipes/bioconductor-bindingsitefinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "2.0.0" %} {% set name = "BindingSiteFinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,58 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: deb1c8c88ca7fbd1701582975f32808f + md5: b54f11a27c1f6f55b4cc60ad8986e029 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bindingsitefinder", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments, ComplexHeatmap, forcats, scales +# Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments, scales, Gviz, xlsx, GGally, patchwork, viridis, ggplotify, SummarizedExperiment, DESeq2, ggpointdensity, ggrastr, ashr requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr + - r-forcats + - r-ggdist - r-ggforce - r-ggplot2 + - r-kableextra + - r-lifecycle - r-matrixstats - r-plyr + - r-rcolorbrewer + - r-rlang - r-tibble - r-tidyr run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr + - r-forcats + - r-ggdist - r-ggforce - r-ggplot2 + - r-kableextra + - r-lifecycle - r-matrixstats - r-plyr + - r-rcolorbrewer + - r-rlang - r-tibble - r-tidyr test: diff --git a/recipes/bioconductor-bioassayr/meta.yaml b/recipes/bioconductor-bioassayr/meta.yaml index da01d4f62b18f..af54b2e1f736c 100644 --- a/recipes/bioconductor-bioassayr/meta.yaml +++ b/recipes/bioconductor-bioassayr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "bioassayR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f2df098a9b7bb4735e92bf3a0b0d87c4 + md5: 94ac7a2ff2a9de7b65d8ebd864513a31 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bioassayr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, RCurl, biomaRt, cellHTS2, knitr, knitcitations, knitrBootstrap, testthat, ggplot2, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - 'r-dbi >=0.3.1' - r-matrix @@ -30,8 +31,8 @@ requirements: - 'r-rsqlite >=1.0.0' - r-xml run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - 'r-dbi >=0.3.1' - r-matrix diff --git a/recipes/bioconductor-biobase/meta.yaml b/recipes/bioconductor-biobase/meta.yaml index 5b76df1093a7a..e09e97936223e 100644 --- a/recipes/bioconductor-biobase/meta.yaml +++ b/recipes/bioconductor-biobase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.60.0" %} +{% set version = "2.62.0" %} {% set name = "Biobase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e427b98c2208f6c1c81cf4ec64caffc + md5: 75a65eb015d58ca611f2bebca41f9d2d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biobase", max_pin="x.x") }}' # Suggests: tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-biobroom/meta.yaml b/recipes/bioconductor-biobroom/meta.yaml index 3cabf34e8bbf7..629191ae0ef98 100644 --- a/recipes/bioconductor-biobroom/meta.yaml +++ b/recipes/bioconductor-biobroom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "biobroom" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5f8edee57c6cc7540b187ea4d0a9c457 + md5: b0a4b29e9aa3bbb99f42cd2cd19ca4d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biobroom", max_pin="x.x") }}' noarch: generic # Suggests: limma, DESeq2, airway, ggplot2, plyr, GenomicRanges, testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase, rmarkdown, SummarizedExperiment requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-broom - r-dplyr - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-broom - r-dplyr diff --git a/recipes/bioconductor-biobtreer/meta.yaml b/recipes/bioconductor-biobtreer/meta.yaml index 70fa6d16cef8a..c14de14924e0e 100644 --- a/recipes/bioconductor-biobtreer/meta.yaml +++ b/recipes/bioconductor-biobtreer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "biobtreeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94456402f79d5430e53b31d80ed2e3c1 + md5: c341e537e79161abfd6f1f3382d3eb90 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biobtreer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr,testthat,rmarkdown,markdown requirements: diff --git a/recipes/bioconductor-biocancer/meta.yaml b/recipes/bioconductor-biocancer/meta.yaml index ce8ab589bd9c7..ff3219486924f 100644 --- a/recipes/bioconductor-biocancer/meta.yaml +++ b/recipes/bioconductor-biocancer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "bioCancer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cec03fe98717844d52ff9f282dc125b0 + md5: 2eff081b55d8bda988f08f1836420b24 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocancer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, prettydoc, rmarkdown, knitr, testthat (>= 0.10.0) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-genetclassifier >=1.40.0,<1.41.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.bt.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-reactomepa >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-genetclassifier >=1.42.0,<1.43.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.bt.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-reactomepa >=1.46.0,<1.47.0' - 'r-algdesign >=1.1.7.3' - r-base - 'r-diagrammer <=1.01' @@ -49,16 +50,16 @@ requirements: - r-visnetwork - 'r-xml >=3.98' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-genetclassifier >=1.40.0,<1.41.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.bt.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-reactomepa >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-genetclassifier >=1.42.0,<1.43.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.bt.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-reactomepa >=1.46.0,<1.47.0' - 'r-algdesign >=1.1.7.3' - r-base - 'r-diagrammer <=1.01' @@ -83,6 +84,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'AGPL-3 | file LICENSE' summary: 'Interactive Multi-Omics Cancers Data Visualization and Analysis' - description: 'bioCancer is a Shiny App to visualize and analyse interactively Multi-Assays of Cancer Genomic Data.' + description: 'This package is a Shiny App to visualize and analyse interactively Multi-Assays of Cancer Genomic Data.' license_file: LICENSE diff --git a/recipes/bioconductor-biocartaimage/build.sh b/recipes/bioconductor-biocartaimage/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biocartaimage/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocartaimage/meta.yaml b/recipes/bioconductor-biocartaimage/meta.yaml new file mode 100644 index 0000000000000..61d3f51296c03 --- /dev/null +++ b/recipes/bioconductor-biocartaimage/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.0" %} +{% set name = "BioCartaImage" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8190c93a49f3d53085b3e6e44d482ffa +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocartaimage", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat, knitr, BiocStyle, ragg +requirements: + host: + - r-base + - r-magick + run: + - r-base + - r-magick +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'BioCarta Pathway Images' + description: 'The core functionality of the package is to provide coordinates of genes on the BioCarta pathway images and to provide methods to add self-defined graphics to the genes of interest.' + license_file: LICENSE + diff --git a/recipes/bioconductor-biocbaseutils/meta.yaml b/recipes/bioconductor-biocbaseutils/meta.yaml index 14c57e3b3e022..66db86820aac2 100644 --- a/recipes/bioconductor-biocbaseutils/meta.yaml +++ b/recipes/bioconductor-biocbaseutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "BiocBaseUtils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6cb786aff723f206bb901ed336af3d23 + md5: 23ed1406ff70165a763ca2040c46353e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocbaseutils", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, tinytest requirements: diff --git a/recipes/bioconductor-biocbook/build.sh b/recipes/bioconductor-biocbook/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biocbook/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocbook/meta.yaml b/recipes/bioconductor-biocbook/meta.yaml new file mode 100644 index 0000000000000..03d10aeca7f90 --- /dev/null +++ b/recipes/bioconductor-biocbook/meta.yaml @@ -0,0 +1,73 @@ +{% set version = "1.0.0" %} +{% set name = "BiocBook" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6bcb226068f30b135b705960de603ff0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocbook", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, testthat (>= 3.0.0), rmarkdown +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - r-available + - r-base + - r-cli + - r-dplyr + - r-gert + - r-gh + - r-gitcreds + - r-glue + - r-httr + - r-purrr + - r-quarto + - r-renv + - r-rlang + - r-rprojroot + - r-stringr + - r-tibble + - r-usethis + - r-yaml + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - r-available + - r-base + - r-cli + - r-dplyr + - r-gert + - r-gh + - r-gitcreds + - r-glue + - r-httr + - r-purrr + - r-quarto + - r-renv + - r-rlang + - r-rprojroot + - r-stringr + - r-tibble + - r-usethis + - r-yaml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Write, containerize, publish and version Quarto books with Bioconductor' + description: 'A BiocBook can be created by authors (e.g. R developers, but also scientists, teachers, communicators, ...) who wish to 1) write (compile a body of biological and/or bioinformatics knowledge), 2) containerize (provide Docker images to reproduce the examples illustrated in the compendium), 3) publish (deploy an online book to disseminate the compendium), and 4) version (automatically generate specific online book versions and Docker images for specific Bioconductor releases).' + license_file: LICENSE + diff --git a/recipes/bioconductor-bioccheck/meta.yaml b/recipes/bioconductor-bioccheck/meta.yaml index e46357757fa10..2512f02beb7da 100644 --- a/recipes/bioconductor-bioccheck/meta.yaml +++ b/recipes/bioconductor-bioccheck/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.1" %} +{% set version = "1.38.0" %} {% set name = "BiocCheck" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a476a077103abf378f09d9ccb3cf05a + md5: d003f035a6c197261bed5fa4cd989738 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bioccheck", max_pin="x.x") }}' noarch: generic -# Suggests: RUnit, BiocGenerics, Biobase, jsonlite, rmarkdown, downloader, devtools (>= 1.4.1), usethis, BiocStyle, callr +# Suggests: RUnit, BiocGenerics, Biobase, jsonlite, rmarkdown, downloader, devtools (>= 1.4.1), usethis, BiocStyle, GenomicRanges, gert requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-biocmanager + - r-callr - r-codetools - r-httr - r-knitr - r-stringdist run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-biocmanager + - r-callr - r-codetools - r-httr - r-knitr diff --git a/recipes/bioconductor-biocfhir/meta.yaml b/recipes/bioconductor-biocfhir/meta.yaml index 63a838470cbd5..10c51d83594e6 100644 --- a/recipes/bioconductor-biocfhir/meta.yaml +++ b/recipes/bioconductor-biocfhir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "BiocFHIR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 29abc8f873ab6dff5597cf23558e6778 + md5: 788951417cde10ad9434dd443db47f80 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocfhir", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rjsoncons, igraph, BiocStyle requirements: host: - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-dplyr - r-dt @@ -31,8 +32,8 @@ requirements: - r-tidyr - r-visnetwork run: - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-dplyr - r-dt diff --git a/recipes/bioconductor-biocfilecache/meta.yaml b/recipes/bioconductor-biocfilecache/meta.yaml index 50cb12f97189f..f7dcc3d5468c6 100644 --- a/recipes/bioconductor-biocfilecache/meta.yaml +++ b/recipes/bioconductor-biocfilecache/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.1" %} {% set name = "BiocFileCache" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8ad06bf5fc23d0aabde7ba149d4d675 + md5: 80f9b9c7ef6f3fcb9aaff7125b409137 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocfilecache", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle, rmarkdown, rtracklayer requirements: diff --git a/recipes/bioconductor-biocgenerics/meta.yaml b/recipes/bioconductor-biocgenerics/meta.yaml index 785b193559280..d2b4a7afa324d 100644 --- a/recipes/bioconductor-biocgenerics/meta.yaml +++ b/recipes/bioconductor-biocgenerics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.46.0" %} +{% set version = "0.48.1" %} {% set name = "BiocGenerics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 619aadefdba5c7cebac0136ada0fb42a + md5: 77629e64c2a9a0324eb11bb59b53b126 build: - number: 0 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocgenerics", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, S4Vectors, IRanges, GenomicRanges, DelayedArray, Biostrings, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2, flowClust, MSnbase, annotate, RUnit requirements: diff --git a/recipes/bioconductor-biocgraph/meta.yaml b/recipes/bioconductor-biocgraph/meta.yaml index adc493c692e0c..e66a514e3c4a8 100644 --- a/recipes/bioconductor-biocgraph/meta.yaml +++ b/recipes/bioconductor-biocgraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "biocGraph" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a46b4f9c1a38fa5576b0323a22ebbedc + md5: 5deb3ff8596eaf678592ad9ae15defe2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocgraph", max_pin="x.x") }}' noarch: generic # Suggests: fibroEset, geneplotter, hgu95av2.db requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-biochail/meta.yaml b/recipes/bioconductor-biochail/meta.yaml index 5ea8066b7b2d6..aeb4d1b333b34 100644 --- a/recipes/bioconductor-biochail/meta.yaml +++ b/recipes/bioconductor-biochail/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "BiocHail" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: deafe3a2c0dccb5619f29ac3f917a3e0 + md5: 4707c299d0bb3b41001065a753d89f33 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biochail", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, BiocStyle, ggplot2, DT requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dplyr - r-reticulate run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dplyr - r-reticulate diff --git a/recipes/bioconductor-biochubsshiny/meta.yaml b/recipes/bioconductor-biochubsshiny/meta.yaml index 65f3ba1f939a8..eda08864d20d6 100644 --- a/recipes/bioconductor-biochubsshiny/meta.yaml +++ b/recipes/bioconductor-biochubsshiny/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "BiocHubsShiny" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 123a3f285b0653c760cbb5a11fcc84e8 + md5: bc7ef9bc6285eb045f191b7c72846d68 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biochubsshiny", max_pin="x.x") }}' noarch: generic # Suggests: BiocManager, BiocStyle, knitr, rmarkdown, sessioninfo, shinytest2 requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dt - r-htmlwidgets @@ -33,9 +34,9 @@ requirements: - r-shinythemes - r-shinytoastr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dt - r-htmlwidgets diff --git a/recipes/bioconductor-biocio/meta.yaml b/recipes/bioconductor-biocio/meta.yaml index 6daf6e7f521b9..71881e468ca28 100644 --- a/recipes/bioconductor-biocio/meta.yaml +++ b/recipes/bioconductor-biocio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "BiocIO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ac5aad476739475cfec311c8f28e770b + md5: 6e0c18bdf6d9f707f9d1e431400fa1c7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocio", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-biocneighbors/meta.yaml b/recipes/bioconductor-biocneighbors/meta.yaml index a44d39cfbe661..83929f7284c5a 100644 --- a/recipes/bioconductor-biocneighbors/meta.yaml +++ b/recipes/bioconductor-biocneighbors/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "BiocNeighbors" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e87784c01c3e3c48735ebb1d01ff80f0 + md5: 3cfb96ab6d42068c5b875fa6fcefd779 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocneighbors", max_pin="x.x") }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy, RcppHNSW # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix - r-rcpp @@ -30,8 +31,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-bioconcotk/meta.yaml b/recipes/bioconductor-bioconcotk/meta.yaml index 5d7192e625bf5..278c1af519595 100644 --- a/recipes/bioconductor-bioconcotk/meta.yaml +++ b/recipes/bioconductor-bioconcotk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "BiocOncoTK" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 271d492c165d6350550a05949466289f + md5: 2cd117f19ec3c614a5bcb1d8b27b6e64 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bioconcotk", max_pin="x.x") }}' noarch: generic # Suggests: knitr, dbplyr, org.Hs.eg.db, MultiAssayExperiment, BiocStyle, ontoProc, ontologyPlot, pogos, GenomeInfoDb, restfulSE (>= 1.3.7), BiocFileCache, TxDb.Hsapiens.UCSC.hg19.knownGene, Biobase, TxDb.Hsapiens.UCSC.hg18.knownGene, reshape2, testthat, AnnotationDbi, FDb.InfiniumMethylation.hg19, EnsDb.Hsapiens.v75, rmarkdown, rhdf5client, AnnotationHub requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-curatedtcgadata >=1.22.0,<1.23.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-curatedtcgadata >=1.24.0,<1.25.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bigrquery - r-car @@ -46,15 +47,15 @@ requirements: - r-scales - r-shiny run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-curatedtcgadata >=1.22.0,<1.23.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-curatedtcgadata >=1.24.0,<1.25.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bigrquery - r-car diff --git a/recipes/bioconductor-biocor/meta.yaml b/recipes/bioconductor-biocor/meta.yaml index 4b62b4d930e79..4f9b1efe69ee1 100644 --- a/recipes/bioconductor-biocor/meta.yaml +++ b/recipes/bioconductor-biocor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "BioCor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1ac6d44e021d256002b563d53a8ac9ef + md5: 5d061581890948dc4341346b82f8d170 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocor", max_pin="x.x") }}' noarch: generic -# Suggests: airway, BiocStyle, boot, DESeq2, GOSemSim, Hmisc, knitr (>= 1.35), org.Hs.eg.db, reactome.db, rmarkdown, spelling, targetscan.Hs.eg.db, testthat, WGCNA +# Suggests: airway, BiocStyle, boot, DESeq2, ggplot2 (>= 3.4.1), GOSemSim, Hmisc, knitr (>= 1.35), org.Hs.eg.db, reactome.db, rmarkdown, spelling, targetscan.Hs.eg.db, testthat, WGCNA requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-matrix run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-biocparallel/meta.yaml b/recipes/bioconductor-biocparallel/meta.yaml index 1af1c54af1acc..08b5cb5440130 100644 --- a/recipes/bioconductor-biocparallel/meta.yaml +++ b/recipes/bioconductor-biocparallel/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.2" %} +{% set version = "1.36.0" %} {% set name = "BiocParallel" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fe2e530471e5ecb6a9f74f1f43cb4efe + md5: a6a331ac453920e713836ddd0de38e25 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocparallel", max_pin="x.x") }}' # Suggests: BiocGenerics, tools, foreach, BBmisc, doParallel, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle, knitr, batchtools, data.table # SystemRequirements: C++11 requirements: diff --git a/recipes/bioconductor-biocpkgtools/meta.yaml b/recipes/bioconductor-biocpkgtools/meta.yaml index 2351fc85c2cd0..4c6bab59e87ca 100644 --- a/recipes/bioconductor-biocpkgtools/meta.yaml +++ b/recipes/bioconductor-biocpkgtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "BiocPkgTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5945211cb859f579d7b1900f8c0877d1 + md5: a0ab7353a78b22b286d22520faff6142 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocpkgtools", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, tm, lubridate, visNetwork, clipr, blastula, kableExtra, DiagrammeR, SummarizedExperiment # SystemRequirements: mailsend-go requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-biocmanager - r-dplyr @@ -45,10 +46,10 @@ requirements: - r-tibble - r-xml2 run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-biocmanager - r-dplyr diff --git a/recipes/bioconductor-biocset/meta.yaml b/recipes/bioconductor-biocset/meta.yaml index 5b0ccad529798..e2086fa5fd45a 100644 --- a/recipes/bioconductor-biocset/meta.yaml +++ b/recipes/bioconductor-biocset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "BiocSet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 643105ff3920c099e3713e749f724aac + md5: 69ab960333325b038fb2379781fe36c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocset", max_pin="x.x") }}' noarch: generic # Suggests: GSEABase, airway, org.Hs.eg.db, DESeq2, limma, BiocFileCache, GO.db, testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ontologyindex @@ -33,10 +34,10 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ontologyindex diff --git a/recipes/bioconductor-biocsingular/meta.yaml b/recipes/bioconductor-biocsingular/meta.yaml index 7fea0c7847a07..984b889689b96 100644 --- a/recipes/bioconductor-biocsingular/meta.yaml +++ b/recipes/bioconductor-biocsingular/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "BiocSingular" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df6d2dd2e0de6864dcc488127f9b0621 + md5: 9b4158e143f2cbefc140228c13090b35 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocsingular", max_pin="x.x") }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix -# SystemRequirements: C++11 +# SystemRequirements: C++17 requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scaledmatrix >=1.8.0,<1.9.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' - r-base - r-irlba - r-matrix @@ -35,12 +36,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scaledmatrix >=1.8.0,<1.9.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' - r-base - r-irlba - r-matrix diff --git a/recipes/bioconductor-biocsklearn/meta.yaml b/recipes/bioconductor-biocsklearn/meta.yaml index d18885bab9193..5974e5fdc00d4 100644 --- a/recipes/bioconductor-biocsklearn/meta.yaml +++ b/recipes/bioconductor-biocsklearn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "BiocSklearn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 92331b92237b4a3e82af8e2679cdb576 + md5: a3df49031172bfd2b2a3b1c242b7dd40 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocsklearn", max_pin="x.x") }}' noarch: generic # Suggests: testthat, restfulSE, HDF5Array, BiocStyle, rmarkdown, knitr # SystemRequirements: python (>= 2.7), sklearn, numpy, pandas, h5py requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-reticulate - 'python >=2.7' run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-reticulate - 'python >=2.7' diff --git a/recipes/bioconductor-biocstyle/meta.yaml b/recipes/bioconductor-biocstyle/meta.yaml index d520d23a37171..0f8df92a25fe6 100644 --- a/recipes/bioconductor-biocstyle/meta.yaml +++ b/recipes/bioconductor-biocstyle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "BiocStyle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91272b7821e6d3955aab1ec46c5c8491 + md5: 22ceacb6ab374657de48283e78dedbb5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocstyle", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, RUnit, htmltools requirements: diff --git a/recipes/bioconductor-biocthis/meta.yaml b/recipes/bioconductor-biocthis/meta.yaml index fbb614fc53920..6e1853af5c371 100644 --- a/recipes/bioconductor-biocthis/meta.yaml +++ b/recipes/bioconductor-biocthis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.3" %} +{% set version = "1.12.0" %} {% set name = "biocthis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5f348f9b54ba6845ace32212b709dd64 + md5: 7ebf8e46d2b20a3a2bae3cc7a36264d5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocthis", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, devtools, knitr, pkgdown, RefManageR, rmarkdown, sessioninfo, testthat, utils requirements: diff --git a/recipes/bioconductor-biocversion/meta.yaml b/recipes/bioconductor-biocversion/meta.yaml index d9949d2b05ba8..2f6a6eaf4f1d2 100644 --- a/recipes/bioconductor-biocversion/meta.yaml +++ b/recipes/bioconductor-biocversion/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.1" %} +{% set version = "3.18.1" %} {% set name = "BiocVersion" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9fea6248fd1d5c6ef5f4c00848f870b4 + md5: 46dbe2f6ca9c058b24da1bd98f79631e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocversion", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-biocviews/meta.yaml b/recipes/bioconductor-biocviews/meta.yaml index d9d6ad8abd1a4..0627cb2e4f0f5 100644 --- a/recipes/bioconductor-biocviews/meta.yaml +++ b/recipes/bioconductor-biocviews/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.1" %} +{% set version = "1.70.0" %} {% set name = "biocViews" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b6115ebd1436da570b59dbbd35a9fa0 + md5: e258342a57f06fa23f3732c75539c58d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocviews", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, knitr, commonmark, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-biocmanager - r-rcurl - r-runit - r-xml run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-biocmanager - r-rcurl diff --git a/recipes/bioconductor-biocworkflowtools/meta.yaml b/recipes/bioconductor-biocworkflowtools/meta.yaml index ae38c9e0456e1..800ffd008347d 100644 --- a/recipes/bioconductor-biocworkflowtools/meta.yaml +++ b/recipes/bioconductor-biocworkflowtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "BiocWorkflowTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6696a65d716c89b060c4cee07dcded96 + md5: 412d30d47953d51e35e9fa188e28841e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocworkflowtools", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - r-base - r-bookdown - r-git2r @@ -31,7 +32,7 @@ requirements: - r-stringr - r-usethis run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - r-base - r-bookdown - r-git2r diff --git a/recipes/bioconductor-biodb/meta.yaml b/recipes/bioconductor-biodb/meta.yaml index fe5c913eb0e61..ad39c52b330b1 100644 --- a/recipes/bioconductor-biodb/meta.yaml +++ b/recipes/bioconductor-biodb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "biodb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2140155f6d5c482557f7838661adbfe7 + md5: 0716a73291fb80cc3d1f0909549cbaa8 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, xml2, git2r + run_exports: '{{ pin_subpackage("bioconductor-biodb", max_pin="x.x") }}' +# Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, xml2 requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-chk + - r-git2r - r-jsonlite - r-lgr - r-lifecycle @@ -42,9 +44,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-chk + - r-git2r - r-jsonlite - r-lgr - r-lifecycle diff --git a/recipes/bioconductor-biodbchebi/meta.yaml b/recipes/bioconductor-biodbchebi/meta.yaml index 4551636ba0935..4371bc0a4a43f 100644 --- a/recipes/bioconductor-biodbchebi/meta.yaml +++ b/recipes/bioconductor-biodbchebi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "biodbChebi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ba9df9eafa05f15f032fec477606a21 + md5: 31f6ed155e1126b62c5a6cd7fbd6c742 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodbchebi", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, lgr requirements: host: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-r6 run: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-r6 test: diff --git a/recipes/bioconductor-biodbexpasy/meta.yaml b/recipes/bioconductor-biodbexpasy/meta.yaml index 8bf72de29d06f..11a9662f7a468 100644 --- a/recipes/bioconductor-biodbexpasy/meta.yaml +++ b/recipes/bioconductor-biodbexpasy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "biodbExpasy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98e5ae0c72615b4f1b7d1d2cf0398f7c + md5: b4c2596f2efc76e3ba7cba00fb3a6177 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodbexpasy", max_pin="x.x") }}' noarch: generic # Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr requirements: host: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-r6 - r-stringr run: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-r6 diff --git a/recipes/bioconductor-biodbhmdb/meta.yaml b/recipes/bioconductor-biodbhmdb/meta.yaml index ad27b96d7ac9f..43819b75e957a 100644 --- a/recipes/bioconductor-biodbhmdb/meta.yaml +++ b/recipes/bioconductor-biodbhmdb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "biodbHmdb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 51bfd87e591eab475ec0498eaf805fd1 + md5: b34c06c2ce8865b7eebedb869a1ab505 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodbhmdb", max_pin="x.x") }}' # Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, lgr requirements: host: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-r6 - r-rcpp - r-testthat + - r-zip - libblas - liblapack run: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-r6 - r-rcpp - r-testthat + - r-zip build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-biodbkegg/meta.yaml b/recipes/bioconductor-biodbkegg/meta.yaml index 4932d2d81b630..89f789f680e40 100644 --- a/recipes/bioconductor-biodbkegg/meta.yaml +++ b/recipes/bioconductor-biodbkegg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "biodbKegg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4e55170ed0b1512e058a3546348556e6 + md5: 868600b40fc5ce4c38ced82df890400d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodbkegg", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, igraph, magick, lgr requirements: host: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-lifecycle - r-r6 run: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-lifecycle diff --git a/recipes/bioconductor-biodblipidmaps/meta.yaml b/recipes/bioconductor-biodblipidmaps/meta.yaml index d5aa32c044891..49e10385518b5 100644 --- a/recipes/bioconductor-biodblipidmaps/meta.yaml +++ b/recipes/bioconductor-biodblipidmaps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "biodbLipidmaps" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4bcb13e4a81639403a3203fe973736d1 + md5: 996886d796e7ffba7a1a19598573f9c8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodblipidmaps", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, lgr, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr requirements: host: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-lifecycle - r-r6 run: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-lifecycle - r-r6 diff --git a/recipes/bioconductor-biodbmirbase/meta.yaml b/recipes/bioconductor-biodbmirbase/meta.yaml index f38a72b0e2629..3fc5c553215d5 100644 --- a/recipes/bioconductor-biodbmirbase/meta.yaml +++ b/recipes/bioconductor-biodbmirbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.5.0" %} {% set name = "biodbMirbase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73a96ab8d432ed80ffc987b3f318044e + md5: af331cadc2f7575e4dbf5345f19c61e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodbmirbase", max_pin="x.x") }}' noarch: generic # Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr requirements: host: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-r6 - r-stringr run: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-r6 diff --git a/recipes/bioconductor-biodbncbi/meta.yaml b/recipes/bioconductor-biodbncbi/meta.yaml index e8985870974a5..95b4d06ff4236 100644 --- a/recipes/bioconductor-biodbncbi/meta.yaml +++ b/recipes/bioconductor-biodbncbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "biodbNcbi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8e830a9655fd75706c8d4c75440ddec + md5: 5d2c3e8eade431a86e13d54be468832e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodbncbi", max_pin="x.x") }}' noarch: generic # Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr requirements: host: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-r6 - r-xml run: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-r6 diff --git a/recipes/bioconductor-biodbnci/meta.yaml b/recipes/bioconductor-biodbnci/meta.yaml index 501ca82a668bf..cc1d3f3405d9c 100644 --- a/recipes/bioconductor-biodbnci/meta.yaml +++ b/recipes/bioconductor-biodbnci/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "biodbNci" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f9eeae84d0fb3daf211823d114a5f772 + md5: 6dcd43d5c282054f4edfef08a2f597cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodbnci", max_pin="x.x") }}' # Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr requirements: host: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-r6 @@ -29,7 +30,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-r6 diff --git a/recipes/bioconductor-biodbuniprot/meta.yaml b/recipes/bioconductor-biodbuniprot/meta.yaml index af50105117d6a..a4e0d9a6b658e 100644 --- a/recipes/bioconductor-biodbuniprot/meta.yaml +++ b/recipes/bioconductor-biodbuniprot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "biodbUniprot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cc363aa65d5193c61a478401c9f20b91 + md5: f4f5bcc32018b6472836efcc8c82671c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodbuniprot", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, lgr, covr requirements: host: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-r6 run: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-r6 test: diff --git a/recipes/bioconductor-biodist/meta.yaml b/recipes/bioconductor-biodist/meta.yaml index b84db1943e599..638ca746d888c 100644 --- a/recipes/bioconductor-biodist/meta.yaml +++ b/recipes/bioconductor-biodist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "bioDist" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b0ac96c334d2d0703297b260b9b9535c + md5: a0c907dc82834b4771074cd8164cf773 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodist", max_pin="x.x") }}' noarch: generic # Suggests: locfit requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-kernsmooth run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-kernsmooth test: diff --git a/recipes/bioconductor-bioimagedbs/meta.yaml b/recipes/bioconductor-bioimagedbs/meta.yaml index 088193acc1f0a..f7ebe42cadf2b 100644 --- a/recipes/bioconductor-bioimagedbs/meta.yaml +++ b/recipes/bioconductor-bioimagedbs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "BioImageDbs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b8af4040411218fcfd81ab927747eb48 + md5: 785e9ea81ef5699d70af969fd8d4703d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bioimagedbs", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, purrr requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-animation - r-base - r-einsum @@ -33,9 +34,9 @@ requirements: - r-markdown - r-rmarkdown run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-animation - r-base - r-einsum @@ -45,7 +46,7 @@ requirements: - r-markdown - r-rmarkdown - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bioimagedbs/post-link.sh b/recipes/bioconductor-bioimagedbs/post-link.sh index 97c361a68d9de..908f4e675bd43 100644 --- a/recipes/bioconductor-bioimagedbs/post-link.sh +++ b/recipes/bioconductor-bioimagedbs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bioimagedbs-1.8.0" +installBiocDataPackage.sh "bioimagedbs-1.10.0" diff --git a/recipes/bioconductor-biomart/meta.yaml b/recipes/bioconductor-biomart/meta.yaml index 061a7013a2d8c..9682b4d2750eb 100644 --- a/recipes/bioconductor-biomart/meta.yaml +++ b/recipes/bioconductor-biomart/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.56.1" %} +{% set version = "2.58.0" %} {% set name = "biomaRt" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3ebbe9c8774fc0f1cb42a6a5c3d4ef2 + md5: dd18037fef27f7c50af56f5da2086e04 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biomart", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, mockery, rmarkdown, testthat, webmockr requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-digest - r-httr @@ -32,8 +33,8 @@ requirements: - 'r-xml >=3.99-0.7' - r-xml2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-digest - r-httr diff --git a/recipes/bioconductor-biomartgogenesets/meta.yaml b/recipes/bioconductor-biomartgogenesets/meta.yaml new file mode 100644 index 0000000000000..df4009848c019 --- /dev/null +++ b/recipes/bioconductor-biomartgogenesets/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "0.99.11" %} +{% set name = "BioMartGOGeneSets" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f96a12703fd2f9c357442a60e5f2c764 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biomartgogenesets", max_pin="x.x") }}' + noarch: generic +# Suggests: biomaRt, GO.db, GenomeInfoDb, knitr, testthat, GetoptLong, DT +requirements: + host: + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + run: + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Gene Ontology Gene Sets from BioMart' + description: 'It contains pre-compiled Gene Ontology gene sets for all organisms available on the Ensembl database. It also includes GO gene sets for organisms on Ensembl Plants, Ensembl Metazoa, Ensembl Fungi and Ensembl Protists. The data was collected with the biomaRt package.' + license_file: LICENSE + diff --git a/recipes/bioconductor-biomartgogenesets/post-link.sh b/recipes/bioconductor-biomartgogenesets/post-link.sh new file mode 100644 index 0000000000000..19d29150eab0b --- /dev/null +++ b/recipes/bioconductor-biomartgogenesets/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "biomartgogenesets-0.99.11" diff --git a/recipes/bioconductor-biomartgogenesets/pre-unlink.sh b/recipes/bioconductor-biomartgogenesets/pre-unlink.sh new file mode 100644 index 0000000000000..ea56fd0d96116 --- /dev/null +++ b/recipes/bioconductor-biomartgogenesets/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BioMartGOGeneSets diff --git a/recipes/bioconductor-biomformat/meta.yaml b/recipes/bioconductor-biomformat/meta.yaml index 3f733d767388d..9baeccbf7f291 100644 --- a/recipes/bioconductor-biomformat/meta.yaml +++ b/recipes/bioconductor-biomformat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "biomformat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eff7e3b0449e543e14b8e3c4169a3e11 + md5: f35aaf72b454bc1872f1247642029006 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biomformat", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6), rmarkdown (>= 0.7) requirements: host: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - 'r-jsonlite >=0.9.16' - 'r-matrix >=1.2' - 'r-plyr >=1.8' run: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - 'r-jsonlite >=0.9.16' - 'r-matrix >=1.2' diff --git a/recipes/bioconductor-biomvcclass/meta.yaml b/recipes/bioconductor-biomvcclass/meta.yaml index 9dda455c81080..63e1563014b71 100644 --- a/recipes/bioconductor-biomvcclass/meta.yaml +++ b/recipes/bioconductor-biomvcclass/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.0" %} {% set name = "BioMVCClass" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7186d0439ac65d30681067b145eefa04 + md5: 72d762b9a59c4b75d79c378792250b48 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biomvcclass", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-mvcclass >=1.74.0,<1.75.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-mvcclass >=1.76.0,<1.77.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-mvcclass >=1.74.0,<1.75.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-mvcclass >=1.76.0,<1.77.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-biomvrcns/build.sh b/recipes/bioconductor-biomvrcns/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biomvrcns/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biomvrcns/meta.yaml b/recipes/bioconductor-biomvrcns/meta.yaml new file mode 100644 index 0000000000000..29c5079d7968d --- /dev/null +++ b/recipes/bioconductor-biomvrcns/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.42.1" %} +{% set name = "biomvRCNS" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 592c6d6f34e855eed52b4591b6b065e1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biomvrcns", max_pin="x.x") }}' +# Suggests: cluster, parallel, GenomicFeatures, dynamicTreeCut, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene +requirements: + host: + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - r-base + - r-mvtnorm + - libblas + - liblapack + run: + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - r-base + - r-mvtnorm + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Copy Number study and Segmentation for multivariate biological data' + description: 'In this package, a Hidden Semi Markov Model (HSMM) and one homogeneous segmentation model are designed and implemented for segmentation genomic data, with the aim of assisting in transcripts detection using high throughput technology like RNA-seq or tiling array, and copy number analysis using aCGH or sequencing.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-bionar/meta.yaml b/recipes/bioconductor-bionar/meta.yaml index db31ce7f4be80..a1ef1fc42337d 100644 --- a/recipes/bioconductor-bionar/meta.yaml +++ b/recipes/bioconductor-bionar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.4" %} +{% set version = "1.4.0" %} {% set name = "BioNAR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f78a59dea815f7b7cfad0682cae32708 + md5: 4cbc1fe5bd753444b3470a317029a885 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bionar", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, igraphdata, testthat (>= 3.0.0), vdiffr, devtools, pander, plotly, randomcoloR +# Suggests: knitr, BiocStyle, magick, rmarkdown, igraphdata, testthat (>= 3.0.0), vdiffr, devtools, pander, plotly, randomcoloR requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-synaptome.db >=0.99.0,<0.100.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-clustercons - r-cowplot @@ -35,6 +35,7 @@ requirements: - r-ggrepel - 'r-igraph >=1.4.0' - r-latex2exp + - r-matrix - r-minpack.lm - r-powerlaw - r-rdpack @@ -45,11 +46,10 @@ requirements: - r-viridis - r-wgcna run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-synaptome.db >=0.99.0,<0.100.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-clustercons - r-cowplot @@ -59,6 +59,7 @@ requirements: - r-ggrepel - 'r-igraph >=1.4.0' - r-latex2exp + - r-matrix - r-minpack.lm - r-powerlaw - r-rdpack diff --git a/recipes/bioconductor-bionero/meta.yaml b/recipes/bioconductor-bionero/meta.yaml index f3df186d26e2b..2ebcf257d05b5 100644 --- a/recipes/bioconductor-bionero/meta.yaml +++ b/recipes/bioconductor-bionero/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.5" %} +{% set version = "1.10.0" %} {% set name = "BioNERO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e673d1c24445c648a2a152f8408d4f09 + md5: 4cc77a8b8eb3cff071fbe5df15a6eb67 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bionero", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle, DESeq2, networkD3, covr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genie3 >=1.22.0,<1.23.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genie3 >=1.24.0,<1.25.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-dynamictreecut - r-ggdendro @@ -43,12 +44,12 @@ requirements: - r-rlang - r-wgcna run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genie3 >=1.22.0,<1.23.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genie3 >=1.24.0,<1.25.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-dynamictreecut - r-ggdendro diff --git a/recipes/bioconductor-bionet/meta.yaml b/recipes/bioconductor-bionet/meta.yaml index d9adb1f066cc9..ba12d6bab333a 100644 --- a/recipes/bioconductor-bionet/meta.yaml +++ b/recipes/bioconductor-bionet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "BioNet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ff51b8ceee1e56fb2330eb25404c8db + md5: 7f2fb01406a2c73946981af9fa9c86c8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bionet", max_pin="x.x") }}' noarch: generic # Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - 'r-igraph >=1.0.1' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - 'r-igraph >=1.0.1' test: diff --git a/recipes/bioconductor-bionetstat/meta.yaml b/recipes/bioconductor-bionetstat/meta.yaml index 431995c0950b8..41bdf3796be71 100644 --- a/recipes/bioconductor-bionetstat/meta.yaml +++ b/recipes/bioconductor-bionetstat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "BioNetStat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed891791ee2df9a37085262b321eb994 + md5: c5de66f95b44aa3d98c077be1a27ae44 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bionetstat", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' - r-base - r-dt - r-ggplot2 @@ -40,8 +41,8 @@ requirements: - r-whisker - r-yaml run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' - r-base - r-dt - r-ggplot2 diff --git a/recipes/bioconductor-bioplex/meta.yaml b/recipes/bioconductor-bioplex/meta.yaml index 4eb82837b603c..2861b800c834c 100644 --- a/recipes/bioconductor-bioplex/meta.yaml +++ b/recipes/bioconductor-bioplex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "BioPlex" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a387711025f30513f09cf397c759e81 + md5: 77e38da3b194e7776fa7007a2cef42bf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bioplex", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi, AnnotationHub, BiocStyle, DEXSeq, ExperimentHub, GenomicFeatures, S4Vectors, depmap, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bioplex/post-link.sh b/recipes/bioconductor-bioplex/post-link.sh index b3b51db1f2b19..fbbc180637819 100644 --- a/recipes/bioconductor-bioplex/post-link.sh +++ b/recipes/bioconductor-bioplex/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bioplex-1.6.0" +installBiocDataPackage.sh "bioplex-1.8.0" diff --git a/recipes/bioconductor-bioqc/meta.yaml b/recipes/bioconductor-bioqc/meta.yaml index 41b4f55fc8ba8..1a1c326723051 100644 --- a/recipes/bioconductor-bioqc/meta.yaml +++ b/recipes/bioconductor-bioqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "BioQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef8c169f2a452603691a880ae671082d + md5: 9e9b338e001fdeb614091e4fa0cf50cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bioqc", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, lattice, latticeExtra, rbenchmark, gplots, gridExtra, org.Hs.eg.db, hgu133plus2.db, ggplot2, reshape2, plyr, ineq, covr, limma, RColorBrewer requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-biosigner/meta.yaml b/recipes/bioconductor-biosigner/meta.yaml index 0e141f036996e..459f194a9ee3b 100644 --- a/recipes/bioconductor-biosigner/meta.yaml +++ b/recipes/bioconductor-biosigner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "biosigner" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c8af3938b2d60391138f896583af1056 + md5: 33d853127b5e108b0fa1c5dfea22517d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biosigner", max_pin="x.x") }}' noarch: generic # Suggests: BioMark, BiocGenerics, BiocStyle, golubEsets, hu6800.db, knitr, omicade4, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-randomforest run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-randomforest diff --git a/recipes/bioconductor-biostrings/meta.yaml b/recipes/bioconductor-biostrings/meta.yaml index e55e0fa2c3827..fc1ca74c09cdb 100644 --- a/recipes/bioconductor-biostrings/meta.yaml +++ b/recipes/bioconductor-biostrings/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.68.1" %} +{% set version = "2.70.1" %} {% set name = "Biostrings" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 12cef3d82ae3ac557ab16fabfb6f8646 + md5: 998fdd127f3613ca157917c847e22ac3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ -# Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit + run_exports: '{{ pin_subpackage("bioconductor-biostrings", max_pin="x.x") }}' +# Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-crayon - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-crayon build: diff --git a/recipes/bioconductor-biotip/meta.yaml b/recipes/bioconductor-biotip/meta.yaml index db19a9a6fc203..89e01b63d03be 100644 --- a/recipes/bioconductor-biotip/meta.yaml +++ b/recipes/bioconductor-biotip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "BioTIP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fbfda3e6fbf559c289827a25ae5b5213 + md5: 9a7765bd55ed7e2d7d09d4eff3b2127c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biotip", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown, base, rmarkdown, ggplot2 requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' - r-base - r-cluster - r-igraph @@ -30,8 +31,8 @@ requirements: - r-psych - r-stringr run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' - r-base - r-cluster - r-igraph diff --git a/recipes/bioconductor-biotmle/meta.yaml b/recipes/bioconductor-biotmle/meta.yaml index a09ecd90c450e..b7e9320cef7ee 100644 --- a/recipes/bioconductor-biotmle/meta.yaml +++ b/recipes/bioconductor-biotmle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "biotmle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8737aaa23cc2f9fbeca57ff59fb924c4 + md5: 10fcb7a34336492cbd49f3170a2f81ba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biotmle", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle, arm, earth, ranger, SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-dplyr @@ -35,11 +36,11 @@ requirements: - r-superheat - r-tibble run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-dplyr diff --git a/recipes/bioconductor-biotmledata/meta.yaml b/recipes/bioconductor-biotmledata/meta.yaml index 8832917877b31..2413693fa7bec 100644 --- a/recipes/bioconductor-biotmledata/meta.yaml +++ b/recipes/bioconductor-biotmledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "biotmleData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e21b4d8009abb77c03a67a9115c289dc + md5: 8c725d5c496f9bfe7ed4b5d5c538244a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biotmledata", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, SummarizedExperiment requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-biotmledata/post-link.sh b/recipes/bioconductor-biotmledata/post-link.sh index 93a932011f94d..f4cbb02679956 100644 --- a/recipes/bioconductor-biotmledata/post-link.sh +++ b/recipes/bioconductor-biotmledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "biotmledata-1.24.0" +installBiocDataPackage.sh "biotmledata-1.26.0" diff --git a/recipes/bioconductor-biovizbase/meta.yaml b/recipes/bioconductor-biovizbase/meta.yaml index 96b433d801613..47c84b5c85b74 100644 --- a/recipes/bioconductor-biovizbase/meta.yaml +++ b/recipes/bioconductor-biovizbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "biovizBase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2849083f8ce8e17c9fbfb8448571f482 + md5: 8430b2a7913fdcfe27b9bf52ba9aff7e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biovizbase", max_pin="x.x") }}' # Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-dichromat - r-hmisc @@ -43,20 +44,20 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-dichromat - r-hmisc diff --git a/recipes/bioconductor-birewire/meta.yaml b/recipes/bioconductor-birewire/meta.yaml index 0884d912fb1f7..94f5cee0bbfa8 100644 --- a/recipes/bioconductor-birewire/meta.yaml +++ b/recipes/bioconductor-birewire/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.32.0" %} +{% set version = "3.34.0" %} {% set name = "BiRewire" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7d54730101e7164be2148f51d78790fe + md5: 2539b609076f98e95e044f33fe443bdf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-birewire", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics requirements: host: diff --git a/recipes/bioconductor-biscuiteer/meta.yaml b/recipes/bioconductor-biscuiteer/meta.yaml index 1760062a11885..ab11d6d9b3f44 100644 --- a/recipes/bioconductor-biscuiteer/meta.yaml +++ b/recipes/bioconductor-biscuiteer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "biscuiteer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 18e07fd7cd831b02d9762a4f25b30116 + md5: a38a486daf7d4c4dd682f20658039234 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biscuiteer", max_pin="x.x") }}' noarch: generic # Suggests: DSS, covr, knitr, rmarkdown, markdown, rlang, scmeth, pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biscuiteerdata >=1.14.0,<1.15.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-dmrseq >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biscuiteerdata >=1.16.0,<1.17.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-dmrseq >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-mus.musculus >=1.3.0,<1.4.0' - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-gtools @@ -50,26 +51,26 @@ requirements: - r-r.utils - r-readr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biscuiteerdata >=1.14.0,<1.15.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-dmrseq >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biscuiteerdata >=1.16.0,<1.17.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-dmrseq >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-mus.musculus >=1.3.0,<1.4.0' - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-gtools diff --git a/recipes/bioconductor-biscuiteerdata/meta.yaml b/recipes/bioconductor-biscuiteerdata/meta.yaml index d0656d7a78a17..c4cfffd5a8b7c 100644 --- a/recipes/bioconductor-biscuiteerdata/meta.yaml +++ b/recipes/bioconductor-biscuiteerdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "biscuiteerData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 143bedc239cf56a25dc8bf6c1e98d392 + md5: 9610f1ea2c2e8303acbb0b52204f8d3e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biscuiteerdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, markdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-curl run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-curl - curl - - bioconductor-data-packages>=20230713 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-biscuiteerdata/post-link.sh b/recipes/bioconductor-biscuiteerdata/post-link.sh index 45806f68b34b3..6c22e115a9ff9 100644 --- a/recipes/bioconductor-biscuiteerdata/post-link.sh +++ b/recipes/bioconductor-biscuiteerdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "biscuiteerdata-1.14.1" +installBiocDataPackage.sh "biscuiteerdata-1.16.0" diff --git a/recipes/bioconductor-biseq/meta.yaml b/recipes/bioconductor-biseq/meta.yaml index c3e2ea0161860..93bf96e0a6e37 100644 --- a/recipes/bioconductor-biseq/meta.yaml +++ b/recipes/bioconductor-biseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "BiSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef582ccfe80af188e2c95e93917112f6 + md5: 76a46bdea0a83b3ead6a8ee87d6000ac build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biseq", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-globaltest >=5.54.0,<5.55.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-globaltest >=5.56.0,<5.57.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-betareg - r-formula - r-lokern run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-globaltest >=5.54.0,<5.55.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-globaltest >=5.56.0,<5.57.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-betareg - r-formula diff --git a/recipes/bioconductor-blacksheepr/meta.yaml b/recipes/bioconductor-blacksheepr/meta.yaml index 6261dbb5aa447..956002139ea7c 100644 --- a/recipes/bioconductor-blacksheepr/meta.yaml +++ b/recipes/bioconductor-blacksheepr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "blacksheepr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ffc59bd1330fbd355d89f419d5378c36 + md5: 464b853300f0d97e2ad8f0a4188701c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-blacksheepr", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, curl requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-pasilla >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-pasilla >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-rcolorbrewer - r-viridis run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-pasilla >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-pasilla >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-rcolorbrewer diff --git a/recipes/bioconductor-bladderbatch/meta.yaml b/recipes/bioconductor-bladderbatch/meta.yaml index e3c40acb29dbe..9eafff22e508e 100644 --- a/recipes/bioconductor-bladderbatch/meta.yaml +++ b/recipes/bioconductor-bladderbatch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "bladderbatch" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ab4457a6eebb75202730d4433d4aa245 + md5: d59d10a87e8d62c6ba10f7e9c0160a44 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bladderbatch", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bladderbatch/post-link.sh b/recipes/bioconductor-bladderbatch/post-link.sh index 1f6b3e2258b10..fac44e79b40e2 100644 --- a/recipes/bioconductor-bladderbatch/post-link.sh +++ b/recipes/bioconductor-bladderbatch/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bladderbatch-1.38.0" +installBiocDataPackage.sh "bladderbatch-1.40.0" diff --git a/recipes/bioconductor-blima/meta.yaml b/recipes/bioconductor-blima/meta.yaml index 0ed1506388c12..dee6d37139ead 100644 --- a/recipes/bioconductor-blima/meta.yaml +++ b/recipes/bioconductor-blima/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "blima" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c2c14f23337c1135f6d65fd58fa7ac05 + md5: a0d7cbb46b78eabdbc06c4ee1b417bcb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-blima", max_pin="x.x") }}' # Suggests: xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi, knitr requirements: host: - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - 'r-rcpp >=0.12.8' - libblas - liblapack run: - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - 'r-rcpp >=0.12.8' build: diff --git a/recipes/bioconductor-blimatestingdata/meta.yaml b/recipes/bioconductor-blimatestingdata/meta.yaml index 7befc4cd40a70..6d25e2e3e3f9e 100644 --- a/recipes/bioconductor-blimatestingdata/meta.yaml +++ b/recipes/bioconductor-blimatestingdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "blimaTestingData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 17e9a4119b1beaf61f30fbe192b9a20a + md5: 3ae3da97d0d020e16feee29b93c24825 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-blimatestingdata", max_pin="x.x") }}' noarch: generic # Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-blimatestingdata/post-link.sh b/recipes/bioconductor-blimatestingdata/post-link.sh index 0137332d50d47..1418b77f265e3 100644 --- a/recipes/bioconductor-blimatestingdata/post-link.sh +++ b/recipes/bioconductor-blimatestingdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "blimatestingdata-1.20.0" +installBiocDataPackage.sh "blimatestingdata-1.22.0" diff --git a/recipes/bioconductor-blma/meta.yaml b/recipes/bioconductor-blma/meta.yaml index f16f88fab8d50..acbf15edf9540 100644 --- a/recipes/bioconductor-blma/meta.yaml +++ b/recipes/bioconductor-blma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "BLMA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9040447a39ecba3f13decf927d02295e + md5: a09cb94872d4a064b9b6300945795cdf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-blma", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-padog >=1.42.0,<1.43.0' - - 'bioconductor-rontotools >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-padog >=1.44.0,<1.45.0' + - 'bioconductor-rontotools >=2.30.0,<2.31.0' - r-base - r-gsa - r-metafor run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-padog >=1.42.0,<1.43.0' - - 'bioconductor-rontotools >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-padog >=1.44.0,<1.45.0' + - 'bioconductor-rontotools >=2.30.0,<2.31.0' - r-base - r-gsa - r-metafor diff --git a/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml b/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml index 776134ad78ca8..d6fbe40747131 100644 --- a/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml +++ b/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "BloodCancerMultiOmics2017" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d7ccf32b2249044c2b86aa4cf933372 + md5: d2b2dcb147bf904df505fedca2d1ea9e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bloodcancermultiomics2017", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, abind, AnnotationDbi, biomaRt, broom, colorspace, cowplot, dendsort, doParallel, foreach, forestplot, genefilter, ggbeeswarm, ggtern, gridExtra, hexbin, IHW, limma, magrittr, Matrix, maxstat, nat, org.Hs.eg.db, pheatmap, piano, readxl, Rtsne, tidyr, xtable requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-beeswarm - r-devtools @@ -39,9 +40,9 @@ requirements: - r-survival - r-tibble run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-beeswarm - r-devtools @@ -57,7 +58,7 @@ requirements: - r-survival - r-tibble - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh b/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh index 6a011d5316aed..84e46bc91c92a 100644 --- a/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh +++ b/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bloodcancermultiomics2017-1.20.0" +installBiocDataPackage.sh "bloodcancermultiomics2017-1.22.0" diff --git a/recipes/bioconductor-bloodgen3module/meta.yaml b/recipes/bioconductor-bloodgen3module/meta.yaml index 88890177b4894..aad99351531e3 100644 --- a/recipes/bioconductor-bloodgen3module/meta.yaml +++ b/recipes/bioconductor-bloodgen3module/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "BloodGen3Module" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37a265fa33d837fb54956f3347976869 + md5: c9957080f8c55f99ebcc89cdc652deb9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bloodgen3module", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, devtools, BiocGenerics, knitr, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-ggplot2 @@ -36,11 +37,11 @@ requirements: - r-testthat - r-v8 run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-ggplot2 diff --git a/recipes/bioconductor-bluster/meta.yaml b/recipes/bioconductor-bluster/meta.yaml index 24fd7a073cdab..2ba7e0232e16b 100644 --- a/recipes/bioconductor-bluster/meta.yaml +++ b/recipes/bioconductor-bluster/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "bluster" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a8d0bcd5ece8d29de23893d218538f35 + md5: baf91e0700b1f49eb80522be9eb8204d build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut, scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans, kohonen, apcluster + run_exports: '{{ pin_subpackage("bioconductor-bluster", max_pin="x.x") }}' +# Suggests: knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut, scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans, kohonen, apcluster, DirichletMultinomial, vegan, fastcluster # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-igraph @@ -32,9 +33,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-igraph diff --git a/recipes/bioconductor-bnbc/meta.yaml b/recipes/bioconductor-bnbc/meta.yaml index d3820552aca7c..b60b06813c282 100644 --- a/recipes/bioconductor-bnbc/meta.yaml +++ b/recipes/bioconductor-bnbc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.23.0" %} {% set name = "bnbc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e2882b1e727097ea7116bdb5941eabb0 + md5: 201f8c694f60da1dfa8112194f29ca18 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bnbc", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-data.table - r-matrixstats @@ -37,16 +38,16 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-data.table - r-matrixstats diff --git a/recipes/bioconductor-bnem/meta.yaml b/recipes/bioconductor-bnem/meta.yaml index 00b86a14d90bc..c24854a74af32 100644 --- a/recipes/bioconductor-bnem/meta.yaml +++ b/recipes/bioconductor-bnem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "bnem" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cd61ea3a67e6032366b423e220d4b4de + md5: 84eb035082edc5cefe35763abde3093f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bnem", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, BiocGenerics, MatrixGenerics, BiocStyle +# Suggests: knitr, BiocGenerics, MatrixGenerics, BiocStyle, RUnit requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' - - 'bioconductor-epinem >=1.24.0,<1.25.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mnem >=1.16.0,<1.17.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' + - 'bioconductor-epinem >=1.26.0,<1.27.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mnem >=1.18.0,<1.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-binom - r-cluster @@ -40,16 +41,16 @@ requirements: - r-rmarkdown - r-snowfall run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' - - 'bioconductor-epinem >=1.24.0,<1.25.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mnem >=1.16.0,<1.17.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' + - 'bioconductor-epinem >=1.26.0,<1.27.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mnem >=1.18.0,<1.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-binom - r-cluster diff --git a/recipes/bioconductor-bobafit/meta.yaml b/recipes/bioconductor-bobafit/meta.yaml index c0cc7a0e533dc..4b504236c4870 100644 --- a/recipes/bioconductor-bobafit/meta.yaml +++ b/recipes/bioconductor-bobafit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "BOBaFIT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61cff94869967960f27a430de74624d4 + md5: 48b9cc5c35adf6469bd1dc2ca566bed1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bobafit", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, markdown, BiocStyle, knitr, testthat (>= 3.0.0), utils, testthat requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' - r-base - r-dplyr - r-ggforce @@ -33,9 +34,9 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' - r-base - r-dplyr - r-ggforce diff --git a/recipes/bioconductor-bodymaprat/meta.yaml b/recipes/bioconductor-bodymaprat/meta.yaml index 30cd298b734df..a13f963c7a9e9 100644 --- a/recipes/bioconductor-bodymaprat/meta.yaml +++ b/recipes/bioconductor-bodymaprat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "bodymapRat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d15dd35c8ce1db80954afb9e4663fe29 + md5: fc575d7f33dd1ee73f1860fb076a840b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bodymaprat", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, BiocStyle, testthat requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bodymaprat/post-link.sh b/recipes/bioconductor-bodymaprat/post-link.sh index 86e3dad9f97d4..d4ee9d2550175 100644 --- a/recipes/bioconductor-bodymaprat/post-link.sh +++ b/recipes/bioconductor-bodymaprat/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bodymaprat-1.16.0" +installBiocDataPackage.sh "bodymaprat-1.18.0" diff --git a/recipes/bioconductor-bovine.db/meta.yaml b/recipes/bioconductor-bovine.db/meta.yaml index ea439d5251876..29be66b899563 100644 --- a/recipes/bioconductor-bovine.db/meta.yaml +++ b/recipes/bioconductor-bovine.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "bovine.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dcc1180e8ac11247f9899f140082647e build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bovine.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.bt.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.bt.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.bt.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.bt.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bovine.db0/meta.yaml b/recipes/bioconductor-bovine.db0/meta.yaml index 5708b4d9c6569..7014ea409a9c4 100644 --- a/recipes/bioconductor-bovine.db0/meta.yaml +++ b/recipes/bioconductor-bovine.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "bovine.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1e268d93f6206875bd73ad2caae53f27 + md5: 658829797db74aec87af1914483d1af7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bovine.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bovine.db0/post-link.sh b/recipes/bioconductor-bovine.db0/post-link.sh index 7506bd29e27b6..0c3dc1fc3f167 100644 --- a/recipes/bioconductor-bovine.db0/post-link.sh +++ b/recipes/bioconductor-bovine.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bovine.db0-3.17.0" +installBiocDataPackage.sh "bovine.db0-3.18.0" diff --git a/recipes/bioconductor-bovinecdf/meta.yaml b/recipes/bioconductor-bovinecdf/meta.yaml index 9ad4d03a221a3..3a8ad02076f2f 100644 --- a/recipes/bioconductor-bovinecdf/meta.yaml +++ b/recipes/bioconductor-bovinecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "bovinecdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e155fc7d5f84ee420d9b250a639af305 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bovinecdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bovineprobe/meta.yaml b/recipes/bioconductor-bovineprobe/meta.yaml index 90f41fdf6fd4b..d4af93a9c72d3 100644 --- a/recipes/bioconductor-bovineprobe/meta.yaml +++ b/recipes/bioconductor-bovineprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "bovineprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9f9e25fc8c7a76acf541745b7c09748b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bovineprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bprmeth/meta.yaml b/recipes/bioconductor-bprmeth/meta.yaml index c01464ce9e050..6a3d18505b240 100644 --- a/recipes/bioconductor-bprmeth/meta.yaml +++ b/recipes/bioconductor-bprmeth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.1" %} +{% set version = "1.28.0" %} {% set name = "BPRMeth" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4b83f314896bec3879303077f2537c62 + md5: 8229c7c5175e3888c86a5a3a42eb7a8c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bprmeth", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - r-cowplot @@ -45,10 +46,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - r-cowplot diff --git a/recipes/bioconductor-brain/meta.yaml b/recipes/bioconductor-brain/meta.yaml index 69cd4b403220d..f5e9400cafc79 100644 --- a/recipes/bioconductor-brain/meta.yaml +++ b/recipes/bioconductor-brain/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "BRAIN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e35f1ec745209c95a944114c34091b41 + md5: 575b879f058d01202c3bc33b0ff8e3f1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-brain", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-lattice - r-polynomf run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-lattice - r-polynomf diff --git a/recipes/bioconductor-brainflowprobes/meta.yaml b/recipes/bioconductor-brainflowprobes/meta.yaml index 6099d55d781b5..5f35b40d260c6 100644 --- a/recipes/bioconductor-brainflowprobes/meta.yaml +++ b/recipes/bioconductor-brainflowprobes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "brainflowprobes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 00cceed929cbf95e9d1dcaf2b0248933 + md5: eb9efebe165aeeae35ccc6b115836937 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-brainflowprobes", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 2.1.0), covr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-derfinderplot >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-derfinderplot >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-genomicstate >=0.99.0,<0.100.0' - r-base - 'r-cowplot >=1.0.0' - 'r-ggplot2 >=3.1.1' - 'r-rcolorbrewer >=1.1' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-derfinderplot >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-derfinderplot >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-genomicstate >=0.99.0,<0.100.0' - r-base - 'r-cowplot >=1.0.0' diff --git a/recipes/bioconductor-branchpointer/meta.yaml b/recipes/bioconductor-branchpointer/meta.yaml index 292fb0401dad9..b5aa55175fda0 100644 --- a/recipes/bioconductor-branchpointer/meta.yaml +++ b/recipes/bioconductor-branchpointer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "branchpointer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a86bfa6b36d075cba930e82d1148b850 + md5: 7a62abd020843736b7ea125ffc4a56e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-branchpointer", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - r-cowplot @@ -39,14 +40,14 @@ requirements: - r-plyr - r-stringr run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - r-cowplot diff --git a/recipes/bioconductor-breakpointr/meta.yaml b/recipes/bioconductor-breakpointr/meta.yaml index d84838d2737df..f401d66f805fd 100644 --- a/recipes/bioconductor-breakpointr/meta.yaml +++ b/recipes/bioconductor-breakpointr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "breakpointR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ba29b07c5e6f5c0972109a7dd43c32c + md5: 96dddc1e7bbd8b880a89f8f1be145e66 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-breakpointr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-breakpointrdata >=1.18.0,<1.19.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-breakpointrdata >=1.20.0,<1.21.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-doparallel @@ -36,14 +37,14 @@ requirements: - r-ggplot2 - r-gtools run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-breakpointrdata >=1.18.0,<1.19.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-breakpointrdata >=1.20.0,<1.21.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-doparallel diff --git a/recipes/bioconductor-breakpointrdata/meta.yaml b/recipes/bioconductor-breakpointrdata/meta.yaml index 2a17fb8938acf..904bd544168f7 100644 --- a/recipes/bioconductor-breakpointrdata/meta.yaml +++ b/recipes/bioconductor-breakpointrdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "breakpointRdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 59535154a02ede7347b6114c11292173 + md5: e3f74132513d150cb5d5cc62bfd49586 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-breakpointrdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breakpointrdata/post-link.sh b/recipes/bioconductor-breakpointrdata/post-link.sh index 12ab5d0df96bb..726ec7f9888bf 100644 --- a/recipes/bioconductor-breakpointrdata/post-link.sh +++ b/recipes/bioconductor-breakpointrdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breakpointrdata-1.18.0" +installBiocDataPackage.sh "breakpointrdata-1.20.0" diff --git a/recipes/bioconductor-breastcancermainz/meta.yaml b/recipes/bioconductor-breastcancermainz/meta.yaml index 0d66189888bfe..e073dd94ff14c 100644 --- a/recipes/bioconductor-breastcancermainz/meta.yaml +++ b/recipes/bioconductor-breastcancermainz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "breastCancerMAINZ" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d906d493af2aa3a2fbf00029aa6f843 + md5: 2b8df5af87b71c6706f909129212b504 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-breastcancermainz", max_pin="x.x") }}' noarch: generic # Suggests: survcomp, genefu, Biobase requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breastcancermainz/post-link.sh b/recipes/bioconductor-breastcancermainz/post-link.sh index c37b0581a960d..4570fff6a22f3 100644 --- a/recipes/bioconductor-breastcancermainz/post-link.sh +++ b/recipes/bioconductor-breastcancermainz/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breastcancermainz-1.38.0" +installBiocDataPackage.sh "breastcancermainz-1.40.0" diff --git a/recipes/bioconductor-breastcancernki/meta.yaml b/recipes/bioconductor-breastcancernki/meta.yaml index 6d47a0d8fb9ff..38686c35da078 100644 --- a/recipes/bioconductor-breastcancernki/meta.yaml +++ b/recipes/bioconductor-breastcancernki/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "breastCancerNKI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61d8e072228b6bbb224793b35625d507 + md5: 0a0940593d75deaed0aa6f01954cf61c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-breastcancernki", max_pin="x.x") }}' noarch: generic # Suggests: survcomp, genefu, Biobase requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breastcancernki/post-link.sh b/recipes/bioconductor-breastcancernki/post-link.sh index 9b89ba199b787..e92a07580eac6 100644 --- a/recipes/bioconductor-breastcancernki/post-link.sh +++ b/recipes/bioconductor-breastcancernki/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breastcancernki-1.38.0" +installBiocDataPackage.sh "breastcancernki-1.40.0" diff --git a/recipes/bioconductor-breastcancertransbig/meta.yaml b/recipes/bioconductor-breastcancertransbig/meta.yaml index 593973e18a542..80be8500b3982 100644 --- a/recipes/bioconductor-breastcancertransbig/meta.yaml +++ b/recipes/bioconductor-breastcancertransbig/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "breastCancerTRANSBIG" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7117b6426a4cf52736db5835ccdc4ccc + md5: 170d89ddd3e554da50a0b2b5d040a96e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-breastcancertransbig", max_pin="x.x") }}' noarch: generic # Suggests: survcomp, genefu, Biobase requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breastcancertransbig/post-link.sh b/recipes/bioconductor-breastcancertransbig/post-link.sh index 586835155b461..819f5330c62a7 100644 --- a/recipes/bioconductor-breastcancertransbig/post-link.sh +++ b/recipes/bioconductor-breastcancertransbig/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breastcancertransbig-1.38.0" +installBiocDataPackage.sh "breastcancertransbig-1.40.0" diff --git a/recipes/bioconductor-breastcancerunt/meta.yaml b/recipes/bioconductor-breastcancerunt/meta.yaml index ea17ee7662462..938bc94e4da08 100644 --- a/recipes/bioconductor-breastcancerunt/meta.yaml +++ b/recipes/bioconductor-breastcancerunt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "breastCancerUNT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fab6de14673763f649a3cfd14fc62579 + md5: 31e1b6d7e34b4acb9207e3e152539166 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-breastcancerunt", max_pin="x.x") }}' noarch: generic # Suggests: survcomp, genefu, Biobase requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breastcancerunt/post-link.sh b/recipes/bioconductor-breastcancerunt/post-link.sh index 6408e7184bd12..0b186b89bdffc 100644 --- a/recipes/bioconductor-breastcancerunt/post-link.sh +++ b/recipes/bioconductor-breastcancerunt/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breastcancerunt-1.38.0" +installBiocDataPackage.sh "breastcancerunt-1.40.0" diff --git a/recipes/bioconductor-breastcancerupp/meta.yaml b/recipes/bioconductor-breastcancerupp/meta.yaml index 20b68e52bd898..0bdf776792724 100644 --- a/recipes/bioconductor-breastcancerupp/meta.yaml +++ b/recipes/bioconductor-breastcancerupp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "breastCancerUPP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37f0587a0149e1abe5525dd7bbc76a7f + md5: c5c10989a8a2dbfd20c228522474fac1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-breastcancerupp", max_pin="x.x") }}' noarch: generic # Suggests: survcomp, genefu, Biobase requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breastcancerupp/post-link.sh b/recipes/bioconductor-breastcancerupp/post-link.sh index b8e19ca711332..7abd029d8fdcd 100644 --- a/recipes/bioconductor-breastcancerupp/post-link.sh +++ b/recipes/bioconductor-breastcancerupp/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breastcancerupp-1.38.0" +installBiocDataPackage.sh "breastcancerupp-1.40.0" diff --git a/recipes/bioconductor-breastcancervdx/meta.yaml b/recipes/bioconductor-breastcancervdx/meta.yaml index 0f60c65a37662..ed8c49c9a563f 100644 --- a/recipes/bioconductor-breastcancervdx/meta.yaml +++ b/recipes/bioconductor-breastcancervdx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "breastCancerVDX" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a20c1e1a3060af883ced8843600a1614 + md5: 446ef46e0bdd1480e12de21ded7b58f0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-breastcancervdx", max_pin="x.x") }}' noarch: generic # Suggests: survcomp, genefu, Biobase requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breastcancervdx/post-link.sh b/recipes/bioconductor-breastcancervdx/post-link.sh index a5e24a547d943..1269d20e15959 100644 --- a/recipes/bioconductor-breastcancervdx/post-link.sh +++ b/recipes/bioconductor-breastcancervdx/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breastcancervdx-1.38.0" +installBiocDataPackage.sh "breastcancervdx-1.40.0" diff --git a/recipes/bioconductor-brendadb/meta.yaml b/recipes/bioconductor-brendadb/meta.yaml index 459cb8316015e..b084097d11c03 100644 --- a/recipes/bioconductor-brendadb/meta.yaml +++ b/recipes/bioconductor-brendadb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "brendaDb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 048a034a1b3a87cfbd31ada86ee4b282 + md5: 35e521feef3f87b0122ac00ad0deae5b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-brendadb", max_pin="x.x") }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown, devtools # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-crayon - r-dplyr @@ -37,8 +38,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-crayon - r-dplyr diff --git a/recipes/bioconductor-brgedata/meta.yaml b/recipes/bioconductor-brgedata/meta.yaml index f353e69bb3c67..39687c989b37a 100644 --- a/recipes/bioconductor-brgedata/meta.yaml +++ b/recipes/bioconductor-brgedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "brgedata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5b448f1cfae2bb44babb2b1720d12234 + md5: b8d26c8dfa756e9eb556e4662e3b3302 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-brgedata", max_pin="x.x") }}' noarch: generic -# Suggests: minfi, MultiAssayExperiment, knitr, rmarkdown, rexposome +# Suggests: minfi, MultiAssayExperiment, knitr, rmarkdown, rexposome, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-brgedata/post-link.sh b/recipes/bioconductor-brgedata/post-link.sh index 1e48f726f3a24..267b22a18da9f 100644 --- a/recipes/bioconductor-brgedata/post-link.sh +++ b/recipes/bioconductor-brgedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "brgedata-1.22.0" +installBiocDataPackage.sh "brgedata-1.24.0" diff --git a/recipes/bioconductor-brgenomics/meta.yaml b/recipes/bioconductor-brgenomics/meta.yaml index 4bccede1a84b9..519fe73af34c1 100644 --- a/recipes/bioconductor-brgenomics/meta.yaml +++ b/recipes/bioconductor-brgenomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.13.0" %} {% set name = "BRGenomics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96099779d34a4ffd00637a2da0d2888d + md5: 33a9bc55e58468faa4cc337617be743a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-brgenomics", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, apeglm, remotes, ggplot2, reshape2, Biostrings requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-bridgedbr/meta.yaml b/recipes/bioconductor-bridgedbr/meta.yaml index 13e09730ca229..f48e3b4fbacd2 100644 --- a/recipes/bioconductor-bridgedbr/meta.yaml +++ b/recipes/bioconductor-bridgedbr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "BridgeDbR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 64a3933b9e01f5e9f8f7ca740fbf2e1a + md5: 2c155c28cb8d117e2dc1b69873b91d84 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bridgedbr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-bronchialil13/meta.yaml b/recipes/bioconductor-bronchialil13/meta.yaml index 16910d2d8dcb5..4084cc6bf0bff 100644 --- a/recipes/bioconductor-bronchialil13/meta.yaml +++ b/recipes/bioconductor-bronchialil13/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "bronchialIL13" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71116894de06b0faf014ae3be0f54b36 + md5: be303e29450fb15b03a10f6caaf30159 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bronchialil13", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bronchialil13/post-link.sh b/recipes/bioconductor-bronchialil13/post-link.sh index 49cb149982f5b..6ec47d8303721 100644 --- a/recipes/bioconductor-bronchialil13/post-link.sh +++ b/recipes/bioconductor-bronchialil13/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bronchialil13-1.38.0" +installBiocDataPackage.sh "bronchialil13-1.40.0" diff --git a/recipes/bioconductor-browserviz/meta.yaml b/recipes/bioconductor-browserviz/meta.yaml index e2aff600e6de8..a84be67b166ab 100644 --- a/recipes/bioconductor-browserviz/meta.yaml +++ b/recipes/bioconductor-browserviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "BrowserViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f26ddbc8b11670673e8aa1ba1d596da + md5: ae6366903bd754cbe0ca0d21168c6883 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-browserviz", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - 'r-httpuv >=1.5.0' - 'r-jsonlite >=1.5' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - 'r-httpuv >=1.5.0' - 'r-jsonlite >=1.5' diff --git a/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml b/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml index dd0c23f97d22c..8b13956ebc368 100644 --- a/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml +++ b/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "BSgenome.Alyrata.JGI.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 64878499c633de66ccf4c5abc32c0aeb build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.alyrata.jgi.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml b/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml index 10447b66c3c39..ab05d12803a09 100644 --- a/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml +++ b/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Amellifera.BeeBase.assembly4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 77495ee5eba48fe52902c9cc4f9ba7cc build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.amellifera.beebase.assembly4", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1/meta.yaml b/recipes/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1/meta.yaml index 9ff51c4de3714..be19401c6fca5 100644 --- a/recipes/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1/meta.yaml +++ b/recipes/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "BSgenome.Amellifera.NCBI.AmelHAv3.1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b119087dfe54805c90cb6bf901e8237e build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.amellifera.ncbi.amelhav3.1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml index 51095fb8ab0e1..5ad72a039a442 100644 --- a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Amellifera.UCSC.apiMel2.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e7a7ff8cfce8e239b22116855456f23d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.amellifera.ucsc.apimel2.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.amellifera.ucsc.apimel2 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.amellifera.ucsc.apimel2 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml index 6c642df024a66..03cf1f3dc82a3 100644 --- a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml +++ b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Amellifera.UCSC.apiMel2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 436ddf54868906e7d1135369d41a2ffe build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.amellifera.ucsc.apimel2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml b/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml index 77d7c5b033f0f..cd38ff3980573 100644 --- a/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml +++ b/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "BSgenome.Aofficinalis.NCBI.V1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3f8fd13e74eee63895a5ef528004b60b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.aofficinalis.ncbi.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml b/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml index ad247c14857a0..4fdd444fe0fb6 100644 --- a/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml +++ b/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Athaliana.TAIR.04232008" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6b8a31a228dbcf4468974f5ec1d98467 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.athaliana.tair.04232008", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml b/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml index e03055053f540..5829649a04069 100644 --- a/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml +++ b/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Athaliana.TAIR.TAIR9" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8c6709a5f544616d59f4d39aac5787a7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.athaliana.tair.tair9", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml index a893da700aa30..5e00c72c1eb23 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau3.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 50f7da5907cbe0d08183dc7161a8ca56 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau3.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau3 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml index a7cfc076d2a11..cf3656257eb57 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fe6c4d5853f91c3db3e716ddbc773580 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau3", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml index 8f79033795b1a..27d7dfefcbef2 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau4.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7c5294349c7061adfb3948bc5659afeb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau4.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau4 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau4 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml index 1c30f83c63ff8..eab5a9891ec02 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 162cd253c719e347df5748ebb407a191 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau4", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml index f75c8d0eaa275..bbfbee0affde2 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau6.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a176de6b1b91854d47e783b8249dbf58 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau6.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau6 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau6 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml index b3832e58994bd..ce246f321d24a 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b22391e0678fc3743daa4b77ecc55f66 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau6", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml index 1c7c2e7b1f8d1..682d89e7f4c24 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau8" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 61ababa7b2b5360fceeb06f0bf49b208 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau8", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9.masked/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9.masked/meta.yaml index 4bda0bf0ac096..62f59fbac5296 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.4" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau9.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c96bd95c3b791d712aa5cb8c96f9c937 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau9.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau9 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau9 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9/meta.yaml index 87bc529b78d3e..3f586fcdbffff 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau9" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9b3343725d85c093999413d91218079d build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau9", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml b/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml index 5a326847bb631..648f18fbe0f64 100644 --- a/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml +++ b/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "BSgenome.Carietinum.NCBI.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: eef018ecce6d32852aa18ac39cf377c6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.carietinum.ncbi.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml index 997b63d67e600..7f4da58f4e64f 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Celegans.UCSC.ce10" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 98a8ca836d6db23e46674552669d7942 build: - number: 16 + number: 17 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.celegans.ucsc.ce10", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml index 4edbab45dbd80..c2b220fe98a18 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Celegans.UCSC.ce11" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b80e24149a0c6ed323d0c9a6d112ef52 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.celegans.ucsc.ce11", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml index d41e5c535f971..32235e1365fe1 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Celegans.UCSC.ce2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b2bf7eec2b07685cf9dcdf42840db208 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.celegans.ucsc.ce2", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml index 77e16d3a2e788..e42da8e5488ee 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Celegans.UCSC.ce6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: cb86ff861d8f660c2abd8fc1907d84a6 build: - number: 16 + number: 17 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.celegans.ucsc.ce6", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Celegans.UCSC.ce6.ensGene requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml index 2392f4d5cf402..069fc1c59c867 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Cfamiliaris.UCSC.canFam2.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6f921533bb83f83f43b8d227b00a48cb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam2 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam2 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml index 4ade310b5153a..982e9034314f8 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Cfamiliaris.UCSC.canFam2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b98f5289ed5d362cd815db9352598634 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cfamiliaris.ucsc.canfam2", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml index 0492d4146ac81..0261f9eff5a17 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Cfamiliaris.UCSC.canFam3.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8e2246f51fc967dc2ed748cf967a7649 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam3 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml index b8e2a85ce5776..89560db448749 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Cfamiliaris.UCSC.canFam3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: efcdc531042be86f99a734cd69c0688c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cfamiliaris.ucsc.canfam3", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/meta.yaml b/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/meta.yaml index 29b734795a981..10417581a99fc 100644 --- a/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/meta.yaml +++ b/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Cjacchus.UCSC.calJac3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 41f927aa0d6ffbdaa6ad93c9135409e6 build: - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cjacchus.ucsc.caljac3", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac4/meta.yaml b/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac4/meta.yaml index 899af20c80879..516f9eb1efe23 100644 --- a/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac4/meta.yaml +++ b/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac4/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "BSgenome.Cjacchus.UCSC.calJac4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b11d16ac2cfa81e04af74e2049e52670 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cjacchus.ucsc.caljac4", max_pin="x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20231202 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1/meta.yaml b/recipes/bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1/meta.yaml index a506ea2b1c87e..462035d069539 100644 --- a/recipes/bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1/meta.yaml +++ b/recipes/bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "BSgenome.CneoformansVarGrubiiKN99.NCBI.ASM221672v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ea536a15bd932af794f672d9b204c141 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.creinhardtii.jgi.v5.6/meta.yaml b/recipes/bioconductor-bsgenome.creinhardtii.jgi.v5.6/meta.yaml index 55e8df05bb417..c415b873854e9 100644 --- a/recipes/bioconductor-bsgenome.creinhardtii.jgi.v5.6/meta.yaml +++ b/recipes/bioconductor-bsgenome.creinhardtii.jgi.v5.6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "BSgenome.Creinhardtii.JGI.v5.6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2bd1be53d19249ac14ad7f39dc00af0e build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.creinhardtii.jgi.v5.6", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml index 11825bf9d2d6e..62a0b17986a8d 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm2.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ae7ca3053e97a0d6bd20bc2b9635ecce build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm2 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm2 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml index e3a3eef94ca81..7b1927e47450e 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ebc88df5595fc7aad588b8f3f7de4784 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.dmelanogaster.ucsc.dm2", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml index 2f2cc231ae70f..6067d2d13f90e 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm3.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 592e7ec451d126b2d314ab6c75d86830 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm3 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml index f16df60d79dc6..c68d6516cefb1 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b7ceebf7bfee766596f602f9e808d069 build: - number: 16 + number: 17 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.dmelanogaster.ucsc.dm3", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Dmelanogaster.UCSC.dm3.ensGene requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml index d84b65dd7a732..feaea65b5861e 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.1" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f9d6e406b7893a17c08edd4521c2802f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.dmelanogaster.ucsc.dm6", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml index 92aca3bfbc9a8..87a3b044b538d 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Drerio.UCSC.danRer10" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b8dbcc8a338a021ed35656b27b3dd4c0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer10", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer11/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer11/meta.yaml index c45c38af3a531..95822ca277bba 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer11/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer11/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Drerio.UCSC.danRer11" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: cd586da56ca88ccebb85804f992ba204 build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer11", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml index 68aa11c6f335a..64e298e1c21eb 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Drerio.UCSC.danRer5.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8f0623bcbe1743754a56c55599b535f3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer5.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer5 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer5 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml index 43690e11e74d6..bf6871a4d5a7d 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Drerio.UCSC.danRer5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b1fee4bcc0d9cebb2bbdec5cb851f00d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer5", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml index fc11125683fda..6b526c573e5c6 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Drerio.UCSC.danRer6.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 71c9b05c27b8d2e05735e6494a8f17ba build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer6.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer6 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer6 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml index f0a07f6245687..478b3e1bddeff 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Drerio.UCSC.danRer6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 537d37d29d97ae0c31d77decc67b25b0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer6", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml index fe467e74c1a8a..019514752ee1c 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Drerio.UCSC.danRer7.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5d68af24477d006ed22e7342ff97ac16 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer7.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml index 05ea9322b3723..6c1a8c0e62b9d 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Drerio.UCSC.danRer7" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 766b407a46f20d69a143eab0809eb10a build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer7", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1/meta.yaml b/recipes/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1/meta.yaml index bfae8430f5959..0ce3c6e24705b 100644 --- a/recipes/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1/meta.yaml +++ b/recipes/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Dvirilis.Ensembl.dvircaf1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6a6a6dc7b2d68a741c85525045a67890 build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.dvirilis.ensembl.dvircaf1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml index b99315e8e48ff..2f3ba681a1364 100644 --- a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml +++ b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Ecoli.NCBI.20080805" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c653e9cbee3faeb6fd5759b7575f234d build: - number: 16 + number: 17 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ecoli.ncbi.20080805", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml index 4e8f686c998da..3a5920d510aaa 100644 --- a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Gaculeatus.UCSC.gasAcu1.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9d9b9e70f4f4624ee4a2b09a59d44510 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.gaculeatus.ucsc.gasacu1 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.gaculeatus.ucsc.gasacu1 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml index 64feabca6f667..6a6732255be3d 100644 --- a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml +++ b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Gaculeatus.UCSC.gasAcu1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 412aa0570d9c556861b7bb9a5bbc2007 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.gaculeatus.ucsc.gasacu1", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml index 58495ba4cfa9f..cf7403c1a2f0a 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Ggallus.UCSC.galGal3.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b3224e3a2b15de379c068e61cedfefa6 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ggallus.ucsc.galgal3.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.ggallus.ucsc.galgal3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.ggallus.ucsc.galgal3 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml index 7d8a3cbcda3e5..e8b20a1070d3b 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Ggallus.UCSC.galGal3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a463e5ccfc8c6d2c62a6ade0da65dbc4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ggallus.ucsc.galgal3", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml index 32c4ca424d92b..4b54412a74eac 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Ggallus.UCSC.galGal4.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0166121ebd8d0b6a4d24d67e175cfe81 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ggallus.ucsc.galgal4.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.ggallus.ucsc.galgal4 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.ggallus.ucsc.galgal4 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml index ad3c3e3edc772..d54b800d51b31 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Ggallus.UCSC.galGal4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c2cb4bfc39db93c060e78d8d12542c11 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ggallus.ucsc.galgal4", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml index 6274a0dcded2f..18a560405740b 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Ggallus.UCSC.galGal5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 93b42354404edd848b21ea6781ca135c build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ggallus.ucsc.galgal5", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal6/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal6/meta.yaml index c5cf92c3d35ad..a44fab45df53d 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal6/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Ggallus.UCSC.galGal6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 25ef08a5430fb337dbf752ca3378ea3e build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ggallus.ucsc.galgal6", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.gmax.ncbi.gmv40/meta.yaml b/recipes/bioconductor-bsgenome.gmax.ncbi.gmv40/meta.yaml index f607776b31e4a..fe9c07be232c6 100644 --- a/recipes/bioconductor-bsgenome.gmax.ncbi.gmv40/meta.yaml +++ b/recipes/bioconductor-bsgenome.gmax.ncbi.gmv40/meta.yaml @@ -1,6 +1,6 @@ {% set version = "4.0" %} {% set name = "BSgenome.Gmax.NCBI.Gmv40" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 421c045b993b2cfbc2b08c8103835c56 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.gmax.ncbi.gmv40", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml index 4d458f7e30969..7fb6b93796e7d 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.1" %} {% set name = "BSgenome.Hsapiens.1000genomes.hs37d5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 164e1692d38fefa499c2c8ac5fc22793 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.1000genomes.hs37d5", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml index 506c403b47d19..04da6b9994ab5 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Hsapiens.NCBI.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 733d324b34d34d7da8c4bf38459f4fae build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ncbi.grch38", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0/meta.yaml index 802f28ed1c51f..4f0ef091db55a 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 22a99174e1e17718e0b4f8b66f32fd9b build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml index fdaff26d7f794..7fb6eb6c52a75 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Hsapiens.UCSC.hg17.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ff6ee5196f234c5a2a3bcdd052c3c08e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg17.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg17 >=1.3.0,<1.4.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg17 >=1.3.0,<1.4.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml index 4a71b4fbb264b..eb46af4af2e48 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Hsapiens.UCSC.hg17" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: cbea3029c3d3125a88e6c061c3d3abde build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg17", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml index 05ee40409117e..e950d5f76a8de 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Hsapiens.UCSC.hg18.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e6a31e3cba34ce5e0eb6f76d2c19870c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg18.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml index a0c785f26697d..33e4cdff26eae 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Hsapiens.UCSC.hg18" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 51bb2e1ed4009860bb21aaac32fffd9c build: - number: 14 + number: 15 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg18", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Hsapiens.UCSC.hg18.knownGene requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml index d4720898a70b4..5664f8236fb7e 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.993" %} {% set name = "BSgenome.Hsapiens.UCSC.hg19.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4424e1bda9cc005d75f5f05ba4a50c77 build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg19.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml index 59cee391fb862..4280e60fd61df 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Hsapiens.UCSC.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: bb3f864ab32450d895816b45f6105f4f build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major/meta.yaml index 972385b4cccfb..2c99c40050795 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.0.9999" %} {% set name = "BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c59f66e52d4982942bea2254223d58df build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor, testthat requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor/meta.yaml index 6e69afb63c9df..9c2021c5d0a73 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.0.9999" %} {% set name = "BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2cc3a612a2064624735d6a92910be7f3 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major, testthat requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml index 0fe10479f56ac..5a69152654b1b 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.5" %} {% set name = "BSgenome.Hsapiens.UCSC.hg38.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,24 +13,25 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7570dd1b4f013b3c6acecd68602180b4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg38.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml index ca742fc10b820..caafd0d4f2854 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.5" %} {% set name = "BSgenome.Hsapiens.UCSC.hg38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b2e670c27944eed77fbe9a9b55be40d2 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg38", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hs1/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hs1/meta.yaml index 71aeb4c9ab68c..6e76b23734749 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hs1/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hs1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.4" %} {% set name = "BSgenome.Hsapiens.UCSC.hs1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5812c5670f51a5c58a9da9e042e7e440 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hs1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/meta.yaml b/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/meta.yaml index 97a0ef2a902cf..c4ab4bc879512 100644 --- a/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/meta.yaml +++ b/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Mdomestica.UCSC.monDom5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ff940f7446a275962f69a6f4cb84724c build: - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mdomestica.ucsc.mondom5", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml index 0784f336cd2a6..c888f310c4025 100644 --- a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml +++ b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Mfascicularis.NCBI.5.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: dba6ade39dc6b4f6d06f488141b5550b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mfascicularis.ncbi.5.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.6.0/meta.yaml b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.6.0/meta.yaml index d1c7ea45dcfd8..d6051b0d89c9a 100644 --- a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.6.0/meta.yaml +++ b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.6.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "BSgenome.Mfascicularis.NCBI.6.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 67272a96950f485d3c0770265f59c85c build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mfascicularis.ncbi.6.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml b/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml index 9c9837bf6ca14..561159c626803 100644 --- a/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml +++ b/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.1" %} {% set name = "BSgenome.Mfuro.UCSC.musFur1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c33e71746ce551bcbcd22be1979aee63 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mfuro.ucsc.musfur1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac10/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac10/meta.yaml index 62544190199ee..075e65553bbe0 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac10/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac10/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac10" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2f2afe40d5dcf8d8620aa5e12e311fbc build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmulatta.ucsc.rhemac10", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml index 80ef70b97663a..0f176b99d2e61 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac2.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7602d86b68df7e4c8d336fede4090a62 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac2 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac2 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml index 3a9195cd66f71..775d3ae08031f 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 90c43e127e76dfd7cea90de9e1af9a50 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmulatta.ucsc.rhemac2", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml index 18733254bbef5..e99cfc364553a 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac3.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 94f8714865655d3144e14f6fc5c24e76 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac3 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml index 2216fcb5a526c..b7f2e7e8cd0b3 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: dfa1ecb9d0bb7a5d9fa628092fb1c354 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmulatta.ucsc.rhemac3", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml index 601e857dbfb7e..1e79bebdc1783 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac8" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e9ad1f70f652c62554e2c5af7638c015 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmulatta.ucsc.rhemac8", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml index d58e64bc4ed81..82ebb44b2a53d 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Mmusculus.UCSC.mm10.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 40d51fb428a5fda8c05101a3dddb8957 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm10.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml index f1efa6f1fac69..8d717d8f96f31 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Mmusculus.UCSC.mm10" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ffddc2e035527ed1a1e201ac4cc0b1f3 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm10", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm39/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm39/meta.yaml index 69b0ae1f316ad..935b7d6e381f3 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm39/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm39/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Mmusculus.UCSC.mm39" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a130ef50dd55da9fd341e6c90b22637b build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm39", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml index 7684f10eb95d2..7f6fd1ee3b55f 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Mmusculus.UCSC.mm8.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5809f925e0fe7c4b73b78a90c9a36fdd build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm8.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm8 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm8 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml index 6e6c613171204..1015d037ec13c 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmusculus.UCSC.mm8" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f6aa91cdce2607f30a34f6dd0d678aff build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm8", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml index 488f175b658b3..a388770cefc1a 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Mmusculus.UCSC.mm9.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a5dadab14e55cdfc39649ede7a8483d5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm9.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml index 48013ddb87342..c84701d12370e 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmusculus.UCSC.mm9" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5a30ba2b4481a17e8e6979eb69eabf78 build: - number: 16 + number: 17 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm9", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Mmusculus.UCSC.mm9.knownGene requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml b/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml index ff0a3d3aa702d..163678ae1635a 100644 --- a/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml +++ b/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.2" %} {% set name = "BSgenome.Osativa.MSU.MSU7" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 80648058756a2f74aa5a246d38ecf576 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.osativa.msu.msu7", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan1/meta.yaml b/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan1/meta.yaml index b59be7d005417..85411a3df2b2e 100644 --- a/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan1/meta.yaml +++ b/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Ppaniscus.UCSC.panPan1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 186adb59264d468d17c0f6374e2eb1f6 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ppaniscus.ucsc.panpan1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan2/meta.yaml b/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan2/meta.yaml index e79c92349f3a6..f6c6a0c21e800 100644 --- a/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan2/meta.yaml +++ b/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Ppaniscus.UCSC.panPan2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 74973376a6377d6820d6cd7fb3655a19 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ppaniscus.ucsc.panpan2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml index f1f2ecf2167d5..456bbdeda57f3 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro2.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e6d069be23712b483b4e4c71554594cf build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro2 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro2 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml index a2cfdf785362c..13287c4def47d 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 780200c315779ac75fcf0bdeb9a2eb8c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ptroglodytes.ucsc.pantro2", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml index 9cbb09f9db090..ccedb52acf0fe 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro3.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 89e96b3796d3b8e8793146597506e3f5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro3 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml index c99aa78937b5e..4cced5a9b52a6 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4677c75befd60742f3fc2a54c7f60666 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ptroglodytes.ucsc.pantro3", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml index 3787d51f36c05..e2c5ae5f72aaa 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5b88573dd9c3ef838699b65934f8abe3 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ptroglodytes.ucsc.pantro5", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml index 693fc7176d78a..12604327f1864 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1df05d985374e9edc1dd7c3df5118338 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ptroglodytes.ucsc.pantro6", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml index f14ab66ec392e..c583c872ec589 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn4.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7e2ea7df588b6b10515e07ea3868c568 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn4 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn4 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml index e86c0d8bc025e..1c86c50cd4dae 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3afe6729237781445d99ec38228ee1a8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.rnorvegicus.ucsc.rn4", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Rnorvegicus.UCSC.rn4.ensGene requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml index a42230bd9c169..89dbbafe4e2e5 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn5.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 663233774b79012cb2cc08224ac275ed build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn5 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn5 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml index ad6b2d180cde1..4297c1fcfc716 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 723b1f3ced395ef638b2d68053b05c86 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.rnorvegicus.ucsc.rn5", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Rnorvegicus.UCSC.rn5.refGene requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml index 3916440396076..1ee39156f2de8 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.1" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 60d3fb201e0b1475912aaf681927096d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.rnorvegicus.ucsc.rn6", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn7/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn7/meta.yaml index 8bb4b62e4b64c..07102a354264c 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn7/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn7/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn7" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c64f7dd9e30ff88ce02ecd3712e4c454 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.rnorvegicus.ucsc.rn7", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml index a990ef8a02074..725432e3a6292 100644 --- a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Scerevisiae.UCSC.sacCer1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ad4c29c16a9635088bf13872b4a02ed4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.scerevisiae.ucsc.saccer1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml index 804779df06c94..f65fa66ad4026 100644 --- a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Scerevisiae.UCSC.sacCer2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f1025b4d0fa7891dc46301550163753e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.scerevisiae.ucsc.saccer2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml index d3c22fceff1e7..b386b9c86ea88 100644 --- a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Scerevisiae.UCSC.sacCer3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7f2d8bba69c3dcebf426d9b19a6bed30 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.scerevisiae.ucsc.saccer3", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml index 56385b29b352b..e2ac5d79e3f68 100644 --- a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Sscrofa.UCSC.susScr11" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: db22832229e31e1a629d107df522dff9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.sscrofa.ucsc.susscr11", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml index a56dd58b2c65b..c116c67adf671 100644 --- a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Sscrofa.UCSC.susScr3.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fd240651d22d169fd1e27a2b66e40dd7 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.sscrofa.ucsc.susscr3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.sscrofa.ucsc.susscr3 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml index 4c832870ef0c0..2903b8432bb02 100644 --- a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Sscrofa.UCSC.susScr3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0457ca52a81c9d7ceadad5830169e6cf build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.sscrofa.ucsc.susscr3", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml b/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml index e4427a2dd78e1..c22953ef89cf7 100644 --- a/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml +++ b/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.1" %} {% set name = "BSgenome.Tgondii.ToxoDB.7.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f67644d1a897fe2ff4139832d4ceaf80 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.tgondii.toxodb.7.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml index 2b2a95e49809c..44e84dd6f5b29 100644 --- a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Tguttata.UCSC.taeGut1.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 63684abb5b330bb54ff89fe78f2e6444 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.tguttata.ucsc.taegut1.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.tguttata.ucsc.taegut1 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.tguttata.ucsc.taegut1 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml index 3cc5e5fc365cb..086df25bd94c0 100644 --- a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Tguttata.UCSC.taeGut1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9753d9568d2a866a627673a518a1dd8a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.tguttata.ucsc.taegut1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml index 7ae6cc8a0698c..fbca5f56adb3d 100644 --- a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Tguttata.UCSC.taeGut2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1d39678fb060e643f7e9c4ec25e828c0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.tguttata.ucsc.taegut2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml index f746388a13d54..ef55869bfb77c 100644 --- a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.1" %} {% set name = "BSgenome.Vvinifera.URGI.IGGP12Xv0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3f791de6d699325a97080cd98be86d89 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.vvinifera.urgi.iggp12xv0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml index d59326e2d635e..32841939100f7 100644 --- a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.1" %} {% set name = "BSgenome.Vvinifera.URGI.IGGP12Xv2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 95472e574ab46327c19e241c381b26a2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.vvinifera.urgi.iggp12xv2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml index 79a636e08497f..34e0332d217bc 100644 --- a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.1" %} {% set name = "BSgenome.Vvinifera.URGI.IGGP8X" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fccaf60e5c9352b9c454f7a8ecac2a20 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.vvinifera.urgi.iggp8x", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome/meta.yaml b/recipes/bioconductor-bsgenome/meta.yaml index 5a909a1c3dcc1..0958486077c61 100644 --- a/recipes/bioconductor-bsgenome/meta.yaml +++ b/recipes/bioconductor-bsgenome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.1" %} {% set name = "BSgenome" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: deb582b34b2d5532bb811c223e8426a0 + md5: a94697b953c4fc9bb0ba15daf35a884d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome", max_pin="x.x") }}' noarch: generic -# Suggests: BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit +# Suggests: BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit, BSgenomeForge requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-matrixstats run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-matrixstats test: diff --git a/recipes/bioconductor-bsgenomeforge/meta.yaml b/recipes/bioconductor-bsgenomeforge/meta.yaml index 7b4754b1911f5..0c189d94200e2 100644 --- a/recipes/bioconductor-bsgenomeforge/meta.yaml +++ b/recipes/bioconductor-bsgenomeforge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "BSgenomeForge" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 630aec996209048e39553239dd20e563 + md5: ed03f4628533403765aae28991855bca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenomeforge", max_pin="x.x") }}' noarch: generic # Suggests: GenomicRanges, GenomicFeatures, testthat, knitr, rmarkdown, BiocStyle, devtools requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-bsseq/meta.yaml b/recipes/bioconductor-bsseq/meta.yaml index e0a4b601e8cd0..a707ba6ca86b9 100644 --- a/recipes/bioconductor-bsseq/meta.yaml +++ b/recipes/bioconductor-bsseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "bsseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3fa1d3c20a5204d8d336c3261174ecfd + md5: 0fee416655d94a260bf4a613b4a6321e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsseq", max_pin="x.x") }}' # Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat (>= 1.5.2), batchtools requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-data.table >=1.11.8' - r-gtools @@ -47,22 +48,22 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-data.table >=1.11.8' - r-gtools diff --git a/recipes/bioconductor-bsseqdata/meta.yaml b/recipes/bioconductor-bsseqdata/meta.yaml index e892d6dcf9b31..2c014a22b1551 100644 --- a/recipes/bioconductor-bsseqdata/meta.yaml +++ b/recipes/bioconductor-bsseqdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "bsseqData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aeca7a29ea03b49344cf7cc223389537 + md5: 514171e8133c8d38e6b1ad31eff722a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsseqdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsseq >=1.36.0,<1.37.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-bsseq >=1.36.0,<1.37.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsseqdata/post-link.sh b/recipes/bioconductor-bsseqdata/post-link.sh index 3679601aa6199..6f79c30564302 100644 --- a/recipes/bioconductor-bsseqdata/post-link.sh +++ b/recipes/bioconductor-bsseqdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bsseqdata-0.38.0" +installBiocDataPackage.sh "bsseqdata-0.40.0" diff --git a/recipes/bioconductor-bsubtiliscdf/meta.yaml b/recipes/bioconductor-bsubtiliscdf/meta.yaml index 706abfe6693c0..d9da46bade688 100644 --- a/recipes/bioconductor-bsubtiliscdf/meta.yaml +++ b/recipes/bioconductor-bsubtiliscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "bsubtiliscdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7d7893d28c601206805819ae0e49b31b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsubtiliscdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsubtilisprobe/meta.yaml b/recipes/bioconductor-bsubtilisprobe/meta.yaml index 6ff55a639a50b..7cfe3dece2b39 100644 --- a/recipes/bioconductor-bsubtilisprobe/meta.yaml +++ b/recipes/bioconductor-bsubtilisprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "bsubtilisprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 83568fcea2122350b7ce982e79b7ec53 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsubtilisprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bubbletree/meta.yaml b/recipes/bioconductor-bubbletree/meta.yaml index 01bb298429bc2..23898ead413c9 100644 --- a/recipes/bioconductor-bubbletree/meta.yaml +++ b/recipes/bioconductor-bubbletree/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "BubbleTree" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 03eea1f59b31aa704ae501d2f8fc5854 + md5: 84649d9271ce193051e18a7bb56ff58e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bubbletree", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-dplyr - r-e1071 @@ -40,13 +41,13 @@ requirements: - r-rcolorbrewer - r-writexls run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-dplyr - r-e1071 diff --git a/recipes/bioconductor-bufferedmatrix/meta.yaml b/recipes/bioconductor-bufferedmatrix/meta.yaml index 2e9069b65c3f1..dbb18ad6dfccf 100644 --- a/recipes/bioconductor-bufferedmatrix/meta.yaml +++ b/recipes/bioconductor-bufferedmatrix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "BufferedMatrix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b33976ecec4bcd9ddabec3ef8747bc78 + md5: a4ad95db528526463e6dfca80975815e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bufferedmatrix", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-bufferedmatrixmethods/meta.yaml b/recipes/bioconductor-bufferedmatrixmethods/meta.yaml index 595e58c396867..55a8f987f77dc 100644 --- a/recipes/bioconductor-bufferedmatrixmethods/meta.yaml +++ b/recipes/bioconductor-bufferedmatrixmethods/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "BufferedMatrixMethods" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c6dfc8b00fbfc5e05576eeef80a6bf9d + md5: 57eb9e8db5a9dc58db25b88bbe5d2436 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bufferedmatrixmethods", max_pin="x.x") }}' # Suggests: affyio, affy requirements: host: - - 'bioconductor-bufferedmatrix >=1.64.0,<1.65.0' + - 'bioconductor-bufferedmatrix >=1.66.0,<1.67.0' - r-base - libblas - liblapack run: - - 'bioconductor-bufferedmatrix >=1.64.0,<1.65.0' + - 'bioconductor-bufferedmatrix >=1.66.0,<1.67.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-bugsigdbr/meta.yaml b/recipes/bioconductor-bugsigdbr/meta.yaml index 45bcd9de2cece..345d5d5fb9b45 100644 --- a/recipes/bioconductor-bugsigdbr/meta.yaml +++ b/recipes/bioconductor-bugsigdbr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.2" %} +{% set version = "1.8.1" %} {% set name = "bugsigdbr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5580a7ce1e29f6e6138a62185f2a9364 + md5: 35aebe840ca55cd93f16af9d239ea806 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bugsigdbr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, ontologyIndex, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - - r-vroom run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - - r-vroom test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bumhmm/meta.yaml b/recipes/bioconductor-bumhmm/meta.yaml index bfb19bbee28a7..853c6756464b6 100644 --- a/recipes/bioconductor-bumhmm/meta.yaml +++ b/recipes/bioconductor-bumhmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "BUMHMM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e43e3eb5d210769b8d9c5b585ecd2af9 + md5: c70dbfec58330fd1fa6cd1aca5e16912 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bumhmm", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-devtools - r-gtools - r-stringi run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-devtools - r-gtools diff --git a/recipes/bioconductor-bumphunter/meta.yaml b/recipes/bioconductor-bumphunter/meta.yaml index def7d740c00be..44699549646a5 100644 --- a/recipes/bioconductor-bumphunter/meta.yaml +++ b/recipes/bioconductor-bumphunter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "bumphunter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0fba211d07df317c3d4722a85357a475 + md5: fea93f84b54daabaaf1686d658aeedfc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bumphunter", max_pin="x.x") }}' noarch: generic # Suggests: testthat, RUnit, doParallel, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dorng - r-foreach @@ -36,14 +37,14 @@ requirements: - r-locfit - r-matrixstats run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dorng - r-foreach diff --git a/recipes/bioconductor-bumpymatrix/meta.yaml b/recipes/bioconductor-bumpymatrix/meta.yaml index aabf599c5e7d0..3087aebf5c9a1 100644 --- a/recipes/bioconductor-bumpymatrix/meta.yaml +++ b/recipes/bioconductor-bumpymatrix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "BumpyMatrix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1575e971c01dd864c690ca5b48627781 + md5: 6069ae96659170c765102c2513e44b58 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bumpymatrix", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-bus/meta.yaml b/recipes/bioconductor-bus/meta.yaml index 95f003cf037ac..d0b152aca8a53 100644 --- a/recipes/bioconductor-bus/meta.yaml +++ b/recipes/bioconductor-bus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "BUS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 10472148950ca1a1ccfecaadf43367d0 + md5: 788ab26ecf05f0df93667a7c37f564ff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bus", max_pin="x.x") }}' requirements: host: - - 'bioconductor-minet >=3.58.0,<3.59.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' - r-base - r-infotheo - libblas - liblapack run: - - 'bioconductor-minet >=3.58.0,<3.59.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' - r-base - r-infotheo build: diff --git a/recipes/bioconductor-buscorrect/meta.yaml b/recipes/bioconductor-buscorrect/meta.yaml index d15129579ac74..9507deeddc21a 100644 --- a/recipes/bioconductor-buscorrect/meta.yaml +++ b/recipes/bioconductor-buscorrect/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "BUScorrect" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dcefe721755de842d0d1952acb19a459 + md5: 6d24bece1ac7982a2a157e5cccc01b99 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-buscorrect", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-gplots - libblas - liblapack run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-gplots build: diff --git a/recipes/bioconductor-busparse/meta.yaml b/recipes/bioconductor-busparse/meta.yaml index 42b0d95564295..6946225b5c956 100644 --- a/recipes/bioconductor-busparse/meta.yaml +++ b/recipes/bioconductor-busparse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "BUSpaRse" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d08b55495020361901d1373d4df4339c + md5: 7d2decd570fd518ad9a06c10a5ecffb3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-busparse", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, BiocStyle, TENxBUSData, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 # SystemRequirements: GNU make requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bh - r-dplyr @@ -50,19 +51,19 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bh - r-dplyr diff --git a/recipes/bioconductor-busseq/meta.yaml b/recipes/bioconductor-busseq/meta.yaml index 1bc0066302432..1efe83d6f0fd2 100644 --- a/recipes/bioconductor-busseq/meta.yaml +++ b/recipes/bioconductor-busseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "BUSseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3623f486d083ce7f0c38903eae323c93 + md5: ba606db2bfb17a5958ba686639ecefbe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-busseq", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, BiocGenerics requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-gplots - libblas - liblapack run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-gplots build: diff --git a/recipes/bioconductor-cadd.v1.6.hg19/meta.yaml b/recipes/bioconductor-cadd.v1.6.hg19/meta.yaml new file mode 100644 index 0000000000000..446a23d0973bb --- /dev/null +++ b/recipes/bioconductor-cadd.v1.6.hg19/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "3.18.1" %} +{% set name = "cadd.v1.6.hg19" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 10cc50d17dbca89406a2290f37d5203c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cadd.v1.6.hg19", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle +requirements: + host: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - r-base + run: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'CADD v1.6 Pathogenicity Scores AnnotationHub Resource Metadata for hg19' + description: 'Store University of Washington CADD v1.6 hg19 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for University of Washington CADD v1.6 hg19 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.' + diff --git a/recipes/bioconductor-cadd.v1.6.hg19/post-link.sh b/recipes/bioconductor-cadd.v1.6.hg19/post-link.sh new file mode 100644 index 0000000000000..1cccd56a142ff --- /dev/null +++ b/recipes/bioconductor-cadd.v1.6.hg19/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "cadd.v1.6.hg19-3.18.1" diff --git a/recipes/bioconductor-cadd.v1.6.hg19/pre-unlink.sh b/recipes/bioconductor-cadd.v1.6.hg19/pre-unlink.sh new file mode 100644 index 0000000000000..010caf8ebc0f2 --- /dev/null +++ b/recipes/bioconductor-cadd.v1.6.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ cadd.v1.6.hg19 diff --git a/recipes/bioconductor-cadd.v1.6.hg38/meta.yaml b/recipes/bioconductor-cadd.v1.6.hg38/meta.yaml new file mode 100644 index 0000000000000..1136468b55f7b --- /dev/null +++ b/recipes/bioconductor-cadd.v1.6.hg38/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "3.18.1" %} +{% set name = "cadd.v1.6.hg38" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 620a889ea8bc55f98811a80a3aec814d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cadd.v1.6.hg38", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle +requirements: + host: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - r-base + run: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'CADD v1.6 Pathogenicity Scores AnnotationHub Resource Metadata for hg38' + description: 'Store University of Washington CADD v1.6 hg38 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for University of Washington CADD v1.6 hg38 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.' + diff --git a/recipes/bioconductor-cadd.v1.6.hg38/post-link.sh b/recipes/bioconductor-cadd.v1.6.hg38/post-link.sh new file mode 100644 index 0000000000000..c954375b37933 --- /dev/null +++ b/recipes/bioconductor-cadd.v1.6.hg38/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "cadd.v1.6.hg38-3.18.1" diff --git a/recipes/bioconductor-cadd.v1.6.hg38/pre-unlink.sh b/recipes/bioconductor-cadd.v1.6.hg38/pre-unlink.sh new file mode 100644 index 0000000000000..3bd10bc74e89d --- /dev/null +++ b/recipes/bioconductor-cadd.v1.6.hg38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ cadd.v1.6.hg38 diff --git a/recipes/bioconductor-cadra/build.sh b/recipes/bioconductor-cadra/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cadra/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cadra/meta.yaml b/recipes/bioconductor-cadra/meta.yaml new file mode 100644 index 0000000000000..72f0b311f64e6 --- /dev/null +++ b/recipes/bioconductor-cadra/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.0.1" %} +{% set name = "CaDrA" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9ac2bc6afe6632e5fbd00c687ca19bba +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cadra", max_pin="x.x") }}' +# Suggests: BiocManager, BiocStyle, devtools, knitr, magick, pheatmap, rmarkdown, testthat (>= 3.1.6) +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-doparallel + - r-ggplot2 + - r-gplots + - r-gtable + - r-mass + - r-misc3d + - r-plyr + - r-ppcor + - r-r.cache + - r-reshape2 + - libblas + - liblapack + run: + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-doparallel + - r-ggplot2 + - r-gplots + - r-gtable + - r-mass + - r-misc3d + - r-plyr + - r-ppcor + - r-r.cache + - r-reshape2 + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'Candidate Driver Analysis' + description: 'Performs both stepwise and backward heuristic search for candidate (epi)genetic drivers based on a binary multi-omics dataset. CaDrA''s main objective is to identify features which, together, are significantly skewed or enriched pertaining to a given vector of continuous scores (e.g. sample-specific scores representing a phenotypic readout of interest, such as protein expression, pathway activity, etc.), based on the union occurence (i.e. logical OR) of the events.' + license_file: LICENSE + diff --git a/recipes/bioconductor-caen/meta.yaml b/recipes/bioconductor-caen/meta.yaml index da3cb9b5852b4..9430206502ac5 100644 --- a/recipes/bioconductor-caen/meta.yaml +++ b/recipes/bioconductor-caen/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "CAEN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0bad38df2fe80cade3ef9db7c9241188 + md5: 66decd595d2315a90c09b7d52df606c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-caen", max_pin="x.x") }}' noarch: generic # Suggests: knitr,rmarkdown,BiocManager,SummarizedExperiment,BiocStyle requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-poiclaclu run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-poiclaclu test: diff --git a/recipes/bioconductor-cafe/meta.yaml b/recipes/bioconductor-cafe/meta.yaml index 42660bfbef0ba..38e52b776a3fc 100644 --- a/recipes/bioconductor-cafe/meta.yaml +++ b/recipes/bioconductor-cafe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "CAFE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3327ab214fb57b43e0e88bd2249c3b17 + md5: 1a64370f203f198ad86163715decbebb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cafe", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-ggplot2 - r-gridextra run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-ggplot2 - r-gridextra diff --git a/recipes/bioconductor-cagefightr/meta.yaml b/recipes/bioconductor-cagefightr/meta.yaml index 36d6bebb1e13f..7c7717aa940e4 100644 --- a/recipes/bioconductor-cagefightr/meta.yaml +++ b/recipes/bioconductor-cagefightr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CAGEfightR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,49 +11,50 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2c46d615668fe693b427295c88416052 + md5: 86c87a4bec49d7c37ef74a6a6081a685 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cagefightr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm9.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicinteractions >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'r-assertthat >=0.2.0' - r-base - 'r-matrix >=1.2-12' - 'r-pryr >=0.1.3' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicinteractions >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'r-assertthat >=0.2.0' - r-base - 'r-matrix >=1.2-12' diff --git a/recipes/bioconductor-cageminer/meta.yaml b/recipes/bioconductor-cageminer/meta.yaml index c31239d6fd788..f6b6d7035888b 100644 --- a/recipes/bioconductor-cageminer/meta.yaml +++ b/recipes/bioconductor-cageminer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "cageminer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d85bf5a81347a582b161160ccf001d83 + md5: 02b96b12bfe145c4c9deefff49cd1015 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cageminer", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle, rmarkdown, covr, sessioninfo requirements: host: - - 'bioconductor-bionero >=1.8.0,<1.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-bionero >=1.10.0,<1.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-ggplot2 - r-ggtext - r-reshape2 - r-rlang run: - - 'bioconductor-bionero >=1.8.0,<1.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-bionero >=1.10.0,<1.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-ggplot2 - r-ggtext diff --git a/recipes/bioconductor-cager/meta.yaml b/recipes/bioconductor-cager/meta.yaml index 7f748a4694dab..760142e82ee20 100644 --- a/recipes/bioconductor-cager/meta.yaml +++ b/recipes/bioconductor-cager/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "CAGEr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b4abf800289121fcb4795c1a30fd35cd + md5: 845c3a47631734b6fe7209f173e24100 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cager", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-cagefightr >=1.20.0,<1.21.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-cagefightr >=1.22.0,<1.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-formula.tools @@ -51,21 +52,21 @@ requirements: - r-vegan - r-vgam run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-cagefightr >=1.20.0,<1.21.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-cagefightr >=1.22.0,<1.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-formula.tools diff --git a/recipes/bioconductor-calm/meta.yaml b/recipes/bioconductor-calm/meta.yaml index 390e16252f8a9..d544112473d73 100644 --- a/recipes/bioconductor-calm/meta.yaml +++ b/recipes/bioconductor-calm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "calm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d6b0e35a1cf15fe23f6ac7138863a58d + md5: 9a2b4c48021193636c88c997331ede2d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-calm", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-camera/meta.yaml b/recipes/bioconductor-camera/meta.yaml index 0d3eca1b9f159..db1fce9160d3f 100644 --- a/recipes/bioconductor-camera/meta.yaml +++ b/recipes/bioconductor-camera/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "CAMERA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b627c870804005f6ef9c1f48ccf6eceb + md5: 1958cafb2c9dd92fa44a35cfc607f894 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-camera", max_pin="x.x") }}' # Suggests: faahKO, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-hmisc - r-igraph - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-hmisc - r-igraph diff --git a/recipes/bioconductor-cancer/meta.yaml b/recipes/bioconductor-cancer/meta.yaml index 0163ea2219ef7..1498a00e3bb28 100644 --- a/recipes/bioconductor-cancer/meta.yaml +++ b/recipes/bioconductor-cancer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "canceR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 942f2c8187c6686017489023ee793d0d + md5: 4311164fc68969a40252dc3761583f24 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cancer", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.1), knitr, rmarkdown, BiocStyle # SystemRequirements: Tktable, BWidget requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genetclassifier >=1.40.0,<1.41.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-phenotest >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genetclassifier >=1.42.0,<1.43.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-phenotest >=1.50.0,<1.51.0' - r-base - r-circlize - r-formula @@ -38,10 +39,10 @@ requirements: - r-survival - r-tkrplot run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genetclassifier >=1.40.0,<1.41.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-phenotest >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genetclassifier >=1.42.0,<1.43.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-phenotest >=1.50.0,<1.51.0' - r-base - r-circlize - r-formula diff --git a/recipes/bioconductor-cancerclass/meta.yaml b/recipes/bioconductor-cancerclass/meta.yaml index 7b84f85d34133..ee3fb82ad436d 100644 --- a/recipes/bioconductor-cancerclass/meta.yaml +++ b/recipes/bioconductor-cancerclass/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "cancerclass" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1b773f50fc0ab3bc1e0555a2807d9c76 + md5: b2e5d6ec200ee08476480fa1f0a1577d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cancerclass", max_pin="x.x") }}' # Suggests: cancerdata requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-binom - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-binom build: diff --git a/recipes/bioconductor-cancerdata/meta.yaml b/recipes/bioconductor-cancerdata/meta.yaml index 6e8a1974a3587..8b5aaa6fb459c 100644 --- a/recipes/bioconductor-cancerdata/meta.yaml +++ b/recipes/bioconductor-cancerdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "cancerdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 23d4242144544786e0327a3144d8a6c6 + md5: 7baa088ef320a0222a897987ea8c3e8b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cancerdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cancerdata/post-link.sh b/recipes/bioconductor-cancerdata/post-link.sh index 634f9917cbc85..f48bb85329be6 100644 --- a/recipes/bioconductor-cancerdata/post-link.sh +++ b/recipes/bioconductor-cancerdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cancerdata-1.38.0" +installBiocDataPackage.sh "cancerdata-1.40.0" diff --git a/recipes/bioconductor-canine.db/meta.yaml b/recipes/bioconductor-canine.db/meta.yaml index 811c40b827bca..9afadfb4280f1 100644 --- a/recipes/bioconductor-canine.db/meta.yaml +++ b/recipes/bioconductor-canine.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "canine.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a876bb01eda62604a32a96b46e34162b build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-canine.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.cf.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.cf.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.cf.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.cf.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-canine.db0/meta.yaml b/recipes/bioconductor-canine.db0/meta.yaml index b83fd7ffeaf32..9e295898ab473 100644 --- a/recipes/bioconductor-canine.db0/meta.yaml +++ b/recipes/bioconductor-canine.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "canine.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: da4af1b026fe2775a020addd13920f71 + md5: dc4fff8ed0a758ddff3f52aa0e8652c6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-canine.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-canine.db0/post-link.sh b/recipes/bioconductor-canine.db0/post-link.sh index e7e67a934420c..e5e86dee05068 100644 --- a/recipes/bioconductor-canine.db0/post-link.sh +++ b/recipes/bioconductor-canine.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "canine.db0-3.17.0" +installBiocDataPackage.sh "canine.db0-3.18.0" diff --git a/recipes/bioconductor-canine2.db/meta.yaml b/recipes/bioconductor-canine2.db/meta.yaml index 6682cbee36fcb..6b4c2bc532688 100644 --- a/recipes/bioconductor-canine2.db/meta.yaml +++ b/recipes/bioconductor-canine2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "canine2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 24727f27cdf1e324f097a76db81dfc1d build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-canine2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.cf.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.cf.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.cf.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.cf.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-canine2cdf/meta.yaml b/recipes/bioconductor-canine2cdf/meta.yaml index 37ab92dcedc44..9d689a5971930 100644 --- a/recipes/bioconductor-canine2cdf/meta.yaml +++ b/recipes/bioconductor-canine2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "canine2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 78740cde98c75e6680470564a4df74c3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-canine2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-canine2probe/meta.yaml b/recipes/bioconductor-canine2probe/meta.yaml index fb4c210c8fd5c..6f54871ac6b19 100644 --- a/recipes/bioconductor-canine2probe/meta.yaml +++ b/recipes/bioconductor-canine2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "canine2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7de0f4ea616e8662dc2eaa9ab78d1f13 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-canine2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-caninecdf/meta.yaml b/recipes/bioconductor-caninecdf/meta.yaml index 70b08561a5922..f80e3709dcb35 100644 --- a/recipes/bioconductor-caninecdf/meta.yaml +++ b/recipes/bioconductor-caninecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "caninecdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 656f845cc66890015a4e13c5304ec262 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-caninecdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-canineprobe/meta.yaml b/recipes/bioconductor-canineprobe/meta.yaml index 1856806650678..a85ebdab28fe3 100644 --- a/recipes/bioconductor-canineprobe/meta.yaml +++ b/recipes/bioconductor-canineprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "canineprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e5467bc9b7e54c5adce6b409ba7df767 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-canineprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cardelino/meta.yaml b/recipes/bioconductor-cardelino/meta.yaml index 2fdbcbb7f4d20..684c1386c8a20 100644 --- a/recipes/bioconductor-cardelino/meta.yaml +++ b/recipes/bioconductor-cardelino/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "cardelino" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ba9264af6b626d01cb7700cd264ca4c7 + md5: 363c06547419f29e1cdfe473651e1861 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cardelino", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, foreach, knitr, pcaMethods, rmarkdown, testthat, VGAM requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-combinat - r-ggplot2 @@ -35,12 +36,12 @@ requirements: - r-pheatmap - r-vcfr run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-combinat - r-ggplot2 diff --git a/recipes/bioconductor-cardinal/meta.yaml b/recipes/bioconductor-cardinal/meta.yaml index a4fa219fb80e4..ebb5c8fde4502 100644 --- a/recipes/bioconductor-cardinal/meta.yaml +++ b/recipes/bioconductor-cardinal/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.2.1" %} +{% set version = "3.4.3" %} {% set name = "Cardinal" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c28538283f8b6b79f6b7e66f5ac7fcb + md5: ee7f799a94a4c3cd1946feb2b1db9dd4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cardinal", max_pin="x.x") }}' # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-matter >=2.2.0,<2.3.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-cardinalio >=1.0.0,<1.1.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-matter >=2.4.0,<2.5.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-irlba - r-magrittr @@ -34,18 +36,18 @@ requirements: - r-mclust - r-nlme - r-signal - - r-sp - r-viridislite - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-matter >=2.2.0,<2.3.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-cardinalio >=1.0.0,<1.1.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-matter >=2.4.0,<2.5.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-irlba - r-magrittr @@ -53,7 +55,6 @@ requirements: - r-mclust - r-nlme - r-signal - - r-sp - r-viridislite build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-cardinalio/build.sh b/recipes/bioconductor-cardinalio/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cardinalio/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cardinalio/meta.yaml b/recipes/bioconductor-cardinalio/meta.yaml new file mode 100644 index 0000000000000..e51480d5e4ba8 --- /dev/null +++ b/recipes/bioconductor-cardinalio/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "CardinalIO" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 746846f9fda38de9fe2c3dd4c49c18e1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cardinalio", max_pin="x.x") }}' +# Suggests: BiocStyle, testthat, knitr, rmarkdown +requirements: + host: + - 'bioconductor-matter >=2.4.0,<2.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-ontologyindex + - libblas + - liblapack + run: + - 'bioconductor-matter >=2.4.0,<2.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-ontologyindex + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Read and write mass spectrometry imaging files' + description: 'Fast and efficient reading and writing of mass spectrometry imaging data files. Supports imzML and Analyze 7.5 formats. Provides ontologies for mass spectrometry imaging.' + diff --git a/recipes/bioconductor-cardinalworkflows/meta.yaml b/recipes/bioconductor-cardinalworkflows/meta.yaml index 55aa4097d3b5f..9935acb2c639a 100644 --- a/recipes/bioconductor-cardinalworkflows/meta.yaml +++ b/recipes/bioconductor-cardinalworkflows/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "CardinalWorkflows" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a8b9945c7f7b5287510917c6bc1e1a4 + md5: 54c51a2ec2f20f96ad9e60c16eeb2ccb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cardinalworkflows", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-cardinal >=3.2.0,<3.3.0' + - 'bioconductor-cardinal >=3.4.0,<3.5.0' - r-base run: - - 'bioconductor-cardinal >=3.2.0,<3.3.0' + - 'bioconductor-cardinal >=3.4.0,<3.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cardinalworkflows/post-link.sh b/recipes/bioconductor-cardinalworkflows/post-link.sh index 375cb5b31f89e..d557ce84baab0 100644 --- a/recipes/bioconductor-cardinalworkflows/post-link.sh +++ b/recipes/bioconductor-cardinalworkflows/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cardinalworkflows-1.32.0" +installBiocDataPackage.sh "cardinalworkflows-1.34.0" diff --git a/recipes/bioconductor-carnival/meta.yaml b/recipes/bioconductor-carnival/meta.yaml index f9fa8303cb483..565eefdb379a4 100644 --- a/recipes/bioconductor-carnival/meta.yaml +++ b/recipes/bioconductor-carnival/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "CARNIVAL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d92b0f48e86019ba880d96574038a7b2 + md5: c5457d5d859c16cbec56532338f64fb0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-carnival", max_pin="x.x") }}' noarch: generic # Suggests: RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0), sessioninfo requirements: diff --git a/recipes/bioconductor-casper/meta.yaml b/recipes/bioconductor-casper/meta.yaml index 557323da87a07..3142caba5767b 100644 --- a/recipes/bioconductor-casper/meta.yaml +++ b/recipes/bioconductor-casper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "casper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f43788dc14c1c51dcfde295920c6f5e6 + md5: 4c9fc29e3b92d5b493953ea97436556a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-casper", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ebarrays >=2.64.0,<2.65.0' - - 'bioconductor-gaga >=2.46.0,<2.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ebarrays >=2.66.0,<2.67.0' + - 'bioconductor-gaga >=2.48.0,<2.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-coda - r-gtools @@ -41,18 +42,18 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ebarrays >=2.64.0,<2.65.0' - - 'bioconductor-gaga >=2.46.0,<2.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ebarrays >=2.66.0,<2.67.0' + - 'bioconductor-gaga >=2.48.0,<2.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-coda - r-gtools diff --git a/recipes/bioconductor-catalyst/meta.yaml b/recipes/bioconductor-catalyst/meta.yaml index 5d2276155f31a..42b526eec0739 100644 --- a/recipes/bioconductor-catalyst/meta.yaml +++ b/recipes/bioconductor-catalyst/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "CATALYST" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 727b6a6736deb00b2a649bffc267ade6 + md5: 6ce647576b86ebdf9fe0933fd87b79ce build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-catalyst", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat, uwot requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowsom >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowsom >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-cowplot @@ -39,7 +40,6 @@ requirements: - r-ggrepel - r-ggridges - r-gridextra - - r-magrittr - r-matrix - r-matrixstats - r-nnls @@ -49,14 +49,14 @@ requirements: - r-rtsne - r-scales run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowsom >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowsom >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-cowplot @@ -67,7 +67,6 @@ requirements: - r-ggrepel - r-ggridges - r-gridextra - - r-magrittr - r-matrix - r-matrixstats - r-nnls @@ -83,6 +82,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Cytometry dATa anALYSis Tools' - description: 'Mass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. While spectral overlap is significantly less pronounced in CyTOF than flow cytometry, spillover due to detection sensitivity, isotopic impurities, and oxide formation can impede data interpretability. We designed CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for preprocessing of cytometry data, including i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation.' + description: 'CATALYST provides tools for preprocessing of and differential discovery in cytometry data such as FACS, CyTOF, and IMC. Preprocessing includes i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation. For differential discovery, the package provides a number of convenient functions for data processing (e.g., clustering, dimension reduction), as well as a suite of visualizations for exploratory data analysis and exploration of results from differential abundance (DA) and state (DS) analysis in order to identify differences in composition and expression profiles at the subpopulation-level, respectively.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-category/meta.yaml b/recipes/bioconductor-category/meta.yaml index 19020d0a70faf..a746fe351958e 100644 --- a/recipes/bioconductor-category/meta.yaml +++ b/recipes/bioconductor-category/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.66.0" %} +{% set version = "2.68.0" %} {% set name = "Category" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6dbd5bb859ad4567680561e085cd0765 + md5: d84fb36419834bb84721436d7f956932 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-category", max_pin="x.x") }}' noarch: generic # Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGGREST, karyoploteR, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-dbi - r-matrix run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-dbi - r-matrix diff --git a/recipes/bioconductor-categorycompare/meta.yaml b/recipes/bioconductor-categorycompare/meta.yaml index 316ebf2f21eaf..1a04329db5a0c 100644 --- a/recipes/bioconductor-categorycompare/meta.yaml +++ b/recipes/bioconductor-categorycompare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "categoryCompare" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 12b838d68868bdf213889ed07657d373 + md5: 9809c7142b4af81d181bf8d8f7e0f815 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-categorycompare", max_pin="x.x") }}' noarch: generic # Suggests: knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter, rmarkdown # SystemRequirements: Cytoscape (>= 3.6.1) (if used for visualization of results, heavily suggested) requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-colorspace - r-hwriter - 'cytoscape >=3.6.1' run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-colorspace - r-hwriter diff --git a/recipes/bioconductor-causalr/meta.yaml b/recipes/bioconductor-causalr/meta.yaml index b96b70a4f9a8b..19336b1df1182 100644 --- a/recipes/bioconductor-causalr/meta.yaml +++ b/recipes/bioconductor-causalr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "CausalR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a1a92153e981da4a487d5c42ca15994a + md5: 408b3cc6bc7a45715e6c07095f61ca2b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-causalr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, RUnit, BiocGenerics requirements: diff --git a/recipes/bioconductor-cbaf/meta.yaml b/recipes/bioconductor-cbaf/meta.yaml index 8a3029fa4092c..8e99a667fb4cb 100644 --- a/recipes/bioconductor-cbaf/meta.yaml +++ b/recipes/bioconductor-cbaf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "cbaf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c4489ed5d1141f61152a666bec15104c + md5: e3c093194c8fdcbd04ca035dddeaf5f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cbaf", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-cbioportaldata >=2.12.0,<2.13.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-cbioportaldata >=2.14.0,<2.15.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - r-base - r-gplots - r-openxlsx - r-rcolorbrewer run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-cbioportaldata >=2.12.0,<2.13.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-cbioportaldata >=2.14.0,<2.15.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - r-base - r-gplots - r-openxlsx diff --git a/recipes/bioconductor-cbea/meta.yaml b/recipes/bioconductor-cbea/meta.yaml index 0b3b567cbbf5d..63e685b38f7f5 100644 --- a/recipes/bioconductor-cbea/meta.yaml +++ b/recipes/bioconductor-cbea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.3.0" %} +{% set version = "1.2.0" %} {% set name = "CBEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: abb5373c75d6328cedad978f32f2c0e7 + md5: 20761b06df9cf37c59172508ff8cd01d build: - number: 0 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cbea", max_pin="x.x") }}' # Suggests: phyloseq, BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), tidyverse, roxygen2, mia, purrr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocset >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocset >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-dplyr - r-fitdistrplus @@ -40,10 +41,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocset >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocset >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-dplyr - r-fitdistrplus diff --git a/recipes/bioconductor-cbioportaldata/meta.yaml b/recipes/bioconductor-cbioportaldata/meta.yaml index 3f964fd3b87ac..4508b5319a9db 100644 --- a/recipes/bioconductor-cbioportaldata/meta.yaml +++ b/recipes/bioconductor-cbioportaldata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "cBioPortalData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 876930b2b73eb4f6d2515d187b925278 + md5: fc51f3b952b9c31900365adc94f85585 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cbioportaldata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, survival, survminer, rmarkdown, testthat requirements: host: - - 'bioconductor-anvil >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-rtcgatoolbox >=2.30.0,<2.31.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgautils >=1.20.0,<1.21.0' + - 'bioconductor-anvil >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-rtcgatoolbox >=2.32.0,<2.33.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgautils >=1.22.0,<1.23.0' - r-base - r-digest - r-dplyr @@ -40,17 +41,17 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-anvil >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-rtcgatoolbox >=2.30.0,<2.31.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgautils >=1.20.0,<1.21.0' + - 'bioconductor-anvil >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-rtcgatoolbox >=2.32.0,<2.33.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgautils >=1.22.0,<1.23.0' - r-base - r-digest - r-dplyr diff --git a/recipes/bioconductor-cbnplot/meta.yaml b/recipes/bioconductor-cbnplot/meta.yaml index e261a401638c6..8ca2a36fb2135 100644 --- a/recipes/bioconductor-cbnplot/meta.yaml +++ b/recipes/bioconductor-cbnplot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "CBNplot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0717efc5c7c4f3b2b957528ff99c8dea + md5: d589e9361caf3409d65345cc48e5ccee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cbnplot", max_pin="x.x") }}' noarch: generic # Suggests: knitr, arules, concaveman, ReactomePA, bnviewer, DESeq2, GEOquery, rmarkdown, withr, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-depmap >=1.14.0,<1.15.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-depmap >=1.16.0,<1.17.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - 'r-bnlearn >=4.7' - r-dplyr @@ -48,13 +49,13 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-depmap >=1.14.0,<1.15.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-depmap >=1.16.0,<1.17.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - 'r-bnlearn >=4.7' - r-dplyr diff --git a/recipes/bioconductor-cbpmanager/meta.yaml b/recipes/bioconductor-cbpmanager/meta.yaml index 5e9b4e7ee8d5f..e35ef4a737405 100644 --- a/recipes/bioconductor-cbpmanager/meta.yaml +++ b/recipes/bioconductor-cbpmanager/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "cbpManager" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 428adb2f63dce7a4cbcba310d13bb32a + md5: 6567afab9427e6ee44a029fa5be314e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cbpmanager", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' - r-base - r-dplyr - r-dt @@ -33,13 +34,14 @@ requirements: - r-rapportools - r-reticulate - r-rintrojs + - r-rlang - r-shiny - r-shinybs - r-shinycssloaders - r-shinydashboard - r-vroom run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' - r-base - r-dplyr - r-dt @@ -51,6 +53,7 @@ requirements: - r-rapportools - r-reticulate - r-rintrojs + - r-rlang - r-shiny - r-shinybs - r-shinycssloaders diff --git a/recipes/bioconductor-ccdata/meta.yaml b/recipes/bioconductor-ccdata/meta.yaml index 5f24f35515072..e552cec2d123c 100644 --- a/recipes/bioconductor-ccdata/meta.yaml +++ b/recipes/bioconductor-ccdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "ccdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d21508b620d5328d66111ed0250bcaa8 + md5: 60cbd595e53467fd61e1edc4f8ea47e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ccdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ccdata/post-link.sh b/recipes/bioconductor-ccdata/post-link.sh index cdc12359a9a68..3c5a6ff31dcdd 100644 --- a/recipes/bioconductor-ccdata/post-link.sh +++ b/recipes/bioconductor-ccdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ccdata-1.26.0" +installBiocDataPackage.sh "ccdata-1.28.0" diff --git a/recipes/bioconductor-ccfindr/build_failure.osx-64.yaml b/recipes/bioconductor-ccfindr/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..f96432c2ea200 --- /dev/null +++ b/recipes/bioconductor-ccfindr/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 284d8b5d60d001aad42c11aa0f88615ff84ff828b15ac43defb45c3fd2d1f416 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-ccfindr-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-ccfindr-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-ccfindr-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-ccfindr-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-ccfindr-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-ccfindr-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + * installing to library /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library + * installing *source* package ccfindR ... + ** using staged installation + ** libs + dyld[12683]: Library not loaded: '@rpath/libclang-cpp.15.dylib' + Referenced from: '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/clang-15' + Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/libclang-cpp.15.dylib' (no such file), '/Users/runner/miniforge3/conda-bld/r-base-split_1700316070281/_build_env/lib/jvm/lib/server/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/libclang-cpp.15.dylib' (no such file), '/Users/runner/miniforge3/conda-bld/r-base-split_1700316070281/_build_env/lib/jvm/lib/server/libclang-cpp.15.dylib' (no such file) + using C compiler: NA + using C11 + using SDK: + x86_64-apple-darwin13.4.0-clang -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1700316070281/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o + dyld[12689]: Library not loaded: '@rpath/libclang-cpp.15.dylib' + Referenced from: '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/clang-15' + Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/libclang-cpp.15.dylib' (no such file), '/Users/runner/miniforge3/conda-bld/r-base-split_1700316070281/_build_env/lib/jvm/lib/server/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/libclang-cpp.15.dylib' (no such file), '/Users/runner/miniforge3/conda-bld/r-base-split_1700316070281/_build_env/lib/jvm/lib/server/libclang-cpp.15.dylib' (no such file) + make: *** [/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/etc/Makeconf:200: RcppExports.o] Abort trap: 6 + ERROR: compilation failed for package ccfindR + * removing /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/ccfindR + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build + utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ccfindr/meta.yaml b/recipes/bioconductor-ccfindr/meta.yaml index 8669dd286eaa1..885a9ad43f114 100644 --- a/recipes/bioconductor-ccfindr/meta.yaml +++ b/recipes/bioconductor-ccfindr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ccfindR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8862cd343902a030a29603942d4dede8 + md5: 0a0dd7c35273c39673f992bed7fa952d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ccfindr", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown +# SystemRequirements: gsl requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-base - r-gtools @@ -36,10 +38,11 @@ requirements: - r-rtsne - libblas - liblapack + - gsl run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-base - r-gtools @@ -51,6 +54,7 @@ requirements: - 'r-rdpack >=0.7' - r-rmpi - r-rtsne + - gsl build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-ccimpute/meta.yaml b/recipes/bioconductor-ccimpute/meta.yaml index 21b4a6711e712..14e1190d5d502 100644 --- a/recipes/bioconductor-ccimpute/meta.yaml +++ b/recipes/bioconductor-ccimpute/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "ccImpute" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 890c259cabc9cd35bab959d4f698f5d9 + md5: f402177e3fc7bbbcac504c956889dfa9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ccimpute", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater, SingleCellExperiment, mclust, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-simlr >=1.26.0,<1.27.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-simlr >=1.28.0,<1.29.0' - r-base - r-matrixstats - r-rcpp @@ -29,8 +30,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-simlr >=1.26.0,<1.27.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-simlr >=1.28.0,<1.29.0' - r-base - r-matrixstats - r-rcpp diff --git a/recipes/bioconductor-ccl4/meta.yaml b/recipes/bioconductor-ccl4/meta.yaml index d9f85af551bc9..6179644dbc14d 100644 --- a/recipes/bioconductor-ccl4/meta.yaml +++ b/recipes/bioconductor-ccl4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "CCl4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a0bfca2abdda039b9376e9cc8ec71333 + md5: 3247cf1db347f959d908e88b5e8febb5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ccl4", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ccl4/post-link.sh b/recipes/bioconductor-ccl4/post-link.sh index e2e4e1647ae6f..8bd8b92dae2ca 100644 --- a/recipes/bioconductor-ccl4/post-link.sh +++ b/recipes/bioconductor-ccl4/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ccl4-1.38.0" +installBiocDataPackage.sh "ccl4-1.40.0" diff --git a/recipes/bioconductor-ccmap/meta.yaml b/recipes/bioconductor-ccmap/meta.yaml index c073c4775e256..765e1c9c198f5 100644 --- a/recipes/bioconductor-ccmap/meta.yaml +++ b/recipes/bioconductor-ccmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "ccmap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a1587c139647a148d00e216b0fc9653d + md5: d01f3e9dca6ce3403096f8fc00766755 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ccmap", max_pin="x.x") }}' noarch: generic # Suggests: crossmeta, knitr, rmarkdown, testthat, lydata requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-ccdata >=1.26.0,<1.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-ccdata >=1.28.0,<1.29.0' - r-base - 'r-biocmanager >=1.30.4' - 'r-data.table >=1.10.4' @@ -31,8 +32,8 @@ requirements: - 'r-lsa >=0.73.1' - 'r-xgboost >=0.6.4' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-ccdata >=1.26.0,<1.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-ccdata >=1.28.0,<1.29.0' - r-base - 'r-biocmanager >=1.30.4' - 'r-data.table >=1.10.4' diff --git a/recipes/bioconductor-ccplotr/build.sh b/recipes/bioconductor-ccplotr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ccplotr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ccplotr/meta.yaml b/recipes/bioconductor-ccplotr/meta.yaml new file mode 100644 index 0000000000000..550ccfa7556d0 --- /dev/null +++ b/recipes/bioconductor-ccplotr/meta.yaml @@ -0,0 +1,75 @@ +{% set version = "1.0.0" %} +{% set name = "CCPlotR" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 913896518f29cd88d7ac9d57298f44de +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ccplotr", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - r-base + - r-circlize + - r-dplyr + - r-forcats + - r-ggbump + - r-ggh4x + - r-ggplot2 + - r-ggraph + - r-ggtext + - r-igraph + - r-patchwork + - r-plyr + - r-rcolorbrewer + - r-scales + - r-scatterpie + - r-stringr + - r-tibble + - r-tidyr + - r-viridis + run: + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - r-base + - r-circlize + - r-dplyr + - r-forcats + - r-ggbump + - r-ggh4x + - r-ggplot2 + - r-ggraph + - r-ggtext + - r-igraph + - r-patchwork + - r-plyr + - r-rcolorbrewer + - r-scales + - r-scatterpie + - r-stringr + - r-tibble + - r-tidyr + - r-viridis +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Plots For Visualising Cell-Cell Interactions' + description: 'CCPlotR is an R package for visualising results from tools that predict cell-cell interactions from single-cell RNA-seq data. These plots are generic and can be used to visualise results from multiple tools such as Liana, CellPhoneDB, NATMI etc.' + license_file: LICENSE + diff --git a/recipes/bioconductor-ccpromise/build_failure.linux-64.yaml b/recipes/bioconductor-ccpromise/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..72fc0dc3a0c09 --- /dev/null +++ b/recipes/bioconductor-ccpromise/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 722fb617600a55303b535b784f5387ef700db6e8486e427c054d57fb5deff1b6 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.1s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.2s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.3s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.4s + [2K[1A[2K[0Gconda-forge/linux-64 + [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.2MB/s 0.0s + [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.1MB/s 0.0s + [?25hMamba failed to solve: + - r-base 4.3.* + - r-ccp + - bioconductor-biobase >=2.62.0,<2.63.0 + - bioconductor-gseabase >=1.64.0,<1.65.0 + - bioconductor-promise >=1.54.0,<1.55.0 + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-promise >=1.54.0,<1.55.0 + - + + Leaving build/test directories: + Work: + /opt/conda/conda-bld/work + Test: + /opt/conda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + Build: + source activate /opt/conda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - r-base 4.3.* + - r-ccp + - bioconductor-biobase >=2.62.0,<2.63.0 + - bioconductor-gseabase >=1.64.0,<1.65.0 + - bioconductor-promise >=1.54.0,<1.55.0 + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-promise >=1.54.0,<1.55.0 + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-promise[version='>=1.54.0,<1.55.0']")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ccpromise/meta.yaml b/recipes/bioconductor-ccpromise/meta.yaml index f24d2e72bf027..a9de2cd528f55 100644 --- a/recipes/bioconductor-ccpromise/meta.yaml +++ b/recipes/bioconductor-ccpromise/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "CCPROMISE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1efc8cd0ffc5444554a53bb13b32d2f4 + md5: 1b85c7bbed3be474abf4e4591882abdf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ccpromise", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-promise >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-promise >=1.54.0,<1.55.0' - r-base - r-ccp run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-promise >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-promise >=1.54.0,<1.55.0' - r-base - r-ccp test: diff --git a/recipes/bioconductor-cctutorial/meta.yaml b/recipes/bioconductor-cctutorial/meta.yaml index a679a121002ad..ba960ac374091 100644 --- a/recipes/bioconductor-cctutorial/meta.yaml +++ b/recipes/bioconductor-cctutorial/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "ccTutorial" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6515deef368eb06b2f0aabaa069b3f63 + md5: 20af731ec83a03f12ec5d87060f5d168 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cctutorial", max_pin="x.x") }}' noarch: generic # Suggests: biomaRt, Biobase(>= 2.5.5), xtable requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ringo >=1.64.0,<1.65.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ringo >=1.66.0,<1.67.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ringo >=1.64.0,<1.65.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ringo >=1.66.0,<1.67.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cctutorial/post-link.sh b/recipes/bioconductor-cctutorial/post-link.sh index b0c9b061fbc1f..3acf97540ef0e 100644 --- a/recipes/bioconductor-cctutorial/post-link.sh +++ b/recipes/bioconductor-cctutorial/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cctutorial-1.38.0" +installBiocDataPackage.sh "cctutorial-1.40.0" diff --git a/recipes/bioconductor-cdi/build.sh b/recipes/bioconductor-cdi/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cdi/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cdi/meta.yaml b/recipes/bioconductor-cdi/meta.yaml new file mode 100644 index 0000000000000..10184abeabdbc --- /dev/null +++ b/recipes/bioconductor-cdi/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.0.2" %} +{% set name = "CDI" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 64ebd520b0ba4613c3bddf06bb82dbc0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cdi", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, RUnit, BiocGenerics, magick, BiocStyle +requirements: + host: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-ggplot2 + - r-ggsci + - r-matrixstats + - r-reshape2 + - r-seurat + - r-seuratobject + run: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-ggplot2 + - r-ggsci + - r-matrixstats + - r-reshape2 + - r-seurat + - r-seuratobject +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'Clustering Deviation Index (CDI)' + description: 'Single-cell RNA-sequencing (scRNA-seq) is widely used to explore cellular variation. The analysis of scRNA-seq data often starts from clustering cells into subpopulations. This initial step has a high impact on downstream analyses, and hence it is important to be accurate. However, there have not been unsupervised metric designed for scRNA-seq to evaluate clustering performance. Hence, we propose clustering deviation index (CDI), an unsupervised metric based on the modeling of scRNA-seq UMI counts to evaluate clustering of cells.' + license_file: LICENSE + diff --git a/recipes/bioconductor-celaref/meta.yaml b/recipes/bioconductor-celaref/meta.yaml index 58aa2360a02dc..f3530a6b4cb5d 100644 --- a/recipes/bioconductor-celaref/meta.yaml +++ b/recipes/bioconductor-celaref/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "celaref" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d4e594ba701e701ca005234d6224c518 + md5: 8c168c1e505d63f6372d6baac7051a06 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-celaref", max_pin="x.x") }}' noarch: generic # Suggests: limma, parallel, knitr, rmarkdown, ExperimentHub, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-mast >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-mast >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -35,11 +36,11 @@ requirements: - r-rlang - r-tibble run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-mast >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-mast >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-celarefdata/meta.yaml b/recipes/bioconductor-celarefdata/meta.yaml index 95c7c8450dbb2..5babbe3604e80 100644 --- a/recipes/bioconductor-celarefdata/meta.yaml +++ b/recipes/bioconductor-celarefdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "celarefData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eb23383ea6cb3e84ef6c66f0617cc69e + md5: 6864c27f1d574314fe10612b37f6c433 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-celarefdata", max_pin="x.x") }}' noarch: generic # Suggests: ExperimentHub, knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-celarefdata/post-link.sh b/recipes/bioconductor-celarefdata/post-link.sh index f4fd72ae7f3c6..da558cc839610 100644 --- a/recipes/bioconductor-celarefdata/post-link.sh +++ b/recipes/bioconductor-celarefdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "celarefdata-1.18.0" +installBiocDataPackage.sh "celarefdata-1.20.0" diff --git a/recipes/bioconductor-celda/meta.yaml b/recipes/bioconductor-celda/meta.yaml index c6993b5108ae5..921775f6f1896 100644 --- a/recipes/bioconductor-celda/meta.yaml +++ b/recipes/bioconductor-celda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.1" %} {% set name = "celda" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7f8c768ce0dd749d8f815232bfe0977e + md5: 5b60cdee9ee9cbb13f4af0a40abdd177 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-celda", max_pin="x.x") }}' # Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-data.table @@ -37,11 +38,11 @@ requirements: - r-foreach - r-ggplot2 - r-ggrepel + - r-gridextra - r-gtable - r-matrix - r-matrixstats - r-mcmcprecision - - r-multipanelfigure - r-plyr - r-rcolorbrewer - r-rcpp @@ -55,13 +56,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-data.table @@ -72,11 +73,11 @@ requirements: - r-foreach - r-ggplot2 - r-ggrepel + - r-gridextra - r-gtable - r-matrix - r-matrixstats - r-mcmcprecision - - r-multipanelfigure - r-plyr - r-rcolorbrewer - r-rcpp diff --git a/recipes/bioconductor-celegans.db/meta.yaml b/recipes/bioconductor-celegans.db/meta.yaml index 6dc9527545231..ea39dc2bada5e 100644 --- a/recipes/bioconductor-celegans.db/meta.yaml +++ b/recipes/bioconductor-celegans.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "celegans.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3cfa9df5a81ef538a890ed8c5d5a98ad build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-celegans.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.ce.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.ce.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.ce.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.ce.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-celeganscdf/meta.yaml b/recipes/bioconductor-celeganscdf/meta.yaml index eea808835386d..3e1337bd905c5 100644 --- a/recipes/bioconductor-celeganscdf/meta.yaml +++ b/recipes/bioconductor-celeganscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "celeganscdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1098cd99bfc5000bf9858e4a3acaf452 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-celeganscdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-celegansprobe/meta.yaml b/recipes/bioconductor-celegansprobe/meta.yaml index eed0867c6997e..b1c063a28735f 100644 --- a/recipes/bioconductor-celegansprobe/meta.yaml +++ b/recipes/bioconductor-celegansprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "celegansprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7454bba10ff2dd7c03bfe0f9d450f148 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-celegansprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cellarepertorium/meta.yaml b/recipes/bioconductor-cellarepertorium/meta.yaml index d3550262c3003..26cde2ad158a4 100644 --- a/recipes/bioconductor-cellarepertorium/meta.yaml +++ b/recipes/bioconductor-cellarepertorium/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "CellaRepertorium" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 51d58a44ea2047858aa0a1c0453290d6 + md5: eceb5905cee5e0f9b9ba1ea47db2f1d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellarepertorium", max_pin="x.x") }}' # Suggests: testthat, readr, knitr, rmarkdown, ggplot2, BiocStyle, ggdendro, broom, lme4, RColorBrewer, SingleCellExperiment, scater, broom.mixed, cowplot, igraph, ggraph requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-forcats @@ -40,9 +41,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-forcats diff --git a/recipes/bioconductor-cellbarcode/meta.yaml b/recipes/bioconductor-cellbarcode/meta.yaml index c412436d62627..27da6a1d0c2b9 100644 --- a/recipes/bioconductor-cellbarcode/meta.yaml +++ b/recipes/bioconductor-cellbarcode/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "CellBarcode" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7b1eac1414aa90b4f31efa4acfbed68a + md5: d219d9d5c998fda5f5c02f817361c56a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellbarcode", max_pin="x.x") }}' # Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bh - r-ckmeans.1d.dp @@ -38,10 +39,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bh - r-ckmeans.1d.dp @@ -64,6 +65,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Cellular DNA Barcode Analysis toolkit' - description: 'This package performs Cellular DNA Barcode (genetic lineage tracing) analysis. The package can handle all kinds of DNA barcodes, as long as the barcode within a single sequencing read and has a pattern which can be matched by a regular expression. This package can handle barcode with flexible length, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing of some amplicon sequencing such as CRISPR gRNA screening, immune repertoire sequencing and meta genome data.' + description: 'The package CellBarcode performs Cellular DNA Barcode analysis. It can handle all kinds of DNA barcodes, as long as the barcode is within a single sequencing read and has a pattern that can be matched by a regular expression. \code{CellBarcode} can handle barcodes with flexible lengths, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing some amplicon data such as CRISPR gRNA screening, immune repertoire sequencing, and metagenome data.' license_file: LICENSE diff --git a/recipes/bioconductor-cellbaser/meta.yaml b/recipes/bioconductor-cellbaser/meta.yaml index bb9f42a99f6bc..a80228b09d7cc 100644 --- a/recipes/bioconductor-cellbaser/meta.yaml +++ b/recipes/bioconductor-cellbaser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "cellbaseR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dc80944f26d7d766c213f9330e8093ad + md5: 1540f788e9e1fba133da3a369fe2c8b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellbaser", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-data.table - r-doparallel @@ -33,8 +34,8 @@ requirements: - r-r.utils - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-cellbench/meta.yaml b/recipes/bioconductor-cellbench/meta.yaml index 18127f02e607d..6dbd1f801f5e5 100644 --- a/recipes/bioconductor-cellbench/meta.yaml +++ b/recipes/bioconductor-cellbench/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "CellBench" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 55a020a53f4d16c4df41022b0287f5dd + md5: 21b854517881e111491fd4b6dba0857c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellbench", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2 requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-assertthat - r-base - r-dplyr @@ -39,10 +40,10 @@ requirements: - r-tidyr - r-tidyselect run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-assertthat - r-base - r-dplyr diff --git a/recipes/bioconductor-celldex/meta.yaml b/recipes/bioconductor-celldex/meta.yaml index 68406f4d3d174..36ae84f27c872 100644 --- a/recipes/bioconductor-celldex/meta.yaml +++ b/recipes/bioconductor-celldex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "celldex" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fef4f15bc2e0a7427627cf1cd7d505dc + md5: 62419c915beb91f7c228e1a125df68f8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-celldex", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle, DT, ensembldb requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-celldex/post-link.sh b/recipes/bioconductor-celldex/post-link.sh index a789c0707212f..d36c9de2e3d47 100644 --- a/recipes/bioconductor-celldex/post-link.sh +++ b/recipes/bioconductor-celldex/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "celldex-1.10.1" +installBiocDataPackage.sh "celldex-1.12.0" diff --git a/recipes/bioconductor-cellhts2/meta.yaml b/recipes/bioconductor-cellhts2/meta.yaml index 187d6f7e88090..9ea087124a5a1 100644 --- a/recipes/bioconductor-cellhts2/meta.yaml +++ b/recipes/bioconductor-cellhts2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.64.0" %} +{% set version = "2.66.0" %} {% set name = "cellHTS2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ba5f251e1fea747094ba827c4bd82eb + md5: 6f9dfcbf4583db914d89c9310e207c02 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellhts2", max_pin="x.x") }}' noarch: generic # Suggests: ggplot2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-splots >=1.66.0,<1.67.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-splots >=1.68.0,<1.69.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-hwriter - r-locfit - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-splots >=1.66.0,<1.67.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-splots >=1.68.0,<1.69.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-hwriter - r-locfit diff --git a/recipes/bioconductor-cellid/meta.yaml b/recipes/bioconductor-cellid/meta.yaml index 656b75d49abd3..7aff6e471d46e 100644 --- a/recipes/bioconductor-cellid/meta.yaml +++ b/recipes/bioconductor-cellid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.1" %} {% set name = "CelliD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 65cfdcb7f5d87427061399fc6603eeea + md5: 91ef83db3f348575f3b90cf4c3753806 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellid", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr, destiny, ggrepel requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-fastmatch @@ -45,11 +46,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-fastmatch diff --git a/recipes/bioconductor-cellity/meta.yaml b/recipes/bioconductor-cellity/meta.yaml index c5cf38ca92df6..3f533b5866143 100644 --- a/recipes/bioconductor-cellity/meta.yaml +++ b/recipes/bioconductor-cellity/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "cellity" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aadb0954509cd1a297ab1adf15449b30 + md5: c6680442e176cef832fc19d82d49815a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellity", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, caret, knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-e1071 - r-ggplot2 - r-mvoutlier - r-robustbase run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-e1071 - r-ggplot2 diff --git a/recipes/bioconductor-cellmapper/meta.yaml b/recipes/bioconductor-cellmapper/meta.yaml index 968c4f0352fd2..6cfb167524086 100644 --- a/recipes/bioconductor-cellmapper/meta.yaml +++ b/recipes/bioconductor-cellmapper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "CellMapper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 93d1fccce26fd0fb0d31bc0a89fdbb95 + md5: ca94af55dbc55bb2bf40c69f4965b553 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellmapper", max_pin="x.x") }}' noarch: generic # Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-cellmapperdata/meta.yaml b/recipes/bioconductor-cellmapperdata/meta.yaml index 45e0955d8f3f6..694aa257b25ef 100644 --- a/recipes/bioconductor-cellmapperdata/meta.yaml +++ b/recipes/bioconductor-cellmapperdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "CellMapperData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b9d311ad83cec787788c967e93cb290b + md5: 5db37729dd49f26b6cba9ff4aff80b1d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellmapperdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-cellmapper >=1.26.0,<1.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-cellmapper >=1.28.0,<1.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-cellmapper >=1.26.0,<1.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-cellmapper >=1.28.0,<1.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cellmapperdata/post-link.sh b/recipes/bioconductor-cellmapperdata/post-link.sh index 7963c56d1b0c3..a5db39ff29df7 100644 --- a/recipes/bioconductor-cellmapperdata/post-link.sh +++ b/recipes/bioconductor-cellmapperdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cellmapperdata-1.26.0" +installBiocDataPackage.sh "cellmapperdata-1.28.0" diff --git a/recipes/bioconductor-cellmigration/meta.yaml b/recipes/bioconductor-cellmigration/meta.yaml index e7215a9ecab0c..c4b413d5dc107 100644 --- a/recipes/bioconductor-cellmigration/meta.yaml +++ b/recipes/bioconductor-cellmigration/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "cellmigRation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f8e86c8cdb38e015e3a1b5927b834cf + md5: 61fc4a74a41e132fc3b760bc444ee5d4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellmigration", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics, BiocManager, kableExtra, rgl requirements: diff --git a/recipes/bioconductor-cellmixs/meta.yaml b/recipes/bioconductor-cellmixs/meta.yaml index d088721b9191d..fbf1f4f06dd59 100644 --- a/recipes/bioconductor-cellmixs/meta.yaml +++ b/recipes/bioconductor-cellmixs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "CellMixS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9882807e195ad678d59c5ef5704bd943 + md5: 67910c3dc01e01dc6be6ca3bb76d7794 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellmixs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-dplyr @@ -38,12 +39,12 @@ requirements: - r-tidyr - r-viridis run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-dplyr diff --git a/recipes/bioconductor-cellnoptr/meta.yaml b/recipes/bioconductor-cellnoptr/meta.yaml index 87c2f623319aa..c4a20e64f1c8a 100644 --- a/recipes/bioconductor-cellnoptr/meta.yaml +++ b/recipes/bioconductor-cellnoptr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "CellNOptR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09bf4fd709ce09ae2e28a60dbe412832 + md5: 22ea1e446726e7b83f26f1f5f614d74f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellnoptr", max_pin="x.x") }}' # Suggests: data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics, # SystemRequirements: Graphviz version >= 2.2 requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-ggplot2 - r-igraph @@ -36,9 +37,9 @@ requirements: - liblapack - 'graphviz >=2.2' run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-ggplot2 - r-igraph diff --git a/recipes/bioconductor-cellscore/meta.yaml b/recipes/bioconductor-cellscore/meta.yaml index 089bf0bf98800..91e7ab9ca06b4 100644 --- a/recipes/bioconductor-cellscore/meta.yaml +++ b/recipes/bioconductor-cellscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CellScore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: afb6d50cd4f4d6af1da07504b10d0650 + md5: c842a56a0f5067b891a0ab7c9f9b1e21 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellscore", max_pin="x.x") }}' noarch: generic -# Suggests: hgu133plus2CellScore, knitr +# Suggests: hgu133plus2CellScore, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-gplots >=3.0.1' - 'r-lsa >=0.73.1' - 'r-rcolorbrewer >=1.1-2' - 'r-squash >=1.0.8' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-gplots >=3.0.1' - 'r-lsa >=0.73.1' diff --git a/recipes/bioconductor-celltrails/meta.yaml b/recipes/bioconductor-celltrails/meta.yaml index ebd283155d0a6..81e50c10fe30a 100644 --- a/recipes/bioconductor-celltrails/meta.yaml +++ b/recipes/bioconductor-celltrails/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "CellTrails" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a9fc651c79c87dc1f49947350f660f6 + md5: 87b23b653d772f9b436b655e5e8af5ae build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-celltrails", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cba - r-dendextend @@ -38,10 +39,10 @@ requirements: - r-reshape2 - r-rtsne run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cba - r-dendextend diff --git a/recipes/bioconductor-cellxgenedp/meta.yaml b/recipes/bioconductor-cellxgenedp/meta.yaml index 331dfc1cac7e3..52a8b40eb76cb 100644 --- a/recipes/bioconductor-cellxgenedp/meta.yaml +++ b/recipes/bioconductor-cellxgenedp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.1" %} {% set name = "cellxgenedp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eadf41eb26e97613a500fa73807a60f5 + md5: dc1730a545f49b0b8c14991289f29a6b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellxgenedp", max_pin="x.x") }}' noarch: generic # Suggests: zellkonverter, SingleCellExperiment, HDF5Array, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery requirements: diff --git a/recipes/bioconductor-cemitool/meta.yaml b/recipes/bioconductor-cemitool/meta.yaml index 911aa97898ae0..0b2b39b75ff26 100644 --- a/recipes/bioconductor-cemitool/meta.yaml +++ b/recipes/bioconductor-cemitool/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "CEMiTool" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 513c292bb3582042a443b20930d66aec + md5: df823e2602a3b994f889644e39e0eb8f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cemitool", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocManager requirements: host: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' - r-base - 'r-data.table >=1.9.4' - r-dplyr @@ -48,8 +49,8 @@ requirements: - r-stringr - r-wgcna run: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' - r-base - 'r-data.table >=1.9.4' - r-dplyr diff --git a/recipes/bioconductor-censcyt/meta.yaml b/recipes/bioconductor-censcyt/meta.yaml index 184a5c03e98bd..5ed00b98241a1 100644 --- a/recipes/bioconductor-censcyt/meta.yaml +++ b/recipes/bioconductor-censcyt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "censcyt" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 25c65055473214240eb1102ffa7b39b1 + md5: e5f2a60dcafc6d878e1e97e85768f078 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-censcyt", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-diffcyt >=1.20.0,<1.21.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-diffcyt >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom.mixed - r-dirmult @@ -43,11 +44,11 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-diffcyt >=1.20.0,<1.21.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-diffcyt >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom.mixed - r-dirmult diff --git a/recipes/bioconductor-cepo/build_failure.linux-64.yaml b/recipes/bioconductor-cepo/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..5ac0014c0d22a --- /dev/null +++ b/recipes/bioconductor-cepo/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b904f129759930c0079c8f1858105b52b54ce300d7c837bd4c417f305be8d2d0 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + yaml: 0.2.5-h7f98852_2 conda-forge + yq: 3.2.3-pyhd8ed1ab_0 conda-forge + zlib: 1.2.13-hd590300_5 conda-forge + zstd: 1.5.5-hfc55251_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + [34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.1MB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.4MB/s 0.0s + [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.0MB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.9MB/s 0.0s + [?25h + ## Package Plan ## + + environment location: /opt/conda/conda-bld/bioconductor-cepo_1703278295981/_build_env + + + Source cache directory is: /opt/conda/conda-bld/src_cache + INFO:conda_build.source:Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: Cepo_1.8.0_9eee9f73ec.tar.gz + INFO:conda_build.source:Downloading source to cache: Cepo_1.8.0_9eee9f73ec.tar.gz + Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/Cepo_1.8.0.tar.gz + INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/Cepo_1.8.0.tar.gz + Success + INFO:conda_build.source:Success + Extracting download + source tree in: /opt/conda/conda-bld/bioconductor-cepo_1703278295981/work + export PREFIX=/opt/conda/conda-bld/bioconductor-cepo_1703278295981/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-cepo_1703278295981/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-cepo_1703278295981/work + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-cepo_1703278295981/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/R/library + * installing *source* package Cepo ... + ** using staged installation + ** R + ** data + ** inst + ** byte-compile and prepare package for lazy loading + During startup - Warning message: + Setting LC_TIME failed, using "C" + ** help + *** installing help indices + *** copying figures + ** building package indices + During startup - Warning message: + Setting LC_TIME failed, using "C" + ** installing vignettes + ** testing if installed package can be loaded from temporary location + During startup - Warning message: + Setting LC_TIME failed, using "C" + ** testing if installed package can be loaded from final location + During startup - Warning message: + Setting LC_TIME failed, using "C" + ** testing if installed package keeps a record of temporary installation path + * creating tarball + packaged installation of Cepo as Cepo_1.8.0_R_x86_64-conda-linux-gnu.tar.gz + * DONE (Cepo) + + Resource usage statistics from building bioconductor-cepo: + Process count: 6 + CPU time: Sys=0:00:02.4, User=0:00:20.2 + Memory: 733.9M + Disk usage: 6.8K + Time elapsed: 0:00:27.8 + + + Packaging bioconductor-cepo + INFO:conda_build.build:Packaging bioconductor-cepo + Packaging bioconductor-cepo-1.8.0-r43hdfd78af_0 + INFO:conda_build.build:Packaging bioconductor-cepo-1.8.0-r43hdfd78af_0 + number of files: 30 + Fixing permissions + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2358, in build + newly_built_packages = bundlers[pkg_type](output_d, m, env, stats) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 1672, in bundle_conda + output['checksums'] = create_info_files(metadata, replacements, files, prefix=metadata.config.host_prefix) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 1272, in create_info_files + copy_license(m) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 762, in copy_license + generic_copy(m, "license", "license_file") + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 800, in generic_copy + raise ValueError( + ValueError: License file given in about/license_file (/opt/recipe/LICENSE) does not exist in source root dir or in recipe root dir (with meta.yaml) +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-cepo/meta.yaml b/recipes/bioconductor-cepo/meta.yaml index b7de86cbeccc6..3e7d32bc32c6d 100644 --- a/recipes/bioconductor-cepo/meta.yaml +++ b/recipes/bioconductor-cepo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "Cepo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa0bd806c84f9024c965b3de7bc6652b + md5: 9eee9f73ecd4d7dd782d14db0f60bd1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cepo", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater, scMerge, fgsea, escape, pheatmap, patchwork requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -36,14 +37,14 @@ requirements: - r-reshape2 - r-rlang run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -58,4 +59,5 @@ about: license: 'MIT + file LICENSE' summary: 'Cepo for the identification of differentially stable genes' description: 'Defining the identity of a cell is fundamental to understand the heterogeneity of cells to various environmental signals and perturbations. We present Cepo, a new method to explore cell identities from single-cell RNA-sequencing data using differential stability as a new metric to define cell identity genes. Cepo computes cell-type specific gene statistics pertaining to differential stable gene expression.' + license_file: LICENSE diff --git a/recipes/bioconductor-cernanetsim/meta.yaml b/recipes/bioconductor-cernanetsim/meta.yaml index 49f97e8b5f8fe..06a85239a44fc 100644 --- a/recipes/bioconductor-cernanetsim/meta.yaml +++ b/recipes/bioconductor-cernanetsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ceRNAnetsim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3bd2c6360a6a11df8ccce61557d105dd + md5: 7a406a65a3e7bad478149f1587317a79 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cernanetsim", max_pin="x.x") }}' noarch: generic # Suggests: knitr, png, rmarkdown, testthat, covr requirements: diff --git a/recipes/bioconductor-cetf/meta.yaml b/recipes/bioconductor-cetf/meta.yaml index 35bc561332f75..a5a4a5da234e4 100644 --- a/recipes/bioconductor-cetf/meta.yaml +++ b/recipes/bioconductor-cetf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "CeTF" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6e155847761cb9f297650b789c967ff7 + md5: b79bf3680b81b7b6945eef89f6babfc1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cetf", max_pin="x.x") }}' # Suggests: airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat # SystemRequirements: libcurl4-openssl-dev, libxml2-dev, libssl-dev, gfortran, build-essential, libz-dev, zlib1g-dev requirements: host: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-dplyr @@ -44,12 +45,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-dplyr diff --git a/recipes/bioconductor-cexor/meta.yaml b/recipes/bioconductor-cexor/meta.yaml index aac4f37c1f333..50afffdcd92be 100644 --- a/recipes/bioconductor-cexor/meta.yaml +++ b/recipes/bioconductor-cexor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "CexoR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 32ef736b70fcc811be756cbed73445c3 + md5: 53f7febbb51a7f925322329e89a8d619 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cexor", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-genomation >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomation >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-idr - r-rcolorbrewer run: - - 'bioconductor-genomation >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomation >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-idr - r-rcolorbrewer diff --git a/recipes/bioconductor-cfassay/meta.yaml b/recipes/bioconductor-cfassay/meta.yaml index c8587570ddc98..96259a3f1aed1 100644 --- a/recipes/bioconductor-cfassay/meta.yaml +++ b/recipes/bioconductor-cfassay/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "CFAssay" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3fbd8b4078901da0139a5fc27d56cda8 + md5: 122c969248ffd92330d93a266db6cb3c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cfassay", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-cfdnakit/build.sh b/recipes/bioconductor-cfdnakit/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cfdnakit/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cfdnakit/meta.yaml b/recipes/bioconductor-cfdnakit/meta.yaml new file mode 100644 index 0000000000000..b7735232ce60f --- /dev/null +++ b/recipes/bioconductor-cfdnakit/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.0.0" %} +{% set name = "cfdnakit" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 967a84e96d20af4a0256e117afe272b7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cfdnakit", max_pin="x.x") }}' + noarch: generic +# Suggests: rmarkdown, knitr, roxygen2, BiocStyle +requirements: + host: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-dplyr + - r-ggplot2 + - r-magrittr + - r-pscbs + - r-rlang + run: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-dplyr + - r-ggplot2 + - r-magrittr + - r-pscbs + - r-rlang +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)' + description: 'This package provides basic functions for analyzing shallow whole-genome sequencing (~0.3X or more) of cell-free DNA (cfDNA). The package basically extracts the length of cfDNA fragments and aids the vistualization of fragment-length information. The package also extract fragment-length information per non-overlapping fixed-sized bins and used it for calculating ctDNA estimation score (CES).' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-cfdnapro/meta.yaml b/recipes/bioconductor-cfdnapro/meta.yaml index 55bda26419c1f..1b8813dc37295 100644 --- a/recipes/bioconductor-cfdnapro/meta.yaml +++ b/recipes/bioconductor-cfdnapro/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "cfDNAPro" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80295d2e20980978b268c420ee6c5acd + md5: 377fb633e850fcef49fbe86f3c4d1505 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cfdnapro", max_pin="x.x") }}' noarch: generic # Suggests: scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools (>= 2.3.0), BiocStyle, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-bsgenome.hsapiens.ncbi.grch38 >=1.3.0,<1.4.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - 'r-dplyr >=0.8.3' - 'r-ggplot2 >=3.2.1' @@ -40,16 +41,16 @@ requirements: - 'r-stringr >=1.4.0' - r-tibble run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-bsgenome.hsapiens.ncbi.grch38 >=1.3.0,<1.4.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - 'r-dplyr >=0.8.3' - 'r-ggplot2 >=3.2.1' diff --git a/recipes/bioconductor-cftools/meta.yaml b/recipes/bioconductor-cftools/meta.yaml index 325303e6f60fc..7ad4099a140e5 100644 --- a/recipes/bioconductor-cftools/meta.yaml +++ b/recipes/bioconductor-cftools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "cfTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc30acea96850944e511ea4bbf58e266 + md5: cf0f03a9654984b3214bcadac889fc28 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cftools", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-cftoolsdata >=1.0.0,<1.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-bh - r-r.utils @@ -29,8 +31,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-cftoolsdata >=1.0.0,<1.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-bh - r-r.utils diff --git a/recipes/bioconductor-cftoolsdata/meta.yaml b/recipes/bioconductor-cftoolsdata/meta.yaml new file mode 100644 index 0000000000000..4150a2a029bdb --- /dev/null +++ b/recipes/bioconductor-cftoolsdata/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.0.0" %} +{% set name = "cfToolsData" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 00bbf328a45fb8731b3c7262b3521e0b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cftoolsdata", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - r-base + run: + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'ExperimentHub data for the cfTools package' + description: 'The cfToolsData package supplies the data for the cfTools package. It contains two pre-trained deep neural network (DNN) models for the cfSort function. Additionally, it includes the shape parameters of beta distribution characterizing methylation markers associated with four tumor types for the CancerDetector function, as well as the parameters characterizing methylation markers specific to 29 primary human tissue types for the cfDeconvolve function.' + license_file: LICENSE + diff --git a/recipes/bioconductor-cftoolsdata/post-link.sh b/recipes/bioconductor-cftoolsdata/post-link.sh new file mode 100644 index 0000000000000..76ff4ad0b782b --- /dev/null +++ b/recipes/bioconductor-cftoolsdata/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "cftoolsdata-1.0.0" diff --git a/recipes/bioconductor-cftoolsdata/pre-unlink.sh b/recipes/bioconductor-cftoolsdata/pre-unlink.sh new file mode 100644 index 0000000000000..d8e309e01fa6c --- /dev/null +++ b/recipes/bioconductor-cftoolsdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ cfToolsData diff --git a/recipes/bioconductor-cgen/meta.yaml b/recipes/bioconductor-cgen/meta.yaml index a45300a10267c..cc332a3a96b16 100644 --- a/recipes/bioconductor-cgen/meta.yaml +++ b/recipes/bioconductor-cgen/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.36.1" %} +{% set version = "3.38.0" %} {% set name = "CGEN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0092d5b8a0127b2ad4b803fc41289f08 + md5: e62dd5874cfcaab65414fff648106633 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cgen", max_pin="x.x") }}' # Suggests: cluster requirements: host: diff --git a/recipes/bioconductor-cghbase/meta.yaml b/recipes/bioconductor-cghbase/meta.yaml index d4196e9ebd2df..6a9c029f439be 100644 --- a/recipes/bioconductor-cghbase/meta.yaml +++ b/recipes/bioconductor-cghbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "CGHbase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ac037567f6cec96bce84af4382d7481 + md5: 806f73dc042c0bf46989606a4aa4dbe8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cghbase", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base test: commands: diff --git a/recipes/bioconductor-cghcall/meta.yaml b/recipes/bioconductor-cghcall/meta.yaml index 2ee30e29f42cf..0177f0dccb3bc 100644 --- a/recipes/bioconductor-cghcall/meta.yaml +++ b/recipes/bioconductor-cghcall/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.62.0" %} +{% set version = "2.64.0" %} {% set name = "CGHcall" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a593c642a5f01c37fd60caece6363f87 + md5: 7a43fd6ae1e6c288b98abd2b8824fed4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cghcall", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cghbase >=1.60.0,<1.61.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-base - r-snowfall run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cghbase >=1.60.0,<1.61.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-base - r-snowfall test: diff --git a/recipes/bioconductor-cghmcr/meta.yaml b/recipes/bioconductor-cghmcr/meta.yaml index ebda3d6609810..ed85eb3edecc1 100644 --- a/recipes/bioconductor-cghmcr/meta.yaml +++ b/recipes/bioconductor-cghmcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "cghMCR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4df2110576ea48c62099f7eafb985866 + md5: b3db4bfc3f23e690592a37414db360c9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cghmcr", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-cntools >=1.56.0,<1.57.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-cntools >=1.58.0,<1.59.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-cntools >=1.56.0,<1.57.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-cntools >=1.58.0,<1.59.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-cghnormaliter/meta.yaml b/recipes/bioconductor-cghnormaliter/meta.yaml index b7cf959966a85..b09f4d2b885e1 100644 --- a/recipes/bioconductor-cghnormaliter/meta.yaml +++ b/recipes/bioconductor-cghnormaliter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "CGHnormaliter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ab70a4d3f244ab250b735ad3b1fbbbd2 + md5: 948d3af66840226e7095e46d281df177 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cghnormaliter", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cghbase >=1.60.0,<1.61.0' - - 'bioconductor-cghcall >=2.62.0,<2.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' + - 'bioconductor-cghcall >=2.64.0,<2.65.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cghbase >=1.60.0,<1.61.0' - - 'bioconductor-cghcall >=2.62.0,<2.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' + - 'bioconductor-cghcall >=2.64.0,<2.65.0' - r-base test: commands: diff --git a/recipes/bioconductor-cghregions/meta.yaml b/recipes/bioconductor-cghregions/meta.yaml index e3f1c469919d2..d10ed89bd1358 100644 --- a/recipes/bioconductor-cghregions/meta.yaml +++ b/recipes/bioconductor-cghregions/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "CGHregions" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e445f33fe45b3f9773e5b433ab94c0aa + md5: 3ec8f1bb5db1987f92932d29a31d74fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cghregions", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cghbase >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cghbase >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-champdata/meta.yaml b/recipes/bioconductor-champdata/meta.yaml index 0bb20b2c6c55e..7e32b96919117 100644 --- a/recipes/bioconductor-champdata/meta.yaml +++ b/recipes/bioconductor-champdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "ChAMPdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf36209a25e3dbc4c8098a3fcb3327df + md5: b12bfec01a1cfdd103bc0cb9bd44d4aa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-champdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-champdata/post-link.sh b/recipes/bioconductor-champdata/post-link.sh index 4d1b7c8156bb8..af3862f5f24b1 100644 --- a/recipes/bioconductor-champdata/post-link.sh +++ b/recipes/bioconductor-champdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "champdata-2.32.0" +installBiocDataPackage.sh "champdata-2.34.0" diff --git a/recipes/bioconductor-chemminedrugs/meta.yaml b/recipes/bioconductor-chemminedrugs/meta.yaml index dcf2b0360e313..97651c57e2bbe 100644 --- a/recipes/bioconductor-chemminedrugs/meta.yaml +++ b/recipes/bioconductor-chemminedrugs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.2" %} {% set name = "ChemmineDrugs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,25 +13,26 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2a3646e5173e93080fb5b49564f5d545 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chemminedrugs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle,knitcitations,knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - r-rsqlite run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - r-rsqlite - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chemmineob/build.sh b/recipes/bioconductor-chemmineob/build.sh index 9ee117c0e7115..ee892d72037fc 100644 --- a/recipes/bioconductor-chemmineob/build.sh +++ b/recipes/bioconductor-chemmineob/build.sh @@ -8,4 +8,4 @@ CXX=$CXX -I$PREFIX/include/openbabel3 -I$PREFIX/include/eigen3 -L$PREFIX/lib CXX98=$CXX CXX11=$CXX CXX14=$CXX -I$PREFIX/include/openbabel3 -I$PREFIX/include/eigen3 -L$PREFIX/lib" > ~/.R/Makevars -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chemmineob/meta.yaml b/recipes/bioconductor-chemmineob/meta.yaml index 0b1c018320b76..e143fc83685a4 100644 --- a/recipes/bioconductor-chemmineob/meta.yaml +++ b/recipes/bioconductor-chemmineob/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "ChemmineOB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,7 +11,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d721ca0fa36f8b42fecca0ab4f98910 + md5: 5bd759ca398ffb70214a8076028bf0b2 patches: - patch build: @@ -19,12 +19,13 @@ build: rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chemmineob", max_pin="x.x") }}' # Suggests: ChemmineR, BiocStyle, knitr, knitrBootstrap, BiocManager, rmarkdown,RUnit # SystemRequirements: OpenBabel (>= 3.0.0) with headers (http://openbabel.org). Eigen3 with headers. requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bh - 'r-rcpp >=0.11.0' @@ -33,8 +34,8 @@ requirements: - openbabel >=3 - eigen run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bh - 'r-rcpp >=0.11.0' diff --git a/recipes/bioconductor-chemminer/meta.yaml b/recipes/bioconductor-chemminer/meta.yaml index 99ce170bcdabf..dec3edb5902fc 100644 --- a/recipes/bioconductor-chemminer/meta.yaml +++ b/recipes/bioconductor-chemminer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.52.0" %} +{% set version = "3.54.0" %} {% set name = "ChemmineR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54601905e8a4a48d85b3c7a80f935eb5 + md5: 8dd1886811bdc4ac23c24fad60a9b238 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chemminer", max_pin="x.x") }}' # Suggests: RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs, png,rmarkdown, BiocManager,bibtex # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-base64enc - r-bh @@ -40,7 +41,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-base64enc - r-bh diff --git a/recipes/bioconductor-chetah/meta.yaml b/recipes/bioconductor-chetah/meta.yaml index d31c3271649f8..2dca0e66b8dbe 100644 --- a/recipes/bioconductor-chetah/meta.yaml +++ b/recipes/bioconductor-chetah/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "CHETAH" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0312f98ec3d18db1839da7f6980cf4d6 + md5: a6b920a4a3f3f931acb3cd950c7a74c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chetah", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, Matrix, testthat, vdiffr requirements: host: - - 'bioconductor-biodist >=1.72.0,<1.73.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biodist >=1.74.0,<1.75.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-corrplot - r-cowplot @@ -35,10 +36,10 @@ requirements: - r-reshape2 - r-shiny run: - - 'bioconductor-biodist >=1.72.0,<1.73.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biodist >=1.74.0,<1.75.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-corrplot - r-cowplot diff --git a/recipes/bioconductor-chic.data/meta.yaml b/recipes/bioconductor-chic.data/meta.yaml index 4a8fcf87e3a4f..f99fd578b9c16 100644 --- a/recipes/bioconductor-chic.data/meta.yaml +++ b/recipes/bioconductor-chic.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ChIC.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c846395a170d9e1601f20f2250b5b3e2 + md5: 34b50ea53e6b5c982dc044addc68c33b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chic.data", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-genomeintervals >=1.56.0,<1.57.0' + - 'bioconductor-genomeintervals >=1.58.0,<1.59.0' - r-base - 'r-caret >=6.0-78' - r-randomforest run: - - 'bioconductor-genomeintervals >=1.56.0,<1.57.0' + - 'bioconductor-genomeintervals >=1.58.0,<1.59.0' - r-base - 'r-caret >=6.0-78' - r-randomforest - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chic.data/post-link.sh b/recipes/bioconductor-chic.data/post-link.sh index 52ba42a28c315..7b754bd9c9d5b 100644 --- a/recipes/bioconductor-chic.data/post-link.sh +++ b/recipes/bioconductor-chic.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chic.data-1.20.0" +installBiocDataPackage.sh "chic.data-1.22.0" diff --git a/recipes/bioconductor-chicago/meta.yaml b/recipes/bioconductor-chicago/meta.yaml index bc24031fe5277..c5b8124eaea7d 100644 --- a/recipes/bioconductor-chicago/meta.yaml +++ b/recipes/bioconductor-chicago/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "Chicago" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cecb7a43534f59b758ad7c05a2c0e4fe + md5: 854dccdecc3b0fc55c9146908bdeec27 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chicago", max_pin="x.x") }}' noarch: generic # Suggests: argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub requirements: diff --git a/recipes/bioconductor-chicken.db/meta.yaml b/recipes/bioconductor-chicken.db/meta.yaml index 0329c2be32619..3269f8ebba784 100644 --- a/recipes/bioconductor-chicken.db/meta.yaml +++ b/recipes/bioconductor-chicken.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "chicken.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 512f887df339529d4883aad3f3eb6fb8 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chicken.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.gg.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.gg.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.gg.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.gg.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chicken.db0/meta.yaml b/recipes/bioconductor-chicken.db0/meta.yaml index 299fd377f924a..f807a281abb07 100644 --- a/recipes/bioconductor-chicken.db0/meta.yaml +++ b/recipes/bioconductor-chicken.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "chicken.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bfacdb3f67e914c4d364a512620ec50d + md5: 0f0c20a519a9490c0909b68ec67c206d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chicken.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chicken.db0/post-link.sh b/recipes/bioconductor-chicken.db0/post-link.sh index b88e8c6ac32e0..23df0c7fd0516 100644 --- a/recipes/bioconductor-chicken.db0/post-link.sh +++ b/recipes/bioconductor-chicken.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chicken.db0-3.17.0" +installBiocDataPackage.sh "chicken.db0-3.18.0" diff --git a/recipes/bioconductor-chickencdf/meta.yaml b/recipes/bioconductor-chickencdf/meta.yaml index 64bc0b66b2e3b..3aa18b57b0fe8 100644 --- a/recipes/bioconductor-chickencdf/meta.yaml +++ b/recipes/bioconductor-chickencdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "chickencdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ab0097b4b7b6c4d94360feb84ab69972 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chickencdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chickenprobe/meta.yaml b/recipes/bioconductor-chickenprobe/meta.yaml index 3b7f3bc49a4ff..21e051513a182 100644 --- a/recipes/bioconductor-chickenprobe/meta.yaml +++ b/recipes/bioconductor-chickenprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "chickenprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b33599081ce1ba768ff7992e143c01d0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chickenprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chihaya/meta.yaml b/recipes/bioconductor-chihaya/meta.yaml index 6166022377359..48ed2f9721a59 100644 --- a/recipes/bioconductor-chihaya/meta.yaml +++ b/recipes/bioconductor-chihaya/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "chihaya" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 52743ecddbcf6548ab5ed19e629ad989 + md5: fc8e24fa8ec373d01c938fbfe12c3b9a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chihaya", max_pin="x.x") }}' # Suggests: BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix, BiocStyle, testthat, rmarkdown, knitr # SystemRequirements: C++17, GNU make requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-chimeraviz/meta.yaml b/recipes/bioconductor-chimeraviz/meta.yaml index 3a0ccce4245d3..e05583b96cc73 100644 --- a/recipes/bioconductor-chimeraviz/meta.yaml +++ b/recipes/bioconductor-chimeraviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "chimeraviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 53ba0b753dbd0c0459d5ba1131a95ea9 + md5: 30227635634cb01d8196626c86dabc26 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chimeraviz", max_pin="x.x") }}' noarch: generic # Suggests: testthat, roxygen2, devtools, knitr, lintr # SystemRequirements: bowtie, samtools, and egrep are required for some functionalities requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-checkmate - r-data.table @@ -51,22 +52,22 @@ requirements: - r-rmarkdown - bowtie2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-checkmate - r-data.table diff --git a/recipes/bioconductor-chimp.db0/meta.yaml b/recipes/bioconductor-chimp.db0/meta.yaml index 6e58d8964a591..ef4f45937f147 100644 --- a/recipes/bioconductor-chimp.db0/meta.yaml +++ b/recipes/bioconductor-chimp.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "chimp.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0a1382e14c2ace3a9cdc3daf7d7e4013 + md5: afb020cefb808101626234257bf71f69 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chimp.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chimp.db0/post-link.sh b/recipes/bioconductor-chimp.db0/post-link.sh index 9fbda934665a5..1298c3be4a0f5 100644 --- a/recipes/bioconductor-chimp.db0/post-link.sh +++ b/recipes/bioconductor-chimp.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chimp.db0-3.17.0" +installBiocDataPackage.sh "chimp.db0-3.18.0" diff --git a/recipes/bioconductor-chimphumanbraindata/meta.yaml b/recipes/bioconductor-chimphumanbraindata/meta.yaml index 80e8eb58a1ccc..36d967d68a6ee 100644 --- a/recipes/bioconductor-chimphumanbraindata/meta.yaml +++ b/recipes/bioconductor-chimphumanbraindata/meta.yaml @@ -34,7 +34,7 @@ requirements: - r-hexbin - r-statmod - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20230706 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chipanalyser/meta.yaml b/recipes/bioconductor-chipanalyser/meta.yaml index 2206c35d793a2..252bfb7c4953c 100644 --- a/recipes/bioconductor-chipanalyser/meta.yaml +++ b/recipes/bioconductor-chipanalyser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "ChIPanalyser" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 75932168cfbb3bf4013b82f2cf95bf97 + md5: 21d3f8fe9fc90548452dab5a3a8e5c0d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipanalyser", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Dmelanogaster.UCSC.dm6,knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-rcolorbrewer - r-rcpproll - r-rocr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-rcolorbrewer diff --git a/recipes/bioconductor-chipcomp/meta.yaml b/recipes/bioconductor-chipcomp/meta.yaml index 2966e785af696..df3945bf8cc83 100644 --- a/recipes/bioconductor-chipcomp/meta.yaml +++ b/recipes/bioconductor-chipcomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "ChIPComp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f3b60264992ea88c72e1d8da73dfa48 + md5: 5294eab6ada6b66e52935843dd9acc6b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipcomp", max_pin="x.x") }}' # Suggests: BiocStyle,RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-chipenrich.data/meta.yaml b/recipes/bioconductor-chipenrich.data/meta.yaml index 9fdd15ef6c4ec..d82da5fbc76ab 100644 --- a/recipes/bioconductor-chipenrich.data/meta.yaml +++ b/recipes/bioconductor-chipenrich.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "chipenrich.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4d9f38a90b43fad02b6448ecfbd36f2d + md5: 4918da98125fee82afaeee84930051a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipenrich.data", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat, GO.db, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-readr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-readr - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chipenrich.data/post-link.sh b/recipes/bioconductor-chipenrich.data/post-link.sh index fba74203f871f..90df321032f62 100644 --- a/recipes/bioconductor-chipenrich.data/post-link.sh +++ b/recipes/bioconductor-chipenrich.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chipenrich.data-2.24.0" +installBiocDataPackage.sh "chipenrich.data-2.26.0" diff --git a/recipes/bioconductor-chipenrich/meta.yaml b/recipes/bioconductor-chipenrich/meta.yaml index 16735153cd287..9f53939b6e86e 100644 --- a/recipes/bioconductor-chipenrich/meta.yaml +++ b/recipes/bioconductor-chipenrich/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "chipenrich" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 85368fc7467101b17025a23231af5ff9 + md5: bb047e41aba2de216b8384322bb6a7aa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipenrich", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chipenrich.data >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.dr.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chipenrich.data >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.dr.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-lattice - r-latticeextra @@ -43,19 +44,19 @@ requirements: - r-rms - r-stringr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chipenrich.data >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.dr.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chipenrich.data >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.dr.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-lattice - r-latticeextra diff --git a/recipes/bioconductor-chipexoqual/meta.yaml b/recipes/bioconductor-chipexoqual/meta.yaml index cab6dcfe66cd7..eaacba6ed4f3c 100644 --- a/recipes/bioconductor-chipexoqual/meta.yaml +++ b/recipes/bioconductor-chipexoqual/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "ChIPexoQual" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 840ba226b952bac3081c94fb133d1c53 + md5: c5fc56e308fbcfdf0630f2559c3556a3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipexoqual", max_pin="x.x") }}' noarch: generic # Suggests: ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-broom >=0.4' - 'r-data.table >=1.9.6' @@ -40,14 +41,14 @@ requirements: - 'r-scales >=0.4.0' - 'r-viridis >=0.3' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-broom >=0.4' - 'r-data.table >=1.9.6' diff --git a/recipes/bioconductor-chipexoqualexample/meta.yaml b/recipes/bioconductor-chipexoqualexample/meta.yaml index 47a99c910c890..b98adbff5998f 100644 --- a/recipes/bioconductor-chipexoqualexample/meta.yaml +++ b/recipes/bioconductor-chipexoqualexample/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "ChIPexoQualExample" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b8a88d767a542955c8dfa93a67c843de + md5: 5ebb67a1848aa0e69557e795d236e24b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipexoqualexample", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chipexoqualexample/post-link.sh b/recipes/bioconductor-chipexoqualexample/post-link.sh index b2682c689a4f7..4cb76a02b9673 100644 --- a/recipes/bioconductor-chipexoqualexample/post-link.sh +++ b/recipes/bioconductor-chipexoqualexample/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chipexoqualexample-1.24.0" +installBiocDataPackage.sh "chipexoqualexample-1.26.0" diff --git a/recipes/bioconductor-chippeakanno/meta.yaml b/recipes/bioconductor-chippeakanno/meta.yaml index 37eec2d81105c..67ad871c9926b 100644 --- a/recipes/bioconductor-chippeakanno/meta.yaml +++ b/recipes/bioconductor-chippeakanno/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.34.1" %} +{% set version = "3.36.0" %} {% set name = "ChIPpeakAnno" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c57887a1682adde2e3a9e3ebf5389575 + md5: d9773752fca7bd32e512d3a5b72236e1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chippeakanno", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationHub, BSgenome, limma, reactome.db, BiocManager, BiocStyle, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg38, DelayedArray, idr, seqinr, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR, knitr, rmarkdown, testthat, trackViewer, motifStack, OrganismDbi requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dbi - r-dplyr @@ -48,26 +49,26 @@ requirements: - r-matrixstats - r-venndiagram run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dbi - r-dplyr diff --git a/recipes/bioconductor-chipqc/meta.yaml b/recipes/bioconductor-chipqc/meta.yaml index 3a35946828413..2eb975a8384db 100644 --- a/recipes/bioconductor-chipqc/meta.yaml +++ b/recipes/bioconductor-chipqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "ChIPQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 10738588f2408b35b805c47ade29958a + md5: b7437c357c5ba27db1f2721a50c15f13 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipqc", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-chipseq >=1.50.0,<1.51.0' - - 'bioconductor-diffbind >=3.10.0,<3.11.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-chipseq >=1.52.0,<1.53.0' + - 'bioconductor-diffbind >=3.12.0,<3.13.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.celegans.ucsc.ce6.ensgene >=3.2.0,<3.3.0' - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' @@ -45,17 +46,17 @@ requirements: - r-nozzle.r1 - r-reshape2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-chipseq >=1.50.0,<1.51.0' - - 'bioconductor-diffbind >=3.10.0,<3.11.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-chipseq >=1.52.0,<1.53.0' + - 'bioconductor-diffbind >=3.12.0,<3.13.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.celegans.ucsc.ce6.ensgene >=3.2.0,<3.3.0' - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' diff --git a/recipes/bioconductor-chipseeker/meta.yaml b/recipes/bioconductor-chipseeker/meta.yaml index ce1d8465acf6d..fe501701d99dd 100644 --- a/recipes/bioconductor-chipseeker/meta.yaml +++ b/recipes/bioconductor-chipseeker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "ChIPseeker" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 40fc097874f59ebe1b216c661f812b8e + md5: 4e7b7622d7d9d1b3de7b8f9bf49eb8c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipseeker", max_pin="x.x") }}' noarch: generic # Suggests: clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram, ReactomePA, org.Hs.eg.db, knitr, rmarkdown, testthat, prettydoc requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-aplot - r-base @@ -43,15 +44,15 @@ requirements: - r-tibble - r-yulab.utils run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-aplot - r-base diff --git a/recipes/bioconductor-chipseq/meta.yaml b/recipes/bioconductor-chipseq/meta.yaml index d651e8addd8b8..9b132ed73d2bc 100644 --- a/recipes/bioconductor-chipseq/meta.yaml +++ b/recipes/bioconductor-chipseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "chipseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bf6ac7d66b1527716768e6218f0468e9 + md5: 5cf8ab297fc95d0a36b4359488c50358 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipseq", max_pin="x.x") }}' # Suggests: BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-lattice - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-lattice build: diff --git a/recipes/bioconductor-chipseqdbdata/meta.yaml b/recipes/bioconductor-chipseqdbdata/meta.yaml index 7fd9e17b951bb..51ec45e800c2a 100644 --- a/recipes/bioconductor-chipseqdbdata/meta.yaml +++ b/recipes/bioconductor-chipseqdbdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "chipseqDBData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9417adbf6ebe305a0caf0d0eba440cac + md5: a6e50016d2d7c0cb085df2c4254b5f84 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipseqdbdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chipseqdbdata/post-link.sh b/recipes/bioconductor-chipseqdbdata/post-link.sh index 2079dff585ed8..3d5e5956052e4 100644 --- a/recipes/bioconductor-chipseqdbdata/post-link.sh +++ b/recipes/bioconductor-chipseqdbdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chipseqdbdata-1.16.0" +installBiocDataPackage.sh "chipseqdbdata-1.18.0" diff --git a/recipes/bioconductor-chipseqr/meta.yaml b/recipes/bioconductor-chipseqr/meta.yaml index a69b3f5e17171..c6349e5dc015c 100644 --- a/recipes/bioconductor-chipseqr/meta.yaml +++ b/recipes/bioconductor-chipseqr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "ChIPseqR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c1a94747eb45fbf4d791cbb05961424 + md5: 8696d6a783d26d8c6225ec4e3f294110 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipseqr", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hilbertvis >=1.58.0,<1.59.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hilbertvis >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-fbasics - r-timsac - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hilbertvis >=1.58.0,<1.59.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hilbertvis >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-fbasics - r-timsac diff --git a/recipes/bioconductor-chipsim/meta.yaml b/recipes/bioconductor-chipsim/meta.yaml index 74820f192e5f3..f81fdb6e13dc2 100644 --- a/recipes/bioconductor-chipsim/meta.yaml +++ b/recipes/bioconductor-chipsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "ChIPsim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f3239589cefb4c8db5fafe013dcd926 + md5: e6f1bd9d18f542abace1039c37ada326 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipsim", max_pin="x.x") }}' noarch: generic # Suggests: actuar, zoo requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base test: commands: diff --git a/recipes/bioconductor-chipxpress/meta.yaml b/recipes/bioconductor-chipxpress/meta.yaml index 05e6214d06fb8..3d91446325661 100644 --- a/recipes/bioconductor-chipxpress/meta.yaml +++ b/recipes/bioconductor-chipxpress/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "ChIPXpress" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 31093ed51ee07a043038f30f431b8df0 + md5: bed7bbe60d0a51fb667cee9b01e4c407 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipxpress", max_pin="x.x") }}' noarch: generic # Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-chipxpressdata >=1.38.0,<1.39.0' - - 'bioconductor-frma >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-chipxpressdata >=1.40.0,<1.41.0' + - 'bioconductor-frma >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base - r-biganalytics - r-bigmemory run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-chipxpressdata >=1.38.0,<1.39.0' - - 'bioconductor-frma >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-chipxpressdata >=1.40.0,<1.41.0' + - 'bioconductor-frma >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base - r-biganalytics - r-bigmemory diff --git a/recipes/bioconductor-chipxpressdata/meta.yaml b/recipes/bioconductor-chipxpressdata/meta.yaml index 45808acdeb8cb..5651a2b0910c0 100644 --- a/recipes/bioconductor-chipxpressdata/meta.yaml +++ b/recipes/bioconductor-chipxpressdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "ChIPXpressData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d764e5abb6fadab9aa4184222665fd25 + md5: 029086a630df9533dedea4babd28f0d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipxpressdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -26,7 +27,7 @@ requirements: - r-base - r-bigmemory - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chipxpressdata/post-link.sh b/recipes/bioconductor-chipxpressdata/post-link.sh index de10fb5bf2753..82a974e07cf07 100644 --- a/recipes/bioconductor-chipxpressdata/post-link.sh +++ b/recipes/bioconductor-chipxpressdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chipxpressdata-1.38.0" +installBiocDataPackage.sh "chipxpressdata-1.40.0" diff --git a/recipes/bioconductor-chopsticks/meta.yaml b/recipes/bioconductor-chopsticks/meta.yaml index ce6e6f825a531..17c378b1395b0 100644 --- a/recipes/bioconductor-chopsticks/meta.yaml +++ b/recipes/bioconductor-chopsticks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "chopsticks" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d89502b5d2b8124bcf02def4af198d1e + md5: b63b111068a6d42f7812010d1dc31047 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chopsticks", max_pin="x.x") }}' # Suggests: hexbin requirements: host: diff --git a/recipes/bioconductor-chromdraw/meta.yaml b/recipes/bioconductor-chromdraw/meta.yaml index 619ff6d5788fa..e92f8c236b474 100644 --- a/recipes/bioconductor-chromdraw/meta.yaml +++ b/recipes/bioconductor-chromdraw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "chromDraw" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 396784bb969985d07948449d9370a7ea + md5: a2cb0f03cdde9853f68662b1783a2edb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chromdraw", max_pin="x.x") }}' # SystemRequirements: Rtools (>= 3.1) requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - 'r-rcpp >=0.11.1' - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - 'r-rcpp >=0.11.1' build: diff --git a/recipes/bioconductor-chromheatmap/meta.yaml b/recipes/bioconductor-chromheatmap/meta.yaml index fcd97fa3d6695..b777bfe8ed021 100644 --- a/recipes/bioconductor-chromheatmap/meta.yaml +++ b/recipes/bioconductor-chromheatmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "ChromHeatMap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a643aa848bc97a9893f442798ab63d51 + md5: ee08133257bb6da21d100e03fd720323 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chromheatmap", max_pin="x.x") }}' noarch: generic # Suggests: ALL, hgu95av2.db requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-chromhmmdata/meta.yaml b/recipes/bioconductor-chromhmmdata/meta.yaml index 31e71bfc05c6f..0dabce226994f 100644 --- a/recipes/bioconductor-chromhmmdata/meta.yaml +++ b/recipes/bioconductor-chromhmmdata/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.2" %} {% set name = "chromhmmData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: eec85c20139b3d826f00264c7b28207c build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chromhmmdata", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chromplot/meta.yaml b/recipes/bioconductor-chromplot/meta.yaml index c679f8ff551d5..38a0a8e56bf16 100644 --- a/recipes/bioconductor-chromplot/meta.yaml +++ b/recipes/bioconductor-chromplot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "chromPlot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e79af2916f986d3381e6b4bad3a0b03 + md5: a9a3e6d499f082698be0bf88f6432103 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chromplot", max_pin="x.x") }}' noarch: generic # Suggests: qtl, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base test: commands: diff --git a/recipes/bioconductor-chromscape/meta.yaml b/recipes/bioconductor-chromscape/meta.yaml index 39884d28d7f71..06a80351408c4 100644 --- a/recipes/bioconductor-chromscape/meta.yaml +++ b/recipes/bioconductor-chromscape/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ChromSCape" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f10af25260d45879be22b5009d675957 + md5: a95b9c5be176f95c178ac7d3a1c26496 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chromscape", max_pin="x.x") }}' # Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, Signac, future, igraph, bluster, httr requirements: host: - - 'bioconductor-batchelor >=1.16.0,<1.17.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-batchelor >=1.18.0,<1.19.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-colorramps - r-colourpicker @@ -75,20 +76,20 @@ requirements: - libblas - liblapack run: - - 'bioconductor-batchelor >=1.16.0,<1.17.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-batchelor >=1.18.0,<1.19.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-colorramps - r-colourpicker diff --git a/recipes/bioconductor-chromstar/meta.yaml b/recipes/bioconductor-chromstar/meta.yaml index 7bf4d86cf9264..c2f40c3c66293 100644 --- a/recipes/bioconductor-chromstar/meta.yaml +++ b/recipes/bioconductor-chromstar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "chromstaR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c7cd6c65772e7ed8857f0c4a7fbde5f2 + md5: 4288983863e4523b5c7e7750691e8987 build: skip: True # [osx] number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chromstar", max_pin="x.x") }}' # Suggests: knitr, BiocStyle, testthat, biomaRt requirements: host: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chromstardata >=1.26.0,<1.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chromstardata >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-foreach @@ -39,15 +40,15 @@ requirements: - libblas - liblapack run: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chromstardata >=1.26.0,<1.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chromstardata >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-chromstardata/meta.yaml b/recipes/bioconductor-chromstardata/meta.yaml index 292e8684ef5a8..1a844f8b5b766 100644 --- a/recipes/bioconductor-chromstardata/meta.yaml +++ b/recipes/bioconductor-chromstardata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "chromstaRData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 316680e584e9e31c3000a87e666fda3b + md5: 7f4a965a6b5aa71874a5cca39046cabf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chromstardata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chromstardata/post-link.sh b/recipes/bioconductor-chromstardata/post-link.sh index 8fe48b9d0b2e1..3707fe3b3448a 100644 --- a/recipes/bioconductor-chromstardata/post-link.sh +++ b/recipes/bioconductor-chromstardata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chromstardata-1.26.0" +installBiocDataPackage.sh "chromstardata-1.28.0" diff --git a/recipes/bioconductor-chromvar/meta.yaml b/recipes/bioconductor-chromvar/meta.yaml index 71bf356fd7b8c..dc83da4dba182 100644 --- a/recipes/bioconductor-chromvar/meta.yaml +++ b/recipes/bioconductor-chromvar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "chromVAR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 457ef63195af94e9b077f852ff950120 + md5: 8e42f2454ce39606fae40e85e437b47b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chromvar", max_pin="x.x") }}' # Suggests: JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-dt - r-ggplot2 @@ -47,17 +48,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-dt - r-ggplot2 diff --git a/recipes/bioconductor-chronos/meta.yaml b/recipes/bioconductor-chronos/meta.yaml index 74f6e5ec5794e..d599b7baf0635 100644 --- a/recipes/bioconductor-chronos/meta.yaml +++ b/recipes/bioconductor-chronos/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "CHRONOS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 36aa4b9e641e13b99c425fceaea51902 + md5: 7d2e5d9c89ea0163868d7b51bfd1c952 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chronos", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, rmarkdown # SystemRequirements: Java version >= 1.7, Pandoc requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-circlize - r-doparallel @@ -36,9 +37,9 @@ requirements: - r-xml - openjdk run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-circlize - r-doparallel diff --git a/recipes/bioconductor-cicero/meta.yaml b/recipes/bioconductor-cicero/meta.yaml index c9a1f8ea9da63..3eccb1e945ea0 100644 --- a/recipes/bioconductor-cicero/meta.yaml +++ b/recipes/bioconductor-cicero/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "cicero" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: df17d0a24bd82617cc2eb0358cb2c01b + md5: 642264199171ac5b31a4f296c855dbb7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cicero", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi (>= 1.38.2), knitr, markdown, rmarkdown, rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-monocle >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-monocle >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'r-assertthat >=0.2.0' - r-base - 'r-data.table >=1.10.4' @@ -45,13 +46,13 @@ requirements: - r-tidyr - 'r-vgam >=1.0-5' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-monocle >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-monocle >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'r-assertthat >=0.2.0' - r-base - 'r-data.table >=1.10.4' diff --git a/recipes/bioconductor-cimice/meta.yaml b/recipes/bioconductor-cimice/meta.yaml index 167de8864400d..fdd7c4e3115bd 100644 --- a/recipes/bioconductor-cimice/meta.yaml +++ b/recipes/bioconductor-cimice/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "CIMICE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2b25b8cfb634948761ef0ab0cea2573a + md5: 510ab010752cd50654467583c6159ba1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cimice", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, webshot requirements: host: - - 'bioconductor-maftools >=2.16.0,<2.17.0' + - 'bioconductor-maftools >=2.18.0,<2.19.0' - r-assertthat - r-base - r-dplyr @@ -38,7 +39,7 @@ requirements: - r-tidyr - r-visnetwork run: - - 'bioconductor-maftools >=2.16.0,<2.17.0' + - 'bioconductor-maftools >=2.18.0,<2.19.0' - r-assertthat - r-base - r-dplyr diff --git a/recipes/bioconductor-cindex/meta.yaml b/recipes/bioconductor-cindex/meta.yaml index 1ac85c185c36e..b76d809749c35 100644 --- a/recipes/bioconductor-cindex/meta.yaml +++ b/recipes/bioconductor-cindex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "CINdex" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e7b2c4eea3f63ef70beb69855c13e8d + md5: 2616a2a02791d966dbf54a54f2ad5f42 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cindex", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, ReactomePA, RUnit, BiocGenerics, AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings,Homo.sapiens, R.utils requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bitops - r-dplyr @@ -34,10 +35,10 @@ requirements: - r-som - r-stringr run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bitops - r-dplyr diff --git a/recipes/bioconductor-circrnaprofiler/meta.yaml b/recipes/bioconductor-circrnaprofiler/meta.yaml index 28a7828103941..169e8226f8928 100644 --- a/recipes/bioconductor-circrnaprofiler/meta.yaml +++ b/recipes/bioconductor-circrnaprofiler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "circRNAprofiler" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 185095e44fb0afd5f381d76f4a9d11b8 + md5: 5cd7f621f355f9d816938675dd550e2f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-circrnaprofiler", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, roxygen2, rmarkdown, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocManager, requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gwascat >=2.32.0,<2.33.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-universalmotif >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gwascat >=2.34.0,<2.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-universalmotif >=1.20.0,<1.21.0' - r-base - r-dplyr - r-ggplot2 @@ -46,19 +47,19 @@ requirements: - r-stringi - r-stringr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gwascat >=2.32.0,<2.33.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-universalmotif >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gwascat >=2.34.0,<2.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-universalmotif >=1.20.0,<1.21.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-circseqaligntk/meta.yaml b/recipes/bioconductor-circseqaligntk/meta.yaml index 8762be109cfe7..1552ea1595ddc 100644 --- a/recipes/bioconductor-circseqaligntk/meta.yaml +++ b/recipes/bioconductor-circseqaligntk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "CircSeqAlignTk" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5afd52c06cc2be5978037ddbaf1c6b9d + md5: 2c3b93fca2c2974a45af093edf7d9558 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-circseqaligntk", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, R.utils, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbowtie2 >=2.6.0,<2.7.0' - - 'bioconductor-rhisat2 >=1.16.0,<1.17.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' + - 'bioconductor-rhisat2 >=1.18.0,<1.19.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-dplyr - r-ggplot2 @@ -36,14 +37,14 @@ requirements: - r-rlang - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbowtie2 >=2.6.0,<2.7.0' - - 'bioconductor-rhisat2 >=1.16.0,<1.17.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' + - 'bioconductor-rhisat2 >=1.18.0,<1.19.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-cispath/meta.yaml b/recipes/bioconductor-cispath/meta.yaml index 198ea08df04db..cc4f2f6708169 100644 --- a/recipes/bioconductor-cispath/meta.yaml +++ b/recipes/bioconductor-cispath/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "cisPath" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d9fb575eb3e75ecca9e49aae03f99e16 + md5: 958a35281b9aa98b2d5c3a5c4e9c8824 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cispath", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-citefuse/meta.yaml b/recipes/bioconductor-citefuse/meta.yaml index c401b9e42dab4..b64daab89d292 100644 --- a/recipes/bioconductor-citefuse/meta.yaml +++ b/recipes/bioconductor-citefuse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "CiteFuse" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a24d3bcaca6d446c6992c8f337deb15 + md5: d612b20352aa6e753d90baa4f24b058f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-citefuse", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle, pkgdown requirements: host: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-compositions - r-cowplot @@ -47,11 +48,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-compositions - r-cowplot diff --git a/recipes/bioconductor-citruscdf/meta.yaml b/recipes/bioconductor-citruscdf/meta.yaml index a1500a296707c..650b3066528a8 100644 --- a/recipes/bioconductor-citruscdf/meta.yaml +++ b/recipes/bioconductor-citruscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "citruscdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4af821a0c1ae1adf42b7dc5ce7458593 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-citruscdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-citrusprobe/meta.yaml b/recipes/bioconductor-citrusprobe/meta.yaml index 762e4af7c0c8f..2c386ee4e5874 100644 --- a/recipes/bioconductor-citrusprobe/meta.yaml +++ b/recipes/bioconductor-citrusprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "citrusprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 259b114f96d5307c447d000bd27a7d15 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-citrusprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml b/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml index 7584a97d8f7b3..85c5b7c172edf 100644 --- a/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml +++ b/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "clariomdhumanprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 01cb1a5cc4674750b6ce5988cd62fad3 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clariomdhumanprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml index ae9a312dc03a3..a76e5a52dc2cb 100644 --- a/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "clariomdhumantranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 80739a70d77ab785231a9367938035a8 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clariomdhumantranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml index daa168f43926a..d70ad9cdca7f4 100644 --- a/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "clariomshumanhttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6a5e8e1f9768694be99277aafcc0a69a build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clariomshumanhttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml index 264f39fc4cc19..794a3936044f0 100644 --- a/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "clariomshumantranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 309b29e044e1227da6d4825bbdf04b76 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clariomshumantranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml index f23ef7e29afe2..1074e66c5774d 100644 --- a/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "clariomsmousehttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c0aa96cbd5ee7e19296dde5a72232d17 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clariomsmousehttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml index 900a5fd7c540e..271042584f0fd 100644 --- a/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "clariomsmousetranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 76d0e2204dcbd5d85d8e53d43710aac5 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clariomsmousetranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml index dda97365b309e..326e026ab0521 100644 --- a/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "clariomsrathttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e7c71721f8201bfd1553a98cfbf47458 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clariomsrathttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml index e1e18af7efc25..15edbc0937e97 100644 --- a/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "clariomsrattranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 72923a3a90f2df27a361b1730cfc0d00 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clariomsrattranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-classifyr/meta.yaml b/recipes/bioconductor-classifyr/meta.yaml index cf51f7b610e65..704f02bfee8e5 100644 --- a/recipes/bioconductor-classifyr/meta.yaml +++ b/recipes/bioconductor-classifyr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.7" %} +{% set version = "3.6.2" %} {% set name = "ClassifyR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61d0fa2d28ce2d1a8f3c984f7dc71e4c + md5: 002678b6aeace9d7967b87654547a4f3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-classifyr", max_pin="x.x") }}' # Suggests: limma, edgeR, car, Rmixmod, gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, parathyroidSE, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, robustbase, glmnet, class, randomForestSRC, MatrixModels, xgboost, data.tree, ggnewscale requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-generics - 'r-ggplot2 >=3.0.0' - r-ggpubr + - r-ggupset - r-ranger - r-reshape2 - r-rlang @@ -37,15 +39,16 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-generics - 'r-ggplot2 >=3.0.0' - r-ggpubr + - r-ggupset - r-ranger - r-reshape2 - r-rlang diff --git a/recipes/bioconductor-cleanupdtseq/meta.yaml b/recipes/bioconductor-cleanupdtseq/meta.yaml index 526d1e356a691..722708178c451 100644 --- a/recipes/bioconductor-cleanupdtseq/meta.yaml +++ b/recipes/bioconductor-cleanupdtseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "cleanUpdTSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4fc6f5fd9421004bf9ab234060d7714d + md5: 52f27e948758be1db9d6b003d69a84b9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cleanupdtseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics (>= 0.1.0) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-e1071 - r-seqinr - r-stringr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-e1071 - r-seqinr diff --git a/recipes/bioconductor-cleaver/meta.yaml b/recipes/bioconductor-cleaver/meta.yaml index 817641b020b8e..e69fedb991a3b 100644 --- a/recipes/bioconductor-cleaver/meta.yaml +++ b/recipes/bioconductor-cleaver/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "cleaver" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cd859842ff42dc19c2d4356fbb9f65f9 + md5: 978f7bba3eb0dae3a3edee5c5721de7b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cleaver", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown, BRAIN, UniProt.ws (>= 2.36.5) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-clevrvis/meta.yaml b/recipes/bioconductor-clevrvis/meta.yaml index 09cd3712f83bb..4cbdb433898df 100644 --- a/recipes/bioconductor-clevrvis/meta.yaml +++ b/recipes/bioconductor-clevrvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "clevRvis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43c9647c43af55cee12813e91c37f569 + md5: 96fde7a442a2cdb69754ebf1e68ccc65 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clevrvis", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: diff --git a/recipes/bioconductor-clippda/meta.yaml b/recipes/bioconductor-clippda/meta.yaml index ee2060d37cffa..4aea5febf6e97 100644 --- a/recipes/bioconductor-clippda/meta.yaml +++ b/recipes/bioconductor-clippda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "clippda" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f31b017726d6b75db0537ae313adc135 + md5: d416c567cfb3615472045bc57c2bce72 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clippda", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-lattice - r-rgl - r-scatterplot3d - r-statmod run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-lattice - r-rgl diff --git a/recipes/bioconductor-clipper/meta.yaml b/recipes/bioconductor-clipper/meta.yaml index d0e6246555f54..63e140182b6f3 100644 --- a/recipes/bioconductor-clipper/meta.yaml +++ b/recipes/bioconductor-clipper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "clipper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 421940d057355924606d4cfe710237d0 + md5: 551f3c6ad3a56f2a70439f48a4aef431 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clipper", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-qpgraph >=2.34.0,<2.35.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-qpgraph >=2.36.0,<2.37.0' - r-base - r-corpcor - 'r-grbase >=1.6.6' @@ -34,11 +34,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-qpgraph >=2.34.0,<2.35.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-qpgraph >=2.36.0,<2.37.0' - r-base - r-corpcor - 'r-grbase >=1.6.6' diff --git a/recipes/bioconductor-cliprofiler/meta.yaml b/recipes/bioconductor-cliprofiler/meta.yaml index a7a37aff8423f..c0910f32ab09f 100644 --- a/recipes/bioconductor-cliprofiler/meta.yaml +++ b/recipes/bioconductor-cliprofiler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "cliProfiler" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54bce2fd9a5c5b30887a3139c0c50301 + md5: 10a33ec5af89503fcb12a8142ec966f8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cliprofiler", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ggplot2 run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-cliquems/meta.yaml b/recipes/bioconductor-cliquems/meta.yaml index a7e4df20a8ce3..0c96850839c51 100644 --- a/recipes/bioconductor-cliquems/meta.yaml +++ b/recipes/bioconductor-cliquems/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.13.0" %} +{% set version = "1.16.0" %} {% set name = "cliqueMS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 21a77001912e964b72c091a32961b42b + md5: f423e41dd4ca04cefe4bd5be77ceec3a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cliquems", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, CAMERA # SystemRequirements: C++11 requirements: host: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-bh - r-igraph @@ -33,8 +34,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-bh - r-igraph diff --git a/recipes/bioconductor-cll/meta.yaml b/recipes/bioconductor-cll/meta.yaml index e87436e996e9b..dfeb4ff22d3ea 100644 --- a/recipes/bioconductor-cll/meta.yaml +++ b/recipes/bioconductor-cll/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "CLL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af6541d53d8bb71eb10e661c0a6efde0 + md5: 4f71fa48ba2205b80c098275c866ac1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cll", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cll/post-link.sh b/recipes/bioconductor-cll/post-link.sh index 253975f1a9713..bfc51d8a40c4f 100644 --- a/recipes/bioconductor-cll/post-link.sh +++ b/recipes/bioconductor-cll/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cll-1.40.0" +installBiocDataPackage.sh "cll-1.42.0" diff --git a/recipes/bioconductor-cllmethylation/meta.yaml b/recipes/bioconductor-cllmethylation/meta.yaml index 30437c33b2d02..1ed25ff3378d0 100644 --- a/recipes/bioconductor-cllmethylation/meta.yaml +++ b/recipes/bioconductor-cllmethylation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CLLmethylation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e3304bdcdaa207660d51a29e1ad2a4c6 + md5: a8c3768dca1df5bb9e911878b68ad4c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cllmethylation", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, ggplot2, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cllmethylation/post-link.sh b/recipes/bioconductor-cllmethylation/post-link.sh index e74887d8fb150..24af32275232b 100644 --- a/recipes/bioconductor-cllmethylation/post-link.sh +++ b/recipes/bioconductor-cllmethylation/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cllmethylation-1.20.0" +installBiocDataPackage.sh "cllmethylation-1.22.0" diff --git a/recipes/bioconductor-clomial/meta.yaml b/recipes/bioconductor-clomial/meta.yaml index 966b40e4e4735..280429af62f00 100644 --- a/recipes/bioconductor-clomial/meta.yaml +++ b/recipes/bioconductor-clomial/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "Clomial" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3b126ecc8f8786eeb190d8a150326562 + md5: 71e609b1bef40cdadcd812f99a5956e8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clomial", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-clst/meta.yaml b/recipes/bioconductor-clst/meta.yaml index 6a88fe2a497e7..40c671b879c52 100644 --- a/recipes/bioconductor-clst/meta.yaml +++ b/recipes/bioconductor-clst/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "clst" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b9c002ff0d92c15fef6fc5abd3c76789 + md5: 5988cf1c0b5207d2f78f75dbe6f2b467 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clst", max_pin="x.x") }}' noarch: generic # Suggests: RUnit requirements: host: - - 'bioconductor-roc >=1.76.0,<1.77.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' - r-base - r-lattice run: - - 'bioconductor-roc >=1.76.0,<1.77.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' - r-base - r-lattice test: diff --git a/recipes/bioconductor-clstutils/meta.yaml b/recipes/bioconductor-clstutils/meta.yaml index c38910cfda1f3..fbd9437560808 100644 --- a/recipes/bioconductor-clstutils/meta.yaml +++ b/recipes/bioconductor-clstutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "clstutils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 40f1c145c0d85feb28a7935705b389fb + md5: 4343490b2b05bf2e4429f2081b3a82c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clstutils", max_pin="x.x") }}' noarch: generic # Suggests: RUnit requirements: host: - - 'bioconductor-clst >=1.48.0,<1.49.0' + - 'bioconductor-clst >=1.50.0,<1.51.0' - r-ape - r-base - r-lattice - r-rjson - r-rsqlite run: - - 'bioconductor-clst >=1.48.0,<1.49.0' + - 'bioconductor-clst >=1.50.0,<1.51.0' - r-ape - r-base - r-lattice diff --git a/recipes/bioconductor-clumsid/meta.yaml b/recipes/bioconductor-clumsid/meta.yaml index 49ee2d606b139..f845097e08a5c 100644 --- a/recipes/bioconductor-clumsid/meta.yaml +++ b/recipes/bioconductor-clumsid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "CluMSID" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b38aa0e170c6aff41ab31e3bcb47ed7 + md5: 0f441929cf30f7ab6c9a035023ef3a20 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clumsid", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr, CluMSIDdata, metaMS, metaMSdata, xcms requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-ape - r-base - r-dbscan @@ -36,10 +37,10 @@ requirements: - r-rcolorbrewer - r-sna run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-ape - r-base - r-dbscan diff --git a/recipes/bioconductor-clumsiddata/meta.yaml b/recipes/bioconductor-clumsiddata/meta.yaml index 2176b782a6929..ea06ae2fe5f88 100644 --- a/recipes/bioconductor-clumsiddata/meta.yaml +++ b/recipes/bioconductor-clumsiddata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "CluMSIDdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f97c24b60d106fe1285496ace8fad79 + md5: 315da29d9f052e0abfbad59be9606f34 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clumsiddata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clumsiddata/post-link.sh b/recipes/bioconductor-clumsiddata/post-link.sh index 13dcc91868f79..2e82be8661106 100644 --- a/recipes/bioconductor-clumsiddata/post-link.sh +++ b/recipes/bioconductor-clumsiddata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "clumsiddata-1.16.0" +installBiocDataPackage.sh "clumsiddata-1.18.0" diff --git a/recipes/bioconductor-clustcomp/meta.yaml b/recipes/bioconductor-clustcomp/meta.yaml index bf6927af6b6c4..b3fc8f1f502a3 100644 --- a/recipes/bioconductor-clustcomp/meta.yaml +++ b/recipes/bioconductor-clustcomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "clustComp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d1d219e2545f57d1d323e65497c50ea + md5: c1783d91366b98b4afbe0b0acc49c452 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clustcomp", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, colonCA, RUnit, BiocGenerics requirements: diff --git a/recipes/bioconductor-clusterexperiment/meta.yaml b/recipes/bioconductor-clusterexperiment/meta.yaml index 8490b0476dbcc..82eb2c72a6339 100644 --- a/recipes/bioconductor-clusterexperiment/meta.yaml +++ b/recipes/bioconductor-clusterexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "clusterExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7f32e3bf65cc1997b021722429f34700 + md5: 0a4bac02f2b310d941afe62b329e7eee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clusterexperiment", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mbkmeans >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zinbwave >=1.22.0,<1.23.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mbkmeans >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zinbwave >=1.24.0,<1.25.0' - 'r-ape >=5.0' - r-base - r-cluster @@ -49,17 +50,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mbkmeans >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zinbwave >=1.22.0,<1.23.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mbkmeans >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zinbwave >=1.24.0,<1.25.0' - 'r-ape >=5.0' - r-base - r-cluster diff --git a/recipes/bioconductor-clusterjudge/meta.yaml b/recipes/bioconductor-clusterjudge/meta.yaml index 5ce838aabca2c..6b919674df414 100644 --- a/recipes/bioconductor-clusterjudge/meta.yaml +++ b/recipes/bioconductor-clusterjudge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "ClusterJudge" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 56ecef405e11e333d5c93fe785ba3c8e + md5: 1f1db5b57d83f67f60de690e6f224bde build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clusterjudge", max_pin="x.x") }}' noarch: generic # Suggests: yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt requirements: diff --git a/recipes/bioconductor-clusterprofiler/meta.yaml b/recipes/bioconductor-clusterprofiler/meta.yaml index fdae3be5aa869..f55cd8017a8be 100644 --- a/recipes/bioconductor-clusterprofiler/meta.yaml +++ b/recipes/bioconductor-clusterprofiler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.8.1" %} +{% set version = "4.10.0" %} {% set name = "clusterProfiler" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,47 +11,52 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ad792319e54d0f39cd6caff54dc1021 + md5: 6eb1c0888849211e04896b3431460048 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clusterprofiler", max_pin="x.x") }}' noarch: generic -# Suggests: AnnotationHub, knitr, rmarkdown, org.Hs.eg.db, prettydoc, ReactomePA, testthat +# Suggests: AnnotationHub, knitr, jsonlite, readr, rmarkdown, org.Hs.eg.db, prettydoc, BiocManager, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-downloader - r-dplyr - 'r-gson >=0.0.7' + - r-httr + - r-igraph - r-magrittr - r-plyr - r-rlang - r-tidyr - - r-yulab.utils + - 'r-yulab.utils >=0.0.7' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-downloader - r-dplyr - 'r-gson >=0.0.7' + - r-httr + - r-igraph - r-magrittr - r-plyr - r-rlang - r-tidyr - - r-yulab.utils + - 'r-yulab.utils >=0.0.7' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clusterseq/build.sh b/recipes/bioconductor-clusterseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-clusterseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clusterseq/meta.yaml b/recipes/bioconductor-clusterseq/meta.yaml new file mode 100644 index 0000000000000..89f709b6c7c02 --- /dev/null +++ b/recipes/bioconductor-clusterseq/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.26.0" %} +{% set name = "clusterSeq" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c0f51fc6b851b707de4f53107c6179f5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clusterseq", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle +requirements: + host: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - r-base + run: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Clustering of high-throughput sequencing data by identifying co-expression patterns' + description: 'Identification of clusters of co-expressed genes based on their expression across multiple (replicated) biological samples.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-clustersignificance/meta.yaml b/recipes/bioconductor-clustersignificance/meta.yaml index 578873112c4d8..452ee4190c486 100644 --- a/recipes/bioconductor-clustersignificance/meta.yaml +++ b/recipes/bioconductor-clustersignificance/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "ClusterSignificance" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e2c35b077596b2fe12be5c9baff99047 + md5: 46f8a23ba4910712f2c65ebbb151ad4f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clustersignificance", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr requirements: diff --git a/recipes/bioconductor-clusterstab/meta.yaml b/recipes/bioconductor-clusterstab/meta.yaml index ac9e1a16e147f..0f20cc38a7835 100644 --- a/recipes/bioconductor-clusterstab/meta.yaml +++ b/recipes/bioconductor-clusterstab/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "clusterStab" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 42577966d771992cbafdf2efdcdda484 + md5: 87f3941fd121e6a60acdefd9a682ba9a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clusterstab", max_pin="x.x") }}' noarch: generic # Suggests: fibroEset, genefilter requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-clustifyr/meta.yaml b/recipes/bioconductor-clustifyr/meta.yaml index 8f891d05b5519..2cb67cd3a2219 100644 --- a/recipes/bioconductor-clustifyr/meta.yaml +++ b/recipes/bioconductor-clustifyr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "clustifyr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6744ece04f6b8aacaff4d235cdf1458b + md5: 5fc803262c7a3b4d11d464f30a110802 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clustifyr", max_pin="x.x") }}' noarch: generic -# Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, Seurat, gprofiler2, purrr +# Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, Seurat, gprofiler2, purrr, data.table, R.utils requirements: host: - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-dplyr @@ -34,17 +35,16 @@ requirements: - r-matrix - r-matrixstats - r-proxy - - r-readr - r-rlang - r-scales - r-stringr - r-tibble - r-tidyr run: - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-dplyr @@ -54,7 +54,6 @@ requirements: - r-matrix - r-matrixstats - r-proxy - - r-readr - r-rlang - r-scales - r-stringr diff --git a/recipes/bioconductor-clustifyrdatahub/meta.yaml b/recipes/bioconductor-clustifyrdatahub/meta.yaml index c271419be117c..c910400fc78c8 100644 --- a/recipes/bioconductor-clustifyrdatahub/meta.yaml +++ b/recipes/bioconductor-clustifyrdatahub/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "clustifyrdatahub" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d1345a885c1b770cd461cf3c69451b39 + md5: aac4529e5c0d71fdc49bda51c3915f61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clustifyrdatahub", max_pin="x.x") }}' noarch: generic # Suggests: clustifyr, Seurat, usethis, rmarkdown, knitr, tidyr, BiocStyle requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clustifyrdatahub/post-link.sh b/recipes/bioconductor-clustifyrdatahub/post-link.sh index 6913cf66ffe04..312ed6f9276d2 100644 --- a/recipes/bioconductor-clustifyrdatahub/post-link.sh +++ b/recipes/bioconductor-clustifyrdatahub/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "clustifyrdatahub-1.10.0" +installBiocDataPackage.sh "clustifyrdatahub-1.12.0" diff --git a/recipes/bioconductor-clustirr/build.sh b/recipes/bioconductor-clustirr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-clustirr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clustirr/meta.yaml b/recipes/bioconductor-clustirr/meta.yaml new file mode 100644 index 0000000000000..58ca1182b4301 --- /dev/null +++ b/recipes/bioconductor-clustirr/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "ClustIRR" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ffd1884844b297c2e593e465a776fb6d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clustirr", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, testthat, ggplot2, patchwork, ggrepel +requirements: + host: + - r-base + - r-future + - r-future.apply + - r-igraph + - r-stringdist + - r-visnetwork + run: + - r-base + - r-future + - r-future.apply + - r-igraph + - r-stringdist + - r-visnetwork +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'Clustering of immune receptor repertoires' + description: 'ClustIRR is a quantitative method for clustering of immune receptor repertoires (IRRs). The algorithm identifies groups of T or B cell receptors (TCRs or BCRs) with similar specificity by comparing their sequences. ClustIRR uses graphs to visualize the specificity structures of IRRs.' + license_file: LICENSE + diff --git a/recipes/bioconductor-cma/meta.yaml b/recipes/bioconductor-cma/meta.yaml index 7cf5de809d7e7..7dcc40d917ad9 100644 --- a/recipes/bioconductor-cma/meta.yaml +++ b/recipes/bioconductor-cma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "CMA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d7b22a1bca581dca052746c3049d15b7 + md5: 6654a3ef8f06edc618b81b8a059b2139 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cma", max_pin="x.x") }}' noarch: generic # Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-cmap/meta.yaml b/recipes/bioconductor-cmap/meta.yaml index 007b0c087943c..d9037cbfaab0a 100644 --- a/recipes/bioconductor-cmap/meta.yaml +++ b/recipes/bioconductor-cmap/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.15.1" %} {% set name = "cMAP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: dbf8df4d4540151936884e1c5d747bcf build: - number: 14 + number: 15 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cmap", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cmap2data/meta.yaml b/recipes/bioconductor-cmap2data/meta.yaml index f8cd0f45b31df..7b58d905ef119 100644 --- a/recipes/bioconductor-cmap2data/meta.yaml +++ b/recipes/bioconductor-cmap2data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "cMap2data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dd007c68b5fd75539c62081497ab1ee5 + md5: c5ecbc59a690426c6def7feb720e1a7d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cmap2data", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cmap2data/post-link.sh b/recipes/bioconductor-cmap2data/post-link.sh index 679c3f090733e..ca70907c04096 100644 --- a/recipes/bioconductor-cmap2data/post-link.sh +++ b/recipes/bioconductor-cmap2data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cmap2data-1.36.0" +installBiocDataPackage.sh "cmap2data-1.38.0" diff --git a/recipes/bioconductor-cmapr/meta.yaml b/recipes/bioconductor-cmapr/meta.yaml index 3b0121b7fb521..03a057ffbe9ef 100644 --- a/recipes/bioconductor-cmapr/meta.yaml +++ b/recipes/bioconductor-cmapr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "cmapR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de47953e61c6df4cd2db9d5551cdcffc + md5: 257c275c11341cac65aae8f0d8cd4e2f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cmapr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-matrixstats run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-matrixstats diff --git a/recipes/bioconductor-cn.farms/meta.yaml b/recipes/bioconductor-cn.farms/meta.yaml index 3e4bdcf6ffbda..43f61d3317be2 100644 --- a/recipes/bioconductor-cn.farms/meta.yaml +++ b/recipes/bioconductor-cn.farms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "cn.farms" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c8dbca1cbb703358e3e24c5fe1d63ee1 + md5: 8a991cf7fb9deb2d6ed855617dcfb853 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cn.farms", max_pin="x.x") }}' # Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, pd.genomewidesnp.6 requirements: host: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dbi - r-ff @@ -34,12 +35,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dbi - r-ff diff --git a/recipes/bioconductor-cn.mops/meta.yaml b/recipes/bioconductor-cn.mops/meta.yaml index 12f2094e41535..d923f5f26fc2d 100644 --- a/recipes/bioconductor-cn.mops/meta.yaml +++ b/recipes/bioconductor-cn.mops/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "cn.mops" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 76e3ef5df3615011d3ba8fbf432ee0d0 + md5: e4e51a7ecd3810464be443ba9a6b6919 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cn.mops", max_pin="x.x") }}' # Suggests: DNAcopy requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-exomecopy >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-exomecopy >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-exomecopy >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-exomecopy >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-cnanorm/meta.yaml b/recipes/bioconductor-cnanorm/meta.yaml index bf9abd406114f..0c80a7be46633 100644 --- a/recipes/bioconductor-cnanorm/meta.yaml +++ b/recipes/bioconductor-cnanorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.1" %} +{% set version = "1.48.0" %} {% set name = "CNAnorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 77feee7f1c624b8b4e380198d923e23c + md5: b9d0f995f3466875285a152415863842 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnanorm", max_pin="x.x") }}' requirements: host: - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - r-base - libblas - liblapack run: - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-cner/meta.yaml b/recipes/bioconductor-cner/meta.yaml index 5363c676fcf79..107812a815c75 100644 --- a/recipes/bioconductor-cner/meta.yaml +++ b/recipes/bioconductor-cner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "CNEr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2382aa80af28d00b3f990268bf61bfbf + md5: 56fdc5f3323b1f3efbb8d85584ff75d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cner", max_pin="x.x") }}' # Suggests: Gviz (>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Ggallus.UCSC.galGal3 requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-dbi >=0.7' - 'r-ggplot2 >=2.1.0' @@ -43,18 +44,18 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-dbi >=0.7' - 'r-ggplot2 >=2.1.0' diff --git a/recipes/bioconductor-cnordt/meta.yaml b/recipes/bioconductor-cnordt/meta.yaml index 6259262861c0d..b6ac951b76ba2 100644 --- a/recipes/bioconductor-cnordt/meta.yaml +++ b/recipes/bioconductor-cnordt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "CNORdt" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bd2389f6b262b0bf323ca0e49a20d3f4 + md5: 74b0c2783638f7d5ce872577eb305ad3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnordt", max_pin="x.x") }}' requirements: host: - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' - r-abind - r-base - libblas - liblapack run: - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' - r-abind - r-base build: diff --git a/recipes/bioconductor-cnorfeeder/meta.yaml b/recipes/bioconductor-cnorfeeder/meta.yaml index 3c97382193da2..5e8b159d1d8a6 100644 --- a/recipes/bioconductor-cnorfeeder/meta.yaml +++ b/recipes/bioconductor-cnorfeeder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "CNORfeeder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ba673e6af1ed038b14678843be82304 + md5: 4dd8271e71505e41edc9509155cb4f9f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnorfeeder", max_pin="x.x") }}' noarch: generic # Suggests: minet, Rgraphviz, RUnit, BiocGenerics, igraph requirements: host: - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base test: commands: diff --git a/recipes/bioconductor-cnorfuzzy/meta.yaml b/recipes/bioconductor-cnorfuzzy/meta.yaml index 3d5879dc204ed..7343bc5ed0dea 100644 --- a/recipes/bioconductor-cnorfuzzy/meta.yaml +++ b/recipes/bioconductor-cnorfuzzy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "CNORfuzzy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c018031c48dc484ad32838a281083afe + md5: c7d388f25498f45c39d8af83c5e14a89 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnorfuzzy", max_pin="x.x") }}' # Suggests: xtable, Rgraphviz, RUnit, BiocGenerics requirements: host: - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' - r-base - 'r-nloptr >=0.8.5' - libblas - liblapack run: - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' - r-base - 'r-nloptr >=0.8.5' build: diff --git a/recipes/bioconductor-cnorode/meta.yaml b/recipes/bioconductor-cnorode/meta.yaml index 4f2da296035a0..7e2f238c23ba1 100644 --- a/recipes/bioconductor-cnorode/meta.yaml +++ b/recipes/bioconductor-cnorode/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "CNORode" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f7b31713feb3c910b5bd09e105cb0a5d + md5: e93b3e3437c26f6cfab6690f78c6a6cc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnorode", max_pin="x.x") }}' requirements: host: - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' - r-base - r-genalg - r-knitr - libblas - liblapack run: - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' - r-base - r-genalg - r-knitr diff --git a/recipes/bioconductor-cntools/meta.yaml b/recipes/bioconductor-cntools/meta.yaml index 436548a21c867..f19724490eaa7 100644 --- a/recipes/bioconductor-cntools/meta.yaml +++ b/recipes/bioconductor-cntools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "CNTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f8beb8f9bd3721c978cb42536062279 + md5: e3ce148937711a84dadf67b5f09c5373 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cntools", max_pin="x.x") }}' requirements: host: - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - r-base - libblas - liblapack run: - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-cnvfilter/meta.yaml b/recipes/bioconductor-cnvfilter/meta.yaml index 04e1f13b266fe..3908bc6abda4c 100644 --- a/recipes/bioconductor-cnvfilter/meta.yaml +++ b/recipes/bioconductor-cnvfilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "CNVfilteR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fba99dc7e437235fee4a92960716f34f + md5: dda71463a83db8c7aaf1bbfa79424ba3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnvfilter", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown +# Suggests: knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-copynumberplots >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-karyoploter >=1.26.0,<1.27.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-copynumberplots >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-karyoploter >=1.28.0,<1.29.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-assertthat - r-base - r-pracma run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-copynumberplots >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-karyoploter >=1.26.0,<1.27.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-copynumberplots >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-karyoploter >=1.28.0,<1.29.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-assertthat - r-base - r-pracma diff --git a/recipes/bioconductor-cnvgsa/meta.yaml b/recipes/bioconductor-cnvgsa/meta.yaml index b7846884afed1..b0cf597118eb0 100644 --- a/recipes/bioconductor-cnvgsa/meta.yaml +++ b/recipes/bioconductor-cnvgsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "cnvGSA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f98d6c70fbf31cfb8cd3282cabffce4f + md5: b3216442e27ff2c602e908aeb6a6f6e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnvgsa", max_pin="x.x") }}' noarch: generic # Suggests: cnvGSAdata, org.Hs.eg.db requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-brglm - r-doparallel - r-foreach - r-splitstackshape run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-brglm - r-doparallel diff --git a/recipes/bioconductor-cnvgsadata/meta.yaml b/recipes/bioconductor-cnvgsadata/meta.yaml index 2cd90be972d1f..cea79ff073286 100644 --- a/recipes/bioconductor-cnvgsadata/meta.yaml +++ b/recipes/bioconductor-cnvgsadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "cnvGSAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 706bef72dd4c818adc1295a3f93bd2cf + md5: 1cc86a2066cae55493d710c475cc7112 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnvgsadata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-cnvgsa >=1.44.0,<1.45.0' + - 'bioconductor-cnvgsa >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-cnvgsa >=1.44.0,<1.45.0' + - 'bioconductor-cnvgsa >=1.46.0,<1.47.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cnvgsadata/post-link.sh b/recipes/bioconductor-cnvgsadata/post-link.sh index c07e462f3f5e4..068b0cb6fee2b 100644 --- a/recipes/bioconductor-cnvgsadata/post-link.sh +++ b/recipes/bioconductor-cnvgsadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cnvgsadata-1.36.0" +installBiocDataPackage.sh "cnvgsadata-1.38.0" diff --git a/recipes/bioconductor-cnviz/meta.yaml b/recipes/bioconductor-cnviz/meta.yaml index 30708fe0762b3..000ef56911ecf 100644 --- a/recipes/bioconductor-cnviz/meta.yaml +++ b/recipes/bioconductor-cnviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "CNViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f269c211d1f940ae3e019441ca4ec85 + md5: e0499b53c29869a1f661e40f4e1f76ca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnviz", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr requirements: host: - - 'bioconductor-copynumberplots >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-karyoploter >=1.26.0,<1.27.0' + - 'bioconductor-copynumberplots >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-karyoploter >=1.28.0,<1.29.0' - r-base - r-dplyr - r-dt @@ -32,9 +33,9 @@ requirements: - r-scales - 'r-shiny >=1.5.0' run: - - 'bioconductor-copynumberplots >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-karyoploter >=1.26.0,<1.27.0' + - 'bioconductor-copynumberplots >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-karyoploter >=1.28.0,<1.29.0' - r-base - r-dplyr - r-dt diff --git a/recipes/bioconductor-cnvmetrics/meta.yaml b/recipes/bioconductor-cnvmetrics/meta.yaml index 7b477048e9c84..5a6a3e47ff376 100644 --- a/recipes/bioconductor-cnvmetrics/meta.yaml +++ b/recipes/bioconductor-cnvmetrics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "CNVMetrics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d745a88974ac4ec80fced32581c02fe + md5: ebb4f847744aaddcc125d870b1a67154 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnvmetrics", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-gridextra - r-magrittr - r-pheatmap + - r-rbeta2009 run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-gridextra - r-magrittr - r-pheatmap + - r-rbeta2009 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cnvpanelizer/meta.yaml b/recipes/bioconductor-cnvpanelizer/meta.yaml index abc49fe1ceaeb..3af7fd5235897 100644 --- a/recipes/bioconductor-cnvpanelizer/meta.yaml +++ b/recipes/bioconductor-cnvpanelizer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "CNVPanelizer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bc8f796d0a9a70d1047059939acaef89 + md5: 1d984f2fa3f3db99f3ccf72b5c9a0890 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnvpanelizer", max_pin="x.x") }}' noarch: generic # Suggests: knitr, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-exomecopy >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-noiseq >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-exomecopy >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-noiseq >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-foreach - r-ggplot2 @@ -42,14 +43,14 @@ requirements: - r-stringr - r-testthat run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-exomecopy >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-noiseq >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-exomecopy >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-noiseq >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-foreach - r-ggplot2 diff --git a/recipes/bioconductor-cnvranger/meta.yaml b/recipes/bioconductor-cnvranger/meta.yaml index 816e951bed0f6..cba6dd7a6a6ec 100644 --- a/recipes/bioconductor-cnvranger/meta.yaml +++ b/recipes/bioconductor-cnvranger/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.4" %} +{% set version = "1.18.0" %} {% set name = "CNVRanger" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fba593b7facaf4bad0bbd16b64b41830 + md5: 3e68952c47447dfad311d1adf7b971d1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnvranger", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment, TCGAutils, TxDb.Hsapiens.UCSC.hg19.knownGene, curatedTCGAData, ensembldb, grid, knitr, org.Hs.eg.db, regioneR, rmarkdown, statmod requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gdsarray >=1.20.0,<1.21.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gdsarray >=1.22.0,<1.23.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-lattice @@ -42,19 +43,19 @@ requirements: - r-rappdirs - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gdsarray >=1.20.0,<1.21.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gdsarray >=1.22.0,<1.23.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-lattice diff --git a/recipes/bioconductor-cnvrd2/meta.yaml b/recipes/bioconductor-cnvrd2/meta.yaml index 60e0572097bea..85d6f7fae13aa 100644 --- a/recipes/bioconductor-cnvrd2/meta.yaml +++ b/recipes/bioconductor-cnvrd2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "CNVrd2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e8eafc38f592bd7322d9f4e8fd12a598 + md5: 9cc2c933a0a521472b5eb6f1382cefd5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnvrd2", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggplot2 - r-gridextra - r-rjags run: - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggplot2 - r-gridextra diff --git a/recipes/bioconductor-cocitestats/meta.yaml b/recipes/bioconductor-cocitestats/meta.yaml index 26df6d2a2141c..5c72102058add 100644 --- a/recipes/bioconductor-cocitestats/meta.yaml +++ b/recipes/bioconductor-cocitestats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "CoCiteStats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2129b78957087707546562a0934e738a + md5: de358f1bd9429dbedc2e7bc91037373a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cocitestats", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base test: commands: diff --git a/recipes/bioconductor-cocoa/build_failure.linux-64.yaml b/recipes/bioconductor-cocoa/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..65ed04bfcc672 --- /dev/null +++ b/recipes/bioconductor-cocoa/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: dd85fa037d453102ef61e3f47e51564c9d31f479966d88c0b89e752d33f8ea37 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + bioconda/noarch 100% + pkgs/main/linux-64 + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gbioconda/noarch + [] 1.5s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/linux-64 100% + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/linux-64 + [] 1.6s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/noarch + [] 1.7s + conda-forge/linux-64 + conda-forge/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.8s + conda-forge/linux-64 + conda-forge/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.9s + conda-forge/linux-64 + conda-forge/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 2.0s + conda-forge/linux-64 + conda-forge/noarch 100% + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 2.1s + conda-forge/linux-64 + conda-forge/noarch 100% + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gconda-forge/noarch + [] 2.2s + conda-forge/linux-64 + pkgs/r/linux-64 + pkgs/r/noarch 100%[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/r/noarch + pkgs/r/linux-64 + [] 2.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.9s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.9s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.9s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.0s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.1s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.2s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.3s + [2K[1A[2K[0Gconda-forge/linux-64 + [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.2MB/s 0.0s + opt/conda/conda-bld/noarch 1.1kB @ 22.3MB/s 0.0s + [?25hTraceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3089, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2879, in test + environ.create_env(metadata.config.test_prefix, actions, config=metadata.config, + File "/opt/conda/lib/python3.8/site-packages/conda_build/environ.py", line 1052, in create_env + display_actions(actions, index) + File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in display_actions + actions['LINK'] = [index[d] for d in actions['LINK']] + File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in + actions['LINK'] = [index[d] for d in actions['LINK']] + KeyError: Dist(channel='conda-forge', dist_name='python-3.12.1-hab00c5b_0_cpython', name='python', fmt='.conda', version='3.12.1', build_string='hab00c5b_0_cpython', build_number=0, base_url=None, platform=None) +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-cocoa/meta.yaml b/recipes/bioconductor-cocoa/meta.yaml index 2da84c65e4b84..6a4528f450642 100644 --- a/recipes/bioconductor-cocoa/meta.yaml +++ b/recipes/bioconductor-cocoa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "COCOA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 528e8eb1e1a358866292395b64570c61 + md5: 6525a033b4b6ab78aa4ecb8e3f35b6e3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cocoa", max_pin="x.x") }}' noarch: generic # Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mira >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mira >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-fitdistrplus @@ -35,13 +36,13 @@ requirements: - r-simplecache - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mira >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mira >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-fitdistrplus diff --git a/recipes/bioconductor-codelink/meta.yaml b/recipes/bioconductor-codelink/meta.yaml index c83b6b10126cb..5aa4146f8d961 100644 --- a/recipes/bioconductor-codelink/meta.yaml +++ b/recipes/bioconductor-codelink/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.0" %} {% set name = "codelink" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 35d35231bf21b1815e02271098872c05 + md5: 7988c997146174710b5faacc70c10328 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-codelink", max_pin="x.x") }}' noarch: generic # Suggests: genefilter, parallel, knitr requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-codex/meta.yaml b/recipes/bioconductor-codex/meta.yaml index dd3350d1a11ec..0b4bb41c7a4db 100644 --- a/recipes/bioconductor-codex/meta.yaml +++ b/recipes/bioconductor-codex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "CODEX" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee6fc5514b4d8982f0d639c34c589b9f + md5: 5b1f67c5fbf4bbe4a3ee4f6da956a886 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-codex", max_pin="x.x") }}' noarch: generic # Suggests: WES.1KG.WUGSC requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-cogaps/meta.yaml b/recipes/bioconductor-cogaps/meta.yaml index f8b21e0ae36c9..c891b02938f1c 100644 --- a/recipes/bioconductor-cogaps/meta.yaml +++ b/recipes/bioconductor-cogaps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.19.1" %} +{% set version = "3.22.0" %} {% set name = "CoGAPS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 22a7d6bb9033c0a2d4c1170856b87b06 + md5: d4c9ec9b2be6c77fbb47c632b62c84b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: testthat, knitr, rmarkdown, BiocStyle + run_exports: '{{ pin_subpackage("bioconductor-cogaps", max_pin="x.x") }}' +# Suggests: testthat, knitr, rmarkdown, BiocStyle, SeuratObject requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-cluster @@ -40,13 +41,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-cluster diff --git a/recipes/bioconductor-cogena/meta.yaml b/recipes/bioconductor-cogena/meta.yaml index e57e9a3bcf655..ea4472b90f122 100644 --- a/recipes/bioconductor-cogena/meta.yaml +++ b/recipes/bioconductor-cogena/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "cogena" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6d25c8d1515cc3b06d4337a28819ea16 + md5: 47a50e5f5d62a9b2f6fcd7bf3f5b9cc6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cogena", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown (>= 2.1) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-amap - r-apcluster - r-base @@ -43,7 +44,7 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-amap - r-apcluster - r-base diff --git a/recipes/bioconductor-cogeqc/meta.yaml b/recipes/bioconductor-cogeqc/meta.yaml index b39477688806a..49d2616f6027b 100644 --- a/recipes/bioconductor-cogeqc/meta.yaml +++ b/recipes/bioconductor-cogeqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "cogeqc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2a92798147ae38ee7e618149ffabcdf5 + md5: 751833fc95e416546193b021e0cbfc69 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cogeqc", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle, rmarkdown, covr # SystemRequirements: BUSCO (>= 5.1.3) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-base - r-ggbeeswarm - r-ggplot2 @@ -34,8 +35,8 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-base - r-ggbeeswarm - r-ggplot2 diff --git a/recipes/bioconductor-cogito/meta.yaml b/recipes/bioconductor-cogito/meta.yaml index c2faac70f8f75..85a806043f509 100644 --- a/recipes/bioconductor-cogito/meta.yaml +++ b/recipes/bioconductor-cogito/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "Cogito" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 436e9cbf49b6a9fbe470772048229db3 + md5: 934ceee8a56ab742bbf3c09af96cb2ba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cogito", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, markdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base - r-biocmanager @@ -35,11 +36,11 @@ requirements: - r-magrittr - r-rmarkdown run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base - r-biocmanager diff --git a/recipes/bioconductor-cogps/meta.yaml b/recipes/bioconductor-cogps/meta.yaml index cef7325cc9a13..558d1ed731974 100644 --- a/recipes/bioconductor-cogps/meta.yaml +++ b/recipes/bioconductor-cogps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "coGPS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2836cad04f3b94cbe305cacaaaee6570 + md5: a824d8a41fee47628eb7f369adef4a2c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cogps", max_pin="x.x") }}' noarch: generic # Suggests: limma requirements: diff --git a/recipes/bioconductor-cohcap/meta.yaml b/recipes/bioconductor-cohcap/meta.yaml index 56afd1c45e2a5..eaafa323c174f 100644 --- a/recipes/bioconductor-cohcap/meta.yaml +++ b/recipes/bioconductor-cohcap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "COHCAP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c6563694a4c95720c88bcc4df639f28 + md5: 6c7c601f8c8aee626d2fa1a6dd306dca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cohcap", max_pin="x.x") }}' # SystemRequirements: Perl requirements: host: - - 'bioconductor-cohcapanno >=1.36.0,<1.37.0' + - 'bioconductor-cohcapanno >=1.38.0,<1.39.0' - r-base - r-bh - r-gplots @@ -32,7 +33,7 @@ requirements: - liblapack - 'perl >=5.6.0' run: - - 'bioconductor-cohcapanno >=1.36.0,<1.37.0' + - 'bioconductor-cohcapanno >=1.38.0,<1.39.0' - r-base - r-bh - r-gplots diff --git a/recipes/bioconductor-cohcapanno/meta.yaml b/recipes/bioconductor-cohcapanno/meta.yaml index b42c2e9817598..4c64d0e2c842f 100644 --- a/recipes/bioconductor-cohcapanno/meta.yaml +++ b/recipes/bioconductor-cohcapanno/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "COHCAPanno" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d95f164282852d44cc982e461157b622 + md5: 78fd4891651a8a62779fe402a13ba6b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cohcapanno", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cohcapanno/post-link.sh b/recipes/bioconductor-cohcapanno/post-link.sh index 5ae5b6c9dbbe4..4b2b9b6c06bfa 100644 --- a/recipes/bioconductor-cohcapanno/post-link.sh +++ b/recipes/bioconductor-cohcapanno/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cohcapanno-1.36.0" +installBiocDataPackage.sh "cohcapanno-1.38.0" diff --git a/recipes/bioconductor-cola/meta.yaml b/recipes/bioconductor-cola/meta.yaml index 11f671e63f537..f5913bc74f273 100644 --- a/recipes/bioconductor-cola/meta.yaml +++ b/recipes/bioconductor-cola/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "cola" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 983ec7f83e64be0637f134ca3576c106 + md5: 57e054e12610fb8d62de83c22f6ed1de build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cola", max_pin="x.x") }}' # Suggests: genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE, AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree, dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot, flexclust, randomForest, e1071 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-base - r-brew - 'r-circlize >=0.4.7' @@ -51,9 +52,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-base - r-brew - 'r-circlize >=0.4.7' diff --git a/recipes/bioconductor-colonca/meta.yaml b/recipes/bioconductor-colonca/meta.yaml index 1a0fd696e7055..642bf020f6e11 100644 --- a/recipes/bioconductor-colonca/meta.yaml +++ b/recipes/bioconductor-colonca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "colonCA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 88a73e6339cf99f42858ddcb073c4e61 + md5: d12f03a7ded676f392dbbb26bbbef174 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-colonca", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-colonca/post-link.sh b/recipes/bioconductor-colonca/post-link.sh index ab2079c657c89..63e3e55b7a7a0 100644 --- a/recipes/bioconductor-colonca/post-link.sh +++ b/recipes/bioconductor-colonca/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "colonca-1.42.0" +installBiocDataPackage.sh "colonca-1.44.0" diff --git a/recipes/bioconductor-comapr/meta.yaml b/recipes/bioconductor-comapr/meta.yaml index a4f6549c9f2c1..130fa29cd2cd1 100644 --- a/recipes/bioconductor-comapr/meta.yaml +++ b/recipes/bioconductor-comapr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.1" %} {% set name = "comapr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eca7d37960ffea05ade6ed24636d08ff + md5: 64dbcfb7f563dc874dc327988ebf8c07 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-comapr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-dplyr @@ -43,13 +44,13 @@ requirements: - r-scales - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-dplyr diff --git a/recipes/bioconductor-combi/meta.yaml b/recipes/bioconductor-combi/meta.yaml index 7bccb67dc97cd..9998659a07a49 100644 --- a/recipes/bioconductor-combi/meta.yaml +++ b/recipes/bioconductor-combi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "combi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,43 +11,44 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2b81ee7cc0b92f982a363f54d42d62dd + md5: 6fe16559db40b31126eb543abf6819fa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-combi", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-alabama - r-base - r-bb - r-cobs - r-dbi - r-ggplot2 - - r-matrix + - 'r-matrix >=1.6.0' - r-nleqslv - r-reshape2 - r-tensor - r-vegan run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-alabama - r-base - r-bb - r-cobs - r-dbi - r-ggplot2 - - r-matrix + - 'r-matrix >=1.6.0' - r-nleqslv - r-reshape2 - r-tensor diff --git a/recipes/bioconductor-comet/meta.yaml b/recipes/bioconductor-comet/meta.yaml index 11290e90520bd..8ba6a888a5ef3 100644 --- a/recipes/bioconductor-comet/meta.yaml +++ b/recipes/bioconductor-comet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "coMET" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d1cbe82dc9eccd6c98d091a7c46516e0 + md5: 34ef806a15489ccd38abd9002fe075ed build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-comet", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, RUnit, BiocGenerics, showtext requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-corrplot - r-gridextra - r-hash - r-psych run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-corrplot - r-gridextra diff --git a/recipes/bioconductor-comethdmr/meta.yaml b/recipes/bioconductor-comethdmr/meta.yaml index 52616731a8f9d..710278af6f46a 100644 --- a/recipes/bioconductor-comethdmr/meta.yaml +++ b/recipes/bioconductor-comethdmr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "coMethDMR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 625273089317239e835e4d368f579230 + md5: 0a6229d90868a4a60eb0f72c4499d1fc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-comethdmr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, corrplot, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-lmertest run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-lmertest test: diff --git a/recipes/bioconductor-compass/meta.yaml b/recipes/bioconductor-compass/meta.yaml index 9919fb7c6de16..2948a0f2be468 100644 --- a/recipes/bioconductor-compass/meta.yaml +++ b/recipes/bioconductor-compass/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.1" %} +{% set version = "1.40.0" %} {% set name = "COMPASS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd27c24d1296f22f905ca0533581224a + md5: 6ab4a9ce40637244377f77b7baaecc38 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-compass", max_pin="x.x") }}' # Suggests: flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2, progress requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - r-abind - r-base - r-clue @@ -42,7 +43,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - r-abind - r-base - r-clue diff --git a/recipes/bioconductor-compcoder/meta.yaml b/recipes/bioconductor-compcoder/meta.yaml index 7c614b91c9c83..5cc77115da02b 100644 --- a/recipes/bioconductor-compcoder/meta.yaml +++ b/recipes/bioconductor-compcoder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.2" %} +{% set version = "1.38.0" %} {% set name = "compcodeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ceef6dc14644528d10b8b0549ddd8cdb + md5: b1ec77496e614cf3399843b8c34e6ab2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-compcoder", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, EBSeq, DESeq2 (>= 1.1.31), baySeq (>= 2.2.0), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), rmarkdown, phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva +# Suggests: BiocStyle, EBSeq, DESeq2 (>= 1.1.31), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva, tcltk requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-ape - r-base - r-catools @@ -37,13 +38,16 @@ requirements: - r-matrixstats - r-modeest - r-phylolm + - r-rmarkdown - r-rocr + - r-shiny + - r-shinydashboard - r-sm - r-stringr - r-vioplot run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-ape - r-base - r-catools @@ -58,7 +62,10 @@ requirements: - r-matrixstats - r-modeest - r-phylolm + - r-rmarkdown - r-rocr + - r-shiny + - r-shinydashboard - r-sm - r-stringr - r-vioplot diff --git a/recipes/bioconductor-compepitools/meta.yaml b/recipes/bioconductor-compepitools/meta.yaml index 10f4dce2ea032..df49a8380538b 100644 --- a/recipes/bioconductor-compepitools/meta.yaml +++ b/recipes/bioconductor-compepitools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.1" %} +{% set version = "1.36.0" %} {% set name = "compEpiTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4073e61c47740e5f0c48db76dfb4b91c + md5: 0ccd28b8de6020ae19f303fc7009ce19 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-compepitools", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-methylpipe >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-methylpipe >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-gplots run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-methylpipe >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-methylpipe >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-gplots test: diff --git a/recipes/bioconductor-complexheatmap/meta.yaml b/recipes/bioconductor-complexheatmap/meta.yaml index 24486629fc4bb..e97a5929f5d7d 100644 --- a/recipes/bioconductor-complexheatmap/meta.yaml +++ b/recipes/bioconductor-complexheatmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "ComplexHeatmap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 87feece17236af22e1d3ad35e3fb7efd + md5: f4f19a1339c99471cb23ffc4a7272881 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-complexheatmap", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff, fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12), gridGraphics, gplots, rmarkdown, Cairo, magick requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-circlize >=0.4.14' - r-clue @@ -36,7 +37,7 @@ requirements: - r-png - r-rcolorbrewer run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-circlize >=0.4.14' - r-clue diff --git a/recipes/bioconductor-compounddb/meta.yaml b/recipes/bioconductor-compounddb/meta.yaml index 71c955494be81..6c581d53b553f 100644 --- a/recipes/bioconductor-compounddb/meta.yaml +++ b/recipes/bioconductor-compounddb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "CompoundDb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 38742446decc04a230b9f43055145158 + md5: 7863bdbb64d2068c22225ece8ed5844c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-compounddb", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19), MsBackendMgf requirements: host: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-metabocoreutils >=1.8.0,<1.9.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base - r-dbi - r-dbplyr @@ -41,17 +42,17 @@ requirements: - r-tibble - r-xml2 run: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-metabocoreutils >=1.8.0,<1.9.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base - r-dbi - r-dbplyr diff --git a/recipes/bioconductor-compran/meta.yaml b/recipes/bioconductor-compran/meta.yaml index 1a13f4a07dfb8..487b8ff516290 100644 --- a/recipes/bioconductor-compran/meta.yaml +++ b/recipes/bioconductor-compran/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ComPrAn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 41183d8093e3f4a754c7eac6a666993e + md5: 24011dcffe9f6c7b22be8e2de0e855b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-compran", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-compspot/build.sh b/recipes/bioconductor-compspot/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-compspot/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-compspot/meta.yaml b/recipes/bioconductor-compspot/meta.yaml new file mode 100644 index 0000000000000..c735ad00891b4 --- /dev/null +++ b/recipes/bioconductor-compspot/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.0.0" %} +{% set name = "compSPOT" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7aa69c9c3ec0c008ad0fdfb4dbbcac57 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-compspot", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - r-base + - r-data.table + - r-ggplot2 + - r-ggpubr + - r-gridextra + - r-magrittr + - r-plotly + run: + - r-base + - r-data.table + - r-ggplot2 + - r-ggpubr + - r-gridextra + - r-magrittr + - r-plotly +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots' + description: 'Clonal cell groups share common mutations within cancer, precancer, and even clinically normal appearing tissues. The frequency and location of these mutations may predict prognosis and cancer risk. It has also been well established that certain genomic regions have increased sensitivity to acquiring mutations. Mutation-sensitive genomic regions may therefore serve as markers for predicting cancer risk. This package contains multiple functions to establish significantly mutated hotspots, compare hotspot mutation burden between samples, and perform exploratory data analysis of the correlation between hotspot mutation burden and personal risk factors for cancer, such as age, gender, and history of carcinogen exposure. This package allows users to identify robust genomic markers to help establish cancer risk.' + diff --git a/recipes/bioconductor-concordexr/meta.yaml b/recipes/bioconductor-concordexr/meta.yaml index 26925b4bf5159..16a7d13375823 100644 --- a/recipes/bioconductor-concordexr/meta.yaml +++ b/recipes/bioconductor-concordexr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "concordexR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a83636d355e3b226da6f6030c17d84d + md5: 5ffab81582264ccb300c9f937c698adf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-concordexr", max_pin="x.x") }}' noarch: generic # Suggests: BiocNeighbors, BiocStyle, bluster, covr, knitr, patchwork, rmarkdown, scater, TENxPBMCData, testthat (>= 3.0.0), vdiffr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - r-base - r-cli - r-ggplot2 @@ -31,8 +32,8 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - r-base - r-cli - r-ggplot2 diff --git a/recipes/bioconductor-condiments/build_failure.linux-64.yaml b/recipes/bioconductor-condiments/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..64bb7869e9bff --- /dev/null +++ b/recipes/bioconductor-condiments/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d70ad20d6aa8d5ec24cc58bdae0002e9ce657a5241a612189057a31a9a2b5902 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - bioconductor-distinct >=1.14.0,<1.15.0 + - r-ecume >=0.9.1 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-mgcv + - bioconductor-slingshot >=2.10.0,<2.11.0 + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - r-matrixstats + - r-base 4.3.* + - r-rann + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-distinct >=1.14.0,<1.15.0 + - + + Leaving build/test directories: + Work: + /opt/conda/conda-bld/work + Test: + /opt/conda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + Build: + source activate /opt/conda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - r-pbapply + - r-igraph + - r-magrittr + - r-dplyr >=1.0 + - bioconductor-trajectoryutils >=1.10.0,<1.11.0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 + - bioconductor-distinct >=1.14.0,<1.15.0 + - r-ecume >=0.9.1 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-mgcv + - bioconductor-slingshot >=2.10.0,<2.11.0 + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - r-matrixstats + - r-base 4.3.* + - r-rann + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-distinct >=1.14.0,<1.15.0 + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-distinct[version='>=1.14.0,<1.15.0']")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-condiments/meta.yaml b/recipes/bioconductor-condiments/meta.yaml index 752243104b7c8..c6cceadc411f7 100644 --- a/recipes/bioconductor-condiments/meta.yaml +++ b/recipes/bioconductor-condiments/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "condiments" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 34ccc7d55f139c0c225b31f5a4d6d54e + md5: 63b9756275a532e7d38c67402cef7efd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-condiments", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-distinct >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-slingshot >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-distinct >=1.14.0,<1.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-slingshot >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' - r-base - 'r-dplyr >=1.0' - 'r-ecume >=0.9.1' @@ -37,12 +38,12 @@ requirements: - r-pbapply - r-rann run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-distinct >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-slingshot >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-distinct >=1.14.0,<1.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-slingshot >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' - r-base - 'r-dplyr >=1.0' - 'r-ecume >=0.9.1' diff --git a/recipes/bioconductor-confess/meta.yaml b/recipes/bioconductor-confess/meta.yaml index bfc0aec5efc7d..6e7de11118b8b 100644 --- a/recipes/bioconductor-confess/meta.yaml +++ b/recipes/bioconductor-confess/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "CONFESS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7778073e6c190fe4ce709a28cd0c644e + md5: 67bd1d40551528aab55620fc0a619713 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-confess", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, CONFESSdata requirements: host: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowmeans >=1.60.0,<1.61.0' - - 'bioconductor-flowmerge >=2.48.0,<2.49.0' - - 'bioconductor-flowpeaks >=1.46.0,<1.47.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-samspectral >=1.54.0,<1.55.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowmeans >=1.62.0,<1.63.0' + - 'bioconductor-flowmerge >=2.50.0,<2.51.0' + - 'bioconductor-flowpeaks >=1.48.0,<1.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-samspectral >=1.56.0,<1.57.0' - r-base - r-changepoint - r-cluster @@ -49,14 +50,14 @@ requirements: - r-wavethresh - r-zoo run: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowmeans >=1.60.0,<1.61.0' - - 'bioconductor-flowmerge >=2.48.0,<2.49.0' - - 'bioconductor-flowpeaks >=1.46.0,<1.47.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-samspectral >=1.54.0,<1.55.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowmeans >=1.62.0,<1.63.0' + - 'bioconductor-flowmerge >=2.50.0,<2.51.0' + - 'bioconductor-flowpeaks >=1.48.0,<1.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-samspectral >=1.56.0,<1.57.0' - r-base - r-changepoint - r-cluster diff --git a/recipes/bioconductor-confessdata/meta.yaml b/recipes/bioconductor-confessdata/meta.yaml index 4d75f88da25a8..68d94dd254c3a 100644 --- a/recipes/bioconductor-confessdata/meta.yaml +++ b/recipes/bioconductor-confessdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "CONFESSdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dde8faa711c55ae0abd4a0b9f8132233 + md5: 07df3f8f783b3e734c4032b3f6ed61bd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-confessdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-confessdata/post-link.sh b/recipes/bioconductor-confessdata/post-link.sh index 83419aae9c66c..bd491dd59a8f3 100644 --- a/recipes/bioconductor-confessdata/post-link.sh +++ b/recipes/bioconductor-confessdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "confessdata-1.28.0" +installBiocDataPackage.sh "confessdata-1.30.0" diff --git a/recipes/bioconductor-connectivitymap/meta.yaml b/recipes/bioconductor-connectivitymap/meta.yaml index 792e086df1b38..ce2ee8169dab4 100644 --- a/recipes/bioconductor-connectivitymap/meta.yaml +++ b/recipes/bioconductor-connectivitymap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "ConnectivityMap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0c98c66f64c50f8ae262bccdd4cd0bae + md5: bac29780256afebfd49b90f268114eaf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-connectivitymap", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-connectivitymap/post-link.sh b/recipes/bioconductor-connectivitymap/post-link.sh index 937ed494e6c7c..6840e2570ebd7 100644 --- a/recipes/bioconductor-connectivitymap/post-link.sh +++ b/recipes/bioconductor-connectivitymap/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "connectivitymap-1.36.0" +installBiocDataPackage.sh "connectivitymap-1.38.0" diff --git a/recipes/bioconductor-consensus/meta.yaml b/recipes/bioconductor-consensus/meta.yaml index 5f5940f7ad49e..3cfdf91faedfc 100644 --- a/recipes/bioconductor-consensus/meta.yaml +++ b/recipes/bioconductor-consensus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "consensus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bd7bce9ef0825d845f3b7db038974ab7 + md5: f930fc9b058bce80ccbb112082cf3dc7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-consensus", max_pin="x.x") }}' noarch: generic # Suggests: knitr, RUnit, rmarkdown, BiocGenerics requirements: diff --git a/recipes/bioconductor-consensusclusterplus/meta.yaml b/recipes/bioconductor-consensusclusterplus/meta.yaml index e9500b459fbd0..03b92e32b0a1c 100644 --- a/recipes/bioconductor-consensusclusterplus/meta.yaml +++ b/recipes/bioconductor-consensusclusterplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "ConsensusClusterPlus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 56f8a569c9a014296b658e520f1993d2 + md5: 0943cc2a0d1dff314f384e65b8d71897 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-consensusclusterplus", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-all >=1.42.0,<1.43.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-all >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-cluster run: - - 'bioconductor-all >=1.42.0,<1.43.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-all >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-cluster test: diff --git a/recipes/bioconductor-consensusde/meta.yaml b/recipes/bioconductor-consensusde/meta.yaml index f31966944b1c0..303d9bae79e62 100644 --- a/recipes/bioconductor-consensusde/meta.yaml +++ b/recipes/bioconductor-consensusde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "consensusDE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,62 +11,63 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef7863253b783fe015aee65395b9c453 + md5: f4aedcdf9823551d0ea0cc2ae64ac475 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-consensusde", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-airway >=1.20.0,<1.21.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-airway >=1.22.0,<1.23.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' - r-base - r-data.table - r-dendextend - r-rcolorbrewer run: - - 'bioconductor-airway >=1.20.0,<1.21.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-airway >=1.22.0,<1.23.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' - r-base - r-data.table diff --git a/recipes/bioconductor-consensusov/meta.yaml b/recipes/bioconductor-consensusov/meta.yaml index ebb65e08d7703..10d4991a9294a 100644 --- a/recipes/bioconductor-consensusov/meta.yaml +++ b/recipes/bioconductor-consensusov/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "consensusOV" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd71f79b5fac603f87f16319580f65ff + md5: 54a03e3c6775a27643ffbf5192967ac2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-consensusov", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, ggplot2, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefu >=2.32.0,<2.33.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefu >=2.34.0,<2.35.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-gdata - r-matrixstats - r-randomforest run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefu >=2.32.0,<2.33.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefu >=2.34.0,<2.35.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-gdata - r-matrixstats diff --git a/recipes/bioconductor-consensusseeker/meta.yaml b/recipes/bioconductor-consensusseeker/meta.yaml index b9a4044f33479..55d0281d77d27 100644 --- a/recipes/bioconductor-consensusseeker/meta.yaml +++ b/recipes/bioconductor-consensusseeker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "consensusSeekeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 60e0fda93cad54f7882cba52186783eb + md5: e752cec43fa487cd071a27a1f955b17e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-consensusseeker", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, ggplot2, knitr, rmarkdown, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-stringr test: diff --git a/recipes/bioconductor-consica/meta.yaml b/recipes/bioconductor-consica/meta.yaml index 1f06a4b25d807..cfe5f1bd4e8c0 100644 --- a/recipes/bioconductor-consica/meta.yaml +++ b/recipes/bioconductor-consica/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "2.0.0" %} {% set name = "consICA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5063262bd3705a643f8fada1e509fce4 + md5: b64f871ca062dc65d6a883b000c761d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-consica", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, BiocStyle, rmarkdown, testthat +# Suggests: knitr, BiocStyle, rmarkdown, testthat, Seurat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - 'r-fastica >=1.2.1' + - r-ggplot2 - r-pheatmap + - r-rfast - r-sm - r-survival run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - 'r-fastica >=1.2.1' + - r-ggplot2 - r-pheatmap + - r-rfast - r-sm - r-survival test: diff --git a/recipes/bioconductor-constand/meta.yaml b/recipes/bioconductor-constand/meta.yaml index b730f63f0843f..f4242d0e9f6d5 100644 --- a/recipes/bioconductor-constand/meta.yaml +++ b/recipes/bioconductor-constand/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "CONSTANd" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd346235e5d208c081a80054f0c3d00f + md5: 6337f6a248f820600a99fa9ef9fc1571 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-constand", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra, magick, Cairo, limma requirements: diff --git a/recipes/bioconductor-contibait/meta.yaml b/recipes/bioconductor-contibait/meta.yaml index 168269e1a26ab..71415b965efc6 100644 --- a/recipes/bioconductor-contibait/meta.yaml +++ b/recipes/bioconductor-contibait/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "contiBAIT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bc21baae59dc116f62b237e1690ac8ec + md5: 8297fd66bbfcd997be0f23cf31fcd644 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-contibait", max_pin="x.x") }}' # Suggests: BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-exomecopy >=1.46.0,<1.47.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-exomecopy >=1.48.0,<1.49.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-bh >=1.51.0.3' - r-clue @@ -47,17 +48,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-exomecopy >=1.46.0,<1.47.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-exomecopy >=1.48.0,<1.49.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-bh >=1.51.0.3' - r-clue diff --git a/recipes/bioconductor-conumee/meta.yaml b/recipes/bioconductor-conumee/meta.yaml index 9d3c9cffbc336..e3dde4f6aeff4 100644 --- a/recipes/bioconductor-conumee/meta.yaml +++ b/recipes/bioconductor-conumee/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "conumee" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2e8642efe6cfe74f1856bae5c4b5ec7d + md5: f7eab6e95ed82f050ef52895ef178ba0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-conumee", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, minfiData, RCurl requirements: host: - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-convert/meta.yaml b/recipes/bioconductor-convert/meta.yaml index 5ed7bfd042ff8..82edc223b9c80 100644 --- a/recipes/bioconductor-convert/meta.yaml +++ b/recipes/bioconductor-convert/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "convert" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bd45e86f579302d2cc0e0418ba7ee45b + md5: 828a21b5a554d63faeb6cc2af0784394 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-convert", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base test: commands: diff --git a/recipes/bioconductor-copa/meta.yaml b/recipes/bioconductor-copa/meta.yaml index ce007cd183029..a06e57133a675 100644 --- a/recipes/bioconductor-copa/meta.yaml +++ b/recipes/bioconductor-copa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.0" %} {% set name = "copa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7eceebde920ee2cdba8ff709c51b0607 + md5: bd372714a4dd7e70b90d9232fcba322d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-copa", max_pin="x.x") }}' # Suggests: colonCA requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml b/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml index 9f08845e78458..2239bacb44612 100644 --- a/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml +++ b/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "COPDSexualDimorphism.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ae2601608f8b3f711b73d24734e7d7c + md5: d7cf1990679c90cbaf5250c4761effec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-copdsexualdimorphism.data", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh b/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh index a3394d9c9cada..646f2cfcfb63e 100644 --- a/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh +++ b/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "copdsexualdimorphism.data-1.36.0" +installBiocDataPackage.sh "copdsexualdimorphism.data-1.38.0" diff --git a/recipes/bioconductor-copyhelper/meta.yaml b/recipes/bioconductor-copyhelper/meta.yaml index 87f295b8ca1a0..7b020ea9f183e 100644 --- a/recipes/bioconductor-copyhelper/meta.yaml +++ b/recipes/bioconductor-copyhelper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "CopyhelpeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c38e2379228446d4d94e5ced48633a54 + md5: bb8d3e8cba0c27898e43cbdcfcac6c62 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-copyhelper", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-copyhelper/post-link.sh b/recipes/bioconductor-copyhelper/post-link.sh index ae2a9b3ec6ac2..e5749ce2fa85f 100644 --- a/recipes/bioconductor-copyhelper/post-link.sh +++ b/recipes/bioconductor-copyhelper/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "copyhelper-1.32.0" +installBiocDataPackage.sh "copyhelper-1.34.0" diff --git a/recipes/bioconductor-copyneutralima/meta.yaml b/recipes/bioconductor-copyneutralima/meta.yaml index 6fa32af26bdfe..ded511225ae06 100644 --- a/recipes/bioconductor-copyneutralima/meta.yaml +++ b/recipes/bioconductor-copyneutralima/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "CopyNeutralIMA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8707f36701c11a45e25e92a63cb81f20 + md5: 5f1921b0aff4c3f39b662cc1ae70bf28 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-copyneutralima", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle,knitr,rmarkdown,minfi,conumee,minfiData requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - 'r-rdpack >=0.8' run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - 'r-rdpack >=0.8' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-copyneutralima/post-link.sh b/recipes/bioconductor-copyneutralima/post-link.sh index 70533c31c5401..4ee3bca445581 100644 --- a/recipes/bioconductor-copyneutralima/post-link.sh +++ b/recipes/bioconductor-copyneutralima/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "copyneutralima-1.18.0" +installBiocDataPackage.sh "copyneutralima-1.20.0" diff --git a/recipes/bioconductor-copynumberplots/meta.yaml b/recipes/bioconductor-copynumberplots/meta.yaml index f7bdde352d85c..cd504f81494c7 100644 --- a/recipes/bioconductor-copynumberplots/meta.yaml +++ b/recipes/bioconductor-copynumberplots/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "CopyNumberPlots" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 72aa4e93152130ecf6edd5f80955c1a2 + md5: d35c96c521087a1183dd2ae465b3d2a7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-copynumberplots", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, panelcn.mops, BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy, testthat requirements: host: - - 'bioconductor-cn.mops >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-karyoploter >=1.26.0,<1.27.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-cn.mops >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-karyoploter >=1.28.0,<1.29.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-cn.mops >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-karyoploter >=1.26.0,<1.27.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-cn.mops >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-karyoploter >=1.28.0,<1.29.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-cordon/meta.yaml b/recipes/bioconductor-cordon/meta.yaml index 2e22b546b679c..5733faeb89818 100644 --- a/recipes/bioconductor-cordon/meta.yaml +++ b/recipes/bioconductor-cordon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "coRdon" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e0567325e9913078d8dfec839b8bf7ae + md5: 19e0e0e91d3cccd4c277710c9273275e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cordon", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-data.table - r-dplyr @@ -30,8 +31,8 @@ requirements: - r-purrr - r-stringr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-coregx/meta.yaml b/recipes/bioconductor-coregx/meta.yaml index eae9d496887ff..42ac17580c6ed 100644 --- a/recipes/bioconductor-coregx/meta.yaml +++ b/recipes/bioconductor-coregx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "CoreGx" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dcab6de8de5c96329785558051193dbe + md5: 3556f412bd014d5294b15feb8342d78e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-coregx", max_pin="x.x") }}' noarch: generic # Suggests: pander, markdown, BiocStyle, rmarkdown, knitr, formatR, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bumpymatrix >=1.8.0,<1.9.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-piano >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-piano >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bench - r-checkmate @@ -39,15 +40,15 @@ requirements: - r-lsa - r-rlang run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bumpymatrix >=1.8.0,<1.9.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-piano >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-piano >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bench - r-checkmate @@ -65,4 +66,3 @@ about: summary: 'Classes and Functions to Serve as the Basis for Other ''Gx'' Packages' description: 'A collection of functions and classes which serve as the foundation for our lab''s suite of R packages, such as ''PharmacoGx'' and ''RadioGx''. This package was created to abstract shared functionality from other lab package releases to increase ease of maintainability and reduce code repetition in current and future ''Gx'' suite programs. Major features include a ''CoreSet'' class, from which ''RadioSet'' and ''PharmacoSet'' are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, as well as: Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A., Aerts, H., Lupien, M., Goldenberg, A. (2015) . Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) .' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - diff --git a/recipes/bioconductor-cormotif/meta.yaml b/recipes/bioconductor-cormotif/meta.yaml index fa6bd5bd21c2c..55b5aa549ab64 100644 --- a/recipes/bioconductor-cormotif/meta.yaml +++ b/recipes/bioconductor-cormotif/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "Cormotif" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f673c43aae08a2209f46845b805650dc + md5: 6e65ec2460aecf6004e416d7c61c4c1d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cormotif", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-corral/meta.yaml b/recipes/bioconductor-corral/meta.yaml index ff154a3ace1c2..9086ae8658de5 100644 --- a/recipes/bioconductor-corral/meta.yaml +++ b/recipes/bioconductor-corral/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "corral" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 41cabd6e030f01ca76f98c551ec32287 + md5: 7f1ebb217a695452605bd8aa94f8a5a1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-corral", max_pin="x.x") }}' noarch: generic # Suggests: ade4, BiocStyle, CellBench, DuoClustering2018, knitr, rmarkdown, scater, testthat requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggthemes @@ -34,9 +35,9 @@ requirements: - r-reshape2 - r-transport run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggthemes diff --git a/recipes/bioconductor-correp/meta.yaml b/recipes/bioconductor-correp/meta.yaml index e56b7ed84b106..948f984973f67 100644 --- a/recipes/bioconductor-correp/meta.yaml +++ b/recipes/bioconductor-correp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "CORREP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f8c70e08f9fea69ce64ede0fa0d2f65 + md5: 2cf1b0a377be4fec857415e908e2d8d2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-correp", max_pin="x.x") }}' noarch: generic # Suggests: cluster, MASS requirements: diff --git a/recipes/bioconductor-coseq/meta.yaml b/recipes/bioconductor-coseq/meta.yaml index 11ee5916f621e..6d453975c5710 100644 --- a/recipes/bioconductor-coseq/meta.yaml +++ b/recipes/bioconductor-coseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "coseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 17d095c8ad593a4b879ea4056758ce0c + md5: 1e4bea8d520a2554f8f1095d6912074b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-coseq", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-htsfilter >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-htsfilter >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-capushe - r-compositions @@ -38,12 +39,12 @@ requirements: - r-rmixmod - r-scales run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-htsfilter >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-htsfilter >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-capushe - r-compositions diff --git a/recipes/bioconductor-cosia/meta.yaml b/recipes/bioconductor-cosia/meta.yaml index 26d86569f0b09..9db22300f331c 100644 --- a/recipes/bioconductor-cosia/meta.yaml +++ b/recipes/bioconductor-cosia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "CoSIA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f8ef5bd89e113c1bf68ce002bd54140 + md5: 217ff53ed0aac2ca3c2d91ce5237c111 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cosia", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 2.22.0), tidyverse (>= 1.3.1), knitr (>= 1.42), rmarkdown (>= 2.20), testthat (>= 3.1.6), qpdf (>= 1.3.0) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationtools >=1.74.0,<1.75.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-org.ce.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.dr.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationtools >=1.76.0,<1.77.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-org.ce.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.dr.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - 'r-dplyr >=1.0.7' - 'r-ggplot2 >=3.3.5' @@ -44,16 +45,16 @@ requirements: - 'r-tidyr >=1.2.0' - 'r-tidyselect >=1.1.2' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationtools >=1.74.0,<1.75.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-org.ce.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.dr.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationtools >=1.76.0,<1.77.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-org.ce.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.dr.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - 'r-dplyr >=1.0.7' - 'r-ggplot2 >=3.3.5' diff --git a/recipes/bioconductor-cosiadata/meta.yaml b/recipes/bioconductor-cosiadata/meta.yaml index 184f0cea9bd1b..22efff4627359 100644 --- a/recipes/bioconductor-cosiadata/meta.yaml +++ b/recipes/bioconductor-cosiadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "CoSIAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a1d517d2c097ad8abf9c8298f4ab46d + md5: f0ec9d5ca01647ec3d52e264c0828273 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cosiadata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 2.26.0), utils (>= 4.3.0), AnnotationHub (>= 3.7.3), knitr (>= 1.42) requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cosiadata/post-link.sh b/recipes/bioconductor-cosiadata/post-link.sh index 372312c2627c9..1ec63202a4c96 100644 --- a/recipes/bioconductor-cosiadata/post-link.sh +++ b/recipes/bioconductor-cosiadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cosiadata-1.0.0" +installBiocDataPackage.sh "cosiadata-1.2.0" diff --git a/recipes/bioconductor-cosmic.67/meta.yaml b/recipes/bioconductor-cosmic.67/meta.yaml index 805c769c75dc5..4782b2a7ffb93 100644 --- a/recipes/bioconductor-cosmic.67/meta.yaml +++ b/recipes/bioconductor-cosmic.67/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "COSMIC.67" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5242999a8b93e384ab8c05a2950ccde + md5: 392f31ffd7e95a7558d248d36dcc37fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cosmic.67", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cosmic.67/post-link.sh b/recipes/bioconductor-cosmic.67/post-link.sh index 7ceb0e5a939f6..fe6c437614e15 100644 --- a/recipes/bioconductor-cosmic.67/post-link.sh +++ b/recipes/bioconductor-cosmic.67/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cosmic.67-1.36.0" +installBiocDataPackage.sh "cosmic.67-1.38.0" diff --git a/recipes/bioconductor-cosmiq/meta.yaml b/recipes/bioconductor-cosmiq/meta.yaml index 304d635d26040..9b3100477fa33 100644 --- a/recipes/bioconductor-cosmiq/meta.yaml +++ b/recipes/bioconductor-cosmiq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "cosmiq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d8f08cd3b2fd8da501b6f24cc86edbe0 + md5: ae02870f3759e09bb2c8f86d38306f01 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cosmiq", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-faahko >=1.40.0,<1.41.0' - - 'bioconductor-massspecwavelet >=1.66.0,<1.67.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-faahko >=1.42.0,<1.43.0' + - 'bioconductor-massspecwavelet >=1.68.0,<1.69.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-pracma - r-rcpp - libblas - liblapack run: - - 'bioconductor-faahko >=1.40.0,<1.41.0' - - 'bioconductor-massspecwavelet >=1.66.0,<1.67.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-faahko >=1.42.0,<1.43.0' + - 'bioconductor-massspecwavelet >=1.68.0,<1.69.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-pracma - r-rcpp diff --git a/recipes/bioconductor-cosmosr/meta.yaml b/recipes/bioconductor-cosmosr/meta.yaml index 6fc21c8828f62..3e3679704e138 100644 --- a/recipes/bioconductor-cosmosr/meta.yaml +++ b/recipes/bioconductor-cosmosr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "cosmosR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f18bfd17d55bd1b64aa31eb80aa19126 + md5: f1e0ed65fc63cbdf3a7936bf45e73f3e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cosmosr", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, piano, ggplot2 requirements: host: - - 'bioconductor-carnival >=2.10.0,<2.11.0' - - 'bioconductor-dorothea >=1.12.0,<1.13.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-carnival >=2.12.0,<2.13.0' + - 'bioconductor-decoupler >=2.8.0,<2.9.0' + - 'bioconductor-dorothea >=1.14.0,<1.15.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-dplyr - r-igraph @@ -33,9 +35,10 @@ requirements: - r-stringr - r-visnetwork run: - - 'bioconductor-carnival >=2.10.0,<2.11.0' - - 'bioconductor-dorothea >=1.12.0,<1.13.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-carnival >=2.12.0,<2.13.0' + - 'bioconductor-decoupler >=2.8.0,<2.9.0' + - 'bioconductor-dorothea >=1.14.0,<1.15.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-dplyr - r-igraph diff --git a/recipes/bioconductor-cosnet/meta.yaml b/recipes/bioconductor-cosnet/meta.yaml index 4ff74fc3d6a72..83ab3129d7fd1 100644 --- a/recipes/bioconductor-cosnet/meta.yaml +++ b/recipes/bioconductor-cosnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "COSNet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed1d625a532916dc04b50ff346f6aedd + md5: 6648998ac68e41642f1a7bad77e0bb7f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cosnet", max_pin="x.x") }}' # Suggests: bionetdata, PerfMeas, RUnit, BiocGenerics requirements: host: diff --git a/recipes/bioconductor-cotan/meta.yaml b/recipes/bioconductor-cotan/meta.yaml index b712c8dc4228b..7b8cee0e472ab 100644 --- a/recipes/bioconductor-cotan/meta.yaml +++ b/recipes/bioconductor-cotan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.4" %} +{% set version = "2.2.1" %} {% set name = "COTAN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 186328978b156456a4490ce7eb44361a + md5: ec3bbfe10c1ede4ae12398534ab5395b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cotan", max_pin="x.x") }}' noarch: generic -# Suggests: testthat (>= 3.0.0), proto, spelling, knitr, data.table, gsubfn, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS, Rtsne, plotly, BiocStyle, cowplot, qpdf, GEOquery +# Suggests: testthat (>= 3.0.0), proto, spelling, knitr, data.table, gsubfn, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS, Rtsne, plotly, BiocStyle, cowplot, qpdf, GEOquery, sf requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - r-assertthat - r-base - r-circlize @@ -33,6 +34,7 @@ requirements: - r-ggthemes - r-irlba - r-matrix + - r-paralleldist - r-parallelly - r-plyr - r-rcolorbrewer @@ -47,7 +49,7 @@ requirements: - r-withr - r-zeallot run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - r-assertthat - r-base - r-circlize @@ -59,6 +61,7 @@ requirements: - r-ggthemes - r-irlba - r-matrix + - r-paralleldist - r-parallelly - r-plyr - r-rcolorbrewer diff --git a/recipes/bioconductor-cottoncdf/meta.yaml b/recipes/bioconductor-cottoncdf/meta.yaml index 1d7edd68e7f91..c8d58aec1b26b 100644 --- a/recipes/bioconductor-cottoncdf/meta.yaml +++ b/recipes/bioconductor-cottoncdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "cottoncdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b9d2a4b43235c6e531b78cca006e84b2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cottoncdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cottonprobe/meta.yaml b/recipes/bioconductor-cottonprobe/meta.yaml index 6c4575d866433..6b4cc385024ae 100644 --- a/recipes/bioconductor-cottonprobe/meta.yaml +++ b/recipes/bioconductor-cottonprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "cottonprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 032fa94876685820d94526fd56dd0b65 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cottonprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-countsimqc/meta.yaml b/recipes/bioconductor-countsimqc/meta.yaml index 38c8cb7b77e2f..718397f70710d 100644 --- a/recipes/bioconductor-countsimqc/meta.yaml +++ b/recipes/bioconductor-countsimqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "countsimQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a076a7246b7f4037ccd8660860a160a + md5: a44b69f7c0a9b3f5f822df61a6fcef73 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-countsimqc", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-catools - r-dplyr @@ -36,11 +37,11 @@ requirements: - 'r-rmarkdown >=2.5' - r-tidyr run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-catools - r-dplyr diff --git a/recipes/bioconductor-coveb/meta.yaml b/recipes/bioconductor-coveb/meta.yaml index 34665cfe61e9a..df6fb540d4b0b 100644 --- a/recipes/bioconductor-coveb/meta.yaml +++ b/recipes/bioconductor-coveb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "covEB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67dcc92152292212d430f023d1cca9b5 + md5: 5469ab09a3d502902dc4d698abd1cbae build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-coveb", max_pin="x.x") }}' noarch: generic # Suggests: curatedBladderData requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-gsl - r-igraph @@ -29,7 +30,7 @@ requirements: - r-matrix - r-mvtnorm run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-gsl - r-igraph diff --git a/recipes/bioconductor-coverageview/meta.yaml b/recipes/bioconductor-coverageview/meta.yaml index eaccfd23cd371..c5783d123cbb9 100644 --- a/recipes/bioconductor-coverageview/meta.yaml +++ b/recipes/bioconductor-coverageview/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "CoverageView" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec25cb60624d5cf284f2f41a60abf969 + md5: 27821acd2787d95d95532f71d22378df build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-coverageview", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-covrna/meta.yaml b/recipes/bioconductor-covrna/meta.yaml index 07bd860be2a35..43b8f2d3c5e2f 100644 --- a/recipes/bioconductor-covrna/meta.yaml +++ b/recipes/bioconductor-covrna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "covRNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ae2b33f4b58cbd6d9f42bb5ba444b717 + md5: dd8405538f8c54345579ee7d0d5dc63f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-covrna", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - r-ade4 - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - r-ade4 - r-base test: diff --git a/recipes/bioconductor-cpvsnp/meta.yaml b/recipes/bioconductor-cpvsnp/meta.yaml index d15cd5ea861d9..c4c3bdc69a5f3 100644 --- a/recipes/bioconductor-cpvsnp/meta.yaml +++ b/recipes/bioconductor-cpvsnp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "cpvSNP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 064f756a6ebeb3d9944e85a45b99e032 + md5: 2edb50570eb609c9962e57d36d70ceba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cpvsnp", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-corpcor - r-ggplot2 - r-plyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-corpcor - r-ggplot2 diff --git a/recipes/bioconductor-cqn/meta.yaml b/recipes/bioconductor-cqn/meta.yaml index 9559ff98266f3..267b7af6d65ba 100644 --- a/recipes/bioconductor-cqn/meta.yaml +++ b/recipes/bioconductor-cqn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "cqn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d0d1324320136000b8b75056cdc3bf78 + md5: a72eb9ae5c393dec7ecc4f992d11328f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cqn", max_pin="x.x") }}' noarch: generic # Suggests: scales, edgeR requirements: host: - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-mclust - r-nor1mix - r-quantreg run: - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-mclust - r-nor1mix diff --git a/recipes/bioconductor-crcl18/meta.yaml b/recipes/bioconductor-crcl18/meta.yaml index 6849b5e08730f..7a7776d0bfc5d 100644 --- a/recipes/bioconductor-crcl18/meta.yaml +++ b/recipes/bioconductor-crcl18/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CRCL18" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df8b3bf91d7c7ac39d0fee78b65c1da0 + md5: 176bd921f08e717ec49e4e3eb4a5e5e5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crcl18", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-crcl18/post-link.sh b/recipes/bioconductor-crcl18/post-link.sh index afb5adf88878a..841a4c62b2bb7 100644 --- a/recipes/bioconductor-crcl18/post-link.sh +++ b/recipes/bioconductor-crcl18/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "crcl18-1.20.0" +installBiocDataPackage.sh "crcl18-1.22.0" diff --git a/recipes/bioconductor-crimage/meta.yaml b/recipes/bioconductor-crimage/meta.yaml index bba214a251f5f..42e7d5fc48fd8 100644 --- a/recipes/bioconductor-crimage/meta.yaml +++ b/recipes/bioconductor-crimage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "CRImage" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67f3739d67a92f8e46b27e2b3ff83d55 + md5: 84d9bedefc25b08b7e6d86c47bf233f9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crimage", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-acgh >=1.78.0,<1.79.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-acgh >=1.80.0,<1.81.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-base - r-e1071 - r-foreach - r-mass - r-sgeostat run: - - 'bioconductor-acgh >=1.78.0,<1.79.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-acgh >=1.80.0,<1.81.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-base - r-e1071 - r-foreach diff --git a/recipes/bioconductor-crisprbase/meta.yaml b/recipes/bioconductor-crisprbase/meta.yaml index e75426f262fca..92d843a59a6cf 100644 --- a/recipes/bioconductor-crisprbase/meta.yaml +++ b/recipes/bioconductor-crisprbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "crisprBase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5fc52160cd713801b9499ed277ebcec9 + md5: 20cc1254ee7d33a966bb795f09f8be44 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprbase", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-stringr test: diff --git a/recipes/bioconductor-crisprbowtie/meta.yaml b/recipes/bioconductor-crisprbowtie/meta.yaml index 152de6564d4a3..c2923cdfff081 100644 --- a/recipes/bioconductor-crisprbowtie/meta.yaml +++ b/recipes/bioconductor-crisprbowtie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "crisprBowtie" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f84e8a18573b68f4d70067e3180b08a3 + md5: eabea0206c16b87d8acaa65245390d30 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprbowtie", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbowtie >=1.40.0,<1.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbowtie >=1.42.0,<1.43.0' - r-base - r-readr - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbowtie >=1.40.0,<1.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbowtie >=1.42.0,<1.43.0' - r-base - r-readr - r-stringr diff --git a/recipes/bioconductor-crisprbwa/meta.yaml b/recipes/bioconductor-crisprbwa/meta.yaml index 1f433fa15b865..58f4eece924b8 100644 --- a/recipes/bioconductor-crisprbwa/meta.yaml +++ b/recipes/bioconductor-crisprbwa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "crisprBwa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9a42166c3ec58a55aeec7eda3e512eae + md5: d77734ef6cfa03fb7b08c21c59155518 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprbwa", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-rbwa >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-rbwa >=1.6.0,<1.7.0' - r-base - r-readr - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-rbwa >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-rbwa >=1.6.0,<1.7.0' - r-base - r-readr - r-stringr diff --git a/recipes/bioconductor-crisprdesign/meta.yaml b/recipes/bioconductor-crisprdesign/meta.yaml index ee30ed17f1f52..ead19116d4702 100644 --- a/recipes/bioconductor-crisprdesign/meta.yaml +++ b/recipes/bioconductor-crisprdesign/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "crisprDesign" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,49 +11,50 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84860ded55e114a288c8d4b22b90f7da + md5: f4efe77ba4d8f440af21a1e80f0e1f5d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprdesign", max_pin="x.x") }}' noarch: generic # Suggests: biomaRt, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa (>= 0.99.7), knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-crisprbowtie >=1.4.0,<1.5.0' - - 'bioconductor-crisprscore >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-crisprbowtie >=1.6.0,<1.7.0' + - 'bioconductor-crisprscore >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-matrix run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-crisprbowtie >=1.4.0,<1.5.0' - - 'bioconductor-crisprscore >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-crisprbowtie >=1.6.0,<1.7.0' + - 'bioconductor-crisprscore >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-crisprscore/meta.yaml b/recipes/bioconductor-crisprscore/meta.yaml index e7547701a84ed..2ac786f7e1988 100644 --- a/recipes/bioconductor-crisprscore/meta.yaml +++ b/recipes/bioconductor-crisprscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "crisprScore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2652f2da85d86eb913f4c5dc403ae5be + md5: c83f7928b03ce0308175835556dfcb54 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprscore", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-basilisk.utils >=1.12.0,<1.13.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-crisprscoredata >=1.4.0,<1.5.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-basilisk.utils >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-crisprscoredata >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-randomforest - r-reticulate - r-stringr run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-basilisk.utils >=1.12.0,<1.13.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-crisprscoredata >=1.4.0,<1.5.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-basilisk.utils >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-crisprscoredata >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-randomforest - r-reticulate diff --git a/recipes/bioconductor-crisprscoredata/meta.yaml b/recipes/bioconductor-crisprscoredata/meta.yaml index 385f8db75cbd4..56963b7b20d4a 100644 --- a/recipes/bioconductor-crisprscoredata/meta.yaml +++ b/recipes/bioconductor-crisprscoredata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "crisprScoreData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: feb17485db66f6e86d92b42af3731f4a + md5: 1f4d86404f045ec36cf7d1b1c64373fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprscoredata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-crisprscoredata/post-link.sh b/recipes/bioconductor-crisprscoredata/post-link.sh index 3e7804e70fdcb..4fd2ecb7ae14e 100644 --- a/recipes/bioconductor-crisprscoredata/post-link.sh +++ b/recipes/bioconductor-crisprscoredata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "crisprscoredata-1.4.0" +installBiocDataPackage.sh "crisprscoredata-1.6.0" diff --git a/recipes/bioconductor-crisprseek/meta.yaml b/recipes/bioconductor-crisprseek/meta.yaml index cd254e810c69b..56325695ce330 100644 --- a/recipes/bioconductor-crisprseek/meta.yaml +++ b/recipes/bioconductor-crisprseek/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "CRISPRseek" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f820f2bad907afb0a89e75f3923152d0 + md5: b14c3c52470140b9c7bc85b9ca4044a5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprseek", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, lattice, MASS, tensorflow, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-data.table - r-dplyr @@ -40,16 +41,16 @@ requirements: - r-reticulate - r-seqinr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-crisprvariants/meta.yaml b/recipes/bioconductor-crisprvariants/meta.yaml index 9750f1f3a78e8..a820551578ab1 100644 --- a/recipes/bioconductor-crisprvariants/meta.yaml +++ b/recipes/bioconductor-crisprvariants/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "CrispRVariants" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f6121ca35c8ed2e06bd42111ac2aeea + md5: ede7cabcf986e2494f2e7b489621dd09 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprvariants", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, gdata, GenomicFeatures, knitr, rmarkdown, rtracklayer, sangerseqR, testthat, VariantAnnotation +# Suggests: BiocStyle, GenomicFeatures, knitr, rmarkdown, readxl, rtracklayer, sangerseqR, testthat, VariantAnnotation requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-ggplot2 >=2.2.0' - r-gridextra - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-ggplot2 >=2.2.0' - r-gridextra diff --git a/recipes/bioconductor-crisprverse/meta.yaml b/recipes/bioconductor-crisprverse/meta.yaml index 49c16fe8000ba..112545aadf561 100644 --- a/recipes/bioconductor-crisprverse/meta.yaml +++ b/recipes/bioconductor-crisprverse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "crisprVerse" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dc5f98e715c08356e21bd39d54ca812e + md5: dff359d1f63b8a58289ef0914c9260c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprverse", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-crisprbowtie >=1.4.0,<1.5.0' - - 'bioconductor-crisprdesign >=1.2.0,<1.3.0' - - 'bioconductor-crisprscore >=1.4.0,<1.5.0' - - 'bioconductor-crisprscoredata >=1.4.0,<1.5.0' - - 'bioconductor-crisprviz >=1.2.0,<1.3.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-crisprbowtie >=1.6.0,<1.7.0' + - 'bioconductor-crisprdesign >=1.4.0,<1.5.0' + - 'bioconductor-crisprscore >=1.6.0,<1.7.0' + - 'bioconductor-crisprscoredata >=1.6.0,<1.7.0' + - 'bioconductor-crisprviz >=1.4.0,<1.5.0' - r-base - r-biocmanager - r-cli - r-rlang run: - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-crisprbowtie >=1.4.0,<1.5.0' - - 'bioconductor-crisprdesign >=1.2.0,<1.3.0' - - 'bioconductor-crisprscore >=1.4.0,<1.5.0' - - 'bioconductor-crisprscoredata >=1.4.0,<1.5.0' - - 'bioconductor-crisprviz >=1.2.0,<1.3.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-crisprbowtie >=1.6.0,<1.7.0' + - 'bioconductor-crisprdesign >=1.4.0,<1.5.0' + - 'bioconductor-crisprscore >=1.6.0,<1.7.0' + - 'bioconductor-crisprscoredata >=1.6.0,<1.7.0' + - 'bioconductor-crisprviz >=1.4.0,<1.5.0' - r-base - r-biocmanager - r-cli diff --git a/recipes/bioconductor-crisprviz/meta.yaml b/recipes/bioconductor-crisprviz/meta.yaml index a32e148c6aea0..1c835bd954fd8 100644 --- a/recipes/bioconductor-crisprviz/meta.yaml +++ b/recipes/bioconductor-crisprviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "crisprViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 418a29f193e424f19794de01c36412ec + md5: a95c0cc87c7934da1e9bbfeb1e27bd3a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprviz", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, rtracklayer, testthat, utils requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-crisprdesign >=1.2.0,<1.3.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-crisprdesign >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-crisprdesign >=1.2.0,<1.3.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-crisprdesign >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-crlmm/meta.yaml b/recipes/bioconductor-crlmm/meta.yaml index f433b5954fc87..6e0ee3be271f6 100644 --- a/recipes/bioconductor-crlmm/meta.yaml +++ b/recipes/bioconductor-crlmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "crlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c77b15041b77a1679d307900099a79a9 + md5: d047359287ee832d97e95c0945dff8cc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crlmm", max_pin="x.x") }}' # Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats, RUnit requirements: host: - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-beanplot - r-ellipse @@ -40,13 +41,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-beanplot - r-ellipse diff --git a/recipes/bioconductor-crossmeta/meta.yaml b/recipes/bioconductor-crossmeta/meta.yaml index 75049a5143101..2175cb526022a 100644 --- a/recipes/bioconductor-crossmeta/meta.yaml +++ b/recipes/bioconductor-crossmeta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "crossmeta" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eb215cbcc990a0a74352342c1c952885 + md5: 5bc5c865fba1a04864f9a0643adf041f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crossmeta", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, lydata, org.Hs.eg.db, testthat # SystemRequirements: libxml2: libxml2-dev (deb), libxml2-devel (rpm) libcurl: libcurl4-openssl-dev (deb), libcurl-devel (rpm) openssl: libssl-dev (deb), openssl-devel (rpm), libssl_dev (csw), openssl@1.1 (brew) requirements: host: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - 'r-biocmanager >=1.30.4' - 'r-data.table >=1.10.4' @@ -54,16 +55,16 @@ requirements: - r-tibble - 'r-xml >=3.98.1.17' run: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - 'r-biocmanager >=1.30.4' - 'r-data.table >=1.10.4' diff --git a/recipes/bioconductor-csar/meta.yaml b/recipes/bioconductor-csar/meta.yaml index 9b25df6a1a1a3..4767cf2e78ac2 100644 --- a/recipes/bioconductor-csar/meta.yaml +++ b/recipes/bioconductor-csar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "CSAR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 796d8b24ecf0424a0227ec54124628fa + md5: cf22689abca527406f9f2b333739d7bc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-csar", max_pin="x.x") }}' # Suggests: ShortRead, Biostrings requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - libblas - liblapack run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-csaw/meta.yaml b/recipes/bioconductor-csaw/meta.yaml index ae24e0b28d739..257d3e9ac5aca 100644 --- a/recipes/bioconductor-csaw/meta.yaml +++ b/recipes/bioconductor-csaw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "csaw" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,48 +11,49 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2303363515d9358462fa8670bddbb041 + md5: 07ad4af3be8e5e799b06826cc97a449e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-csaw", max_pin="x.x") }}' # Suggests: AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager # SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-metapod >=1.8.0,<1.9.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-metapod >=1.10.0,<1.11.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-metapod >=1.8.0,<1.9.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-metapod >=1.10.0,<1.11.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-csdr/meta.yaml b/recipes/bioconductor-csdr/meta.yaml index 58600b6179b91..8f28df3937931 100644 --- a/recipes/bioconductor-csdr/meta.yaml +++ b/recipes/bioconductor-csdr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "csdR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a19cb2405a198584f25a03df4b0569d + md5: 02132c2d953434d0bb7de9b58e8b5769 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-csdr", max_pin="x.x") }}' # Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr, igraph, dplyr requirements: host: diff --git a/recipes/bioconductor-cssq/meta.yaml b/recipes/bioconductor-cssq/meta.yaml index 411139143feae..52270a9d7e002 100644 --- a/recipes/bioconductor-cssq/meta.yaml +++ b/recipes/bioconductor-cssq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "CSSQ" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b33aa7496759ea3e7af2e4670956254 + md5: d9a6f6200f67cc06173c30dcd6775e5a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cssq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, markdown requirements: host: - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 run: - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-ctc/meta.yaml b/recipes/bioconductor-ctc/meta.yaml index 00893b46b8267..67bcc2e93f176 100644 --- a/recipes/bioconductor-ctc/meta.yaml +++ b/recipes/bioconductor-ctc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "ctc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 56004c787150f55f1ae6b3c5b1452c3a + md5: ea94b8b636b26d4f827ecd4569804d1e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ctc", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-ctcf/meta.yaml b/recipes/bioconductor-ctcf/meta.yaml index eed0fcb6af070..1c4437ce61d37 100644 --- a/recipes/bioconductor-ctcf/meta.yaml +++ b/recipes/bioconductor-ctcf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.11" %} {% set name = "CTCF" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5ec44245864395de390e68fa56e465af build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ctcf", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown, knitr, AnnotationHub, GenomicRanges, plyranges, sessioninfo requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ctdata/meta.yaml b/recipes/bioconductor-ctdata/meta.yaml index 03168c81f245e..051c707054ba5 100644 --- a/recipes/bioconductor-ctdata/meta.yaml +++ b/recipes/bioconductor-ctdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.2" %} +{% set version = "1.2.0" %} {% set name = "CTdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e5666dc0fc962f452b36e1469947dd28 + md5: d130308cf078329f4cc6a1cc8055475d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ctdata", max_pin="x.x") }}' noarch: generic -# Suggests: testthat (>= 3.0.0), DT, BiocStyle, knitr, rmarkdown, SummarizedExperiment +# Suggests: testthat (>= 3.0.0), DT, BiocStyle, knitr, rmarkdown, SummarizedExperiment, SingleCellExperiment requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base test: commands: diff --git a/recipes/bioconductor-ctdquerier/meta.yaml b/recipes/bioconductor-ctdquerier/meta.yaml index a66cbb012eee3..9cfc17e349b4e 100644 --- a/recipes/bioconductor-ctdquerier/meta.yaml +++ b/recipes/bioconductor-ctdquerier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "CTDquerier" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ae71eaec9c380d827d4ba3f6c6034be + md5: 42c5654d014714b22e5c1c2c2e7a2118 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ctdquerier", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-gridextra @@ -31,8 +32,8 @@ requirements: - r-stringdist - r-stringr run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-gridextra diff --git a/recipes/bioconductor-ctrap/meta.yaml b/recipes/bioconductor-ctrap/meta.yaml index a589d5f0d98b3..07edfeb916d8a 100644 --- a/recipes/bioconductor-ctrap/meta.yaml +++ b/recipes/bioconductor-ctrap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "cTRAP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 69a1a37a36696d321c04734075ec6802 + md5: 049de878508ce8d8031d7d93f6a1fd01 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ctrap", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-binr - r-cowplot @@ -50,11 +51,11 @@ requirements: - r-shinycssloaders - r-tibble run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-binr - r-cowplot diff --git a/recipes/bioconductor-ctsge/meta.yaml b/recipes/bioconductor-ctsge/meta.yaml index 8af0af8538976..44c7878302301 100644 --- a/recipes/bioconductor-ctsge/meta.yaml +++ b/recipes/bioconductor-ctsge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "ctsGE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eb8561fe9bd7f3b4eccbbb40f8573ede + md5: 31cfbfb8002cbb54747b9a4a41fb17d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ctsge", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown, testthat requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ccapp - r-ggplot2 @@ -29,7 +30,7 @@ requirements: - r-shiny - r-stringr run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ccapp - r-ggplot2 diff --git a/recipes/bioconductor-ctsv/meta.yaml b/recipes/bioconductor-ctsv/meta.yaml index bf775fa227b23..209549d623061 100644 --- a/recipes/bioconductor-ctsv/meta.yaml +++ b/recipes/bioconductor-ctsv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "CTSV" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 343c9934a4e4ad3ea145927cb7605bad + md5: 4a3f8c7b5398449ea01b312ed7da1f43 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ctsv", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-knitr - r-pscl run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-knitr - r-pscl diff --git a/recipes/bioconductor-cummerbund/meta.yaml b/recipes/bioconductor-cummerbund/meta.yaml index e56d26fdc5b6b..b02fb64575016 100644 --- a/recipes/bioconductor-cummerbund/meta.yaml +++ b/recipes/bioconductor-cummerbund/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.42.0" %} +{% set version = "2.44.0" %} {% set name = "cummeRbund" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5221eb3a427c7a29beb2404715794561 + md5: 367d124a098eca55a6da149e35621c65 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cummerbund", max_pin="x.x") }}' noarch: generic # Suggests: cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fastcluster - r-ggplot2 @@ -33,11 +34,11 @@ requirements: - r-reshape2 - r-rsqlite run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fastcluster - r-ggplot2 diff --git a/recipes/bioconductor-curatedadipoarray/meta.yaml b/recipes/bioconductor-curatedadipoarray/meta.yaml index 43353cd4929d2..771e50a148b5c 100644 --- a/recipes/bioconductor-curatedadipoarray/meta.yaml +++ b/recipes/bioconductor-curatedadipoarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "curatedAdipoArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84600c36847d6fff69d646f1ff65dcbd + md5: 109be77c099e9d7b6da437577f619a54 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedadipoarray", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, ExperimentHub, SummarizedExperiment requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedadipoarray/post-link.sh b/recipes/bioconductor-curatedadipoarray/post-link.sh index 2720124804a73..7471a605b14e7 100644 --- a/recipes/bioconductor-curatedadipoarray/post-link.sh +++ b/recipes/bioconductor-curatedadipoarray/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedadipoarray-1.12.0" +installBiocDataPackage.sh "curatedadipoarray-1.14.0" diff --git a/recipes/bioconductor-curatedadipochip/meta.yaml b/recipes/bioconductor-curatedadipochip/meta.yaml index 11bfe0d9b2e9f..5c312a510e921 100644 --- a/recipes/bioconductor-curatedadipochip/meta.yaml +++ b/recipes/bioconductor-curatedadipochip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "curatedAdipoChIP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9c5ffe38c97500d4fadfdd2c6af165b4 + md5: 0074cb63250ac197dad12e4138d47463 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedadipochip", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, GenomicFeatures, ChIPseeker, AnnotationDbi, S4Vectors, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2 requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedadipochip/post-link.sh b/recipes/bioconductor-curatedadipochip/post-link.sh index c018890261d24..452dbadac0268 100644 --- a/recipes/bioconductor-curatedadipochip/post-link.sh +++ b/recipes/bioconductor-curatedadipochip/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedadipochip-1.16.0" +installBiocDataPackage.sh "curatedadipochip-1.18.0" diff --git a/recipes/bioconductor-curatedadiporna/meta.yaml b/recipes/bioconductor-curatedadiporna/meta.yaml index 3ac6e6b4b45b8..b7c5d9884fddc 100644 --- a/recipes/bioconductor-curatedadiporna/meta.yaml +++ b/recipes/bioconductor-curatedadiporna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "curatedAdipoRNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 81535f56828fc6043a8461b0f9e09ca7 + md5: 61c2e750fc2cf09a6bde6c0bf46e6b8b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedadiporna", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2, S4Vectors requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedadiporna/post-link.sh b/recipes/bioconductor-curatedadiporna/post-link.sh index cf9b4d8383a8c..71d70dbe2607b 100644 --- a/recipes/bioconductor-curatedadiporna/post-link.sh +++ b/recipes/bioconductor-curatedadiporna/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedadiporna-1.16.0" +installBiocDataPackage.sh "curatedadiporna-1.18.0" diff --git a/recipes/bioconductor-curatedatlasqueryr/build.sh b/recipes/bioconductor-curatedatlasqueryr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-curatedatlasqueryr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-curatedatlasqueryr/meta.yaml b/recipes/bioconductor-curatedatlasqueryr/meta.yaml new file mode 100644 index 0000000000000..4599ae6b3e273 --- /dev/null +++ b/recipes/bioconductor-curatedatlasqueryr/meta.yaml @@ -0,0 +1,75 @@ +{% set version = "1.0.0" %} +{% set name = "CuratedAtlasQueryR" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 21e5bf1d5aa58d59098176dca867c42c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedatlasqueryr", max_pin="x.x") }}' + noarch: generic +# Suggests: zellkonverter, rmarkdown, knitr, testthat, basilisk, arrow, reticulate, spelling, forcats, ggplot2, tidySingleCellExperiment, rprojroot +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-assertthat + - r-base + - r-cli + - r-dbi + - 'r-dbplyr >=2.3.0' + - r-dplyr + - r-duckdb + - r-glue + - r-httr + - 'r-purrr >=1.0.0' + - r-rlang + - r-seurat + - r-seuratobject + - r-stringr + - r-tibble + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-assertthat + - r-base + - r-cli + - r-dbi + - 'r-dbplyr >=2.3.0' + - r-dplyr + - r-duckdb + - r-glue + - r-httr + - 'r-purrr >=1.0.0' + - r-rlang + - r-seurat + - r-seuratobject + - r-stringr + - r-tibble +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Queries the Human Cell Atlas' + description: 'Provides access to a copy of the Human Cell Atlas, but with harmonised metadata. This allows for uniform querying across numerous datasets within the Atlas using common fields such as cell type, tissue type, and patient ethnicity. Usage involves first querying the metadata table for cells of interest, and then downloading the corresponding cells into a SingleCellExperiment object.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-curatedbladderdata/meta.yaml b/recipes/bioconductor-curatedbladderdata/meta.yaml index f911f00d9dc99..a19912b009d71 100644 --- a/recipes/bioconductor-curatedbladderdata/meta.yaml +++ b/recipes/bioconductor-curatedbladderdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "curatedBladderData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7db958b1758a3b7bc3f2b552962ed51a + md5: bd8965c4ad49840b4985f90f3dc5a441 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedbladderdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, survival, xtable, sva, genefilter, logging requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedbladderdata/post-link.sh b/recipes/bioconductor-curatedbladderdata/post-link.sh index 72edc5f4d75d6..a5a74357ee58b 100644 --- a/recipes/bioconductor-curatedbladderdata/post-link.sh +++ b/recipes/bioconductor-curatedbladderdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedbladderdata-1.36.0" +installBiocDataPackage.sh "curatedbladderdata-1.38.0" diff --git a/recipes/bioconductor-curatedbreastdata/meta.yaml b/recipes/bioconductor-curatedbreastdata/meta.yaml index 24984a5870644..147d8dbd24191 100644 --- a/recipes/bioconductor-curatedbreastdata/meta.yaml +++ b/recipes/bioconductor-curatedbreastdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "curatedBreastData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e53cc4c883e3b3c94842727f34ad6a6 + md5: 41383ff9e1295448ec0e8004789ab9d5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedbreastdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-base - r-ggplot2 - r-xml run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-base - r-ggplot2 - r-xml - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedbreastdata/post-link.sh b/recipes/bioconductor-curatedbreastdata/post-link.sh index 08d6436b4b509..58788177cdca3 100644 --- a/recipes/bioconductor-curatedbreastdata/post-link.sh +++ b/recipes/bioconductor-curatedbreastdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedbreastdata-2.28.0" +installBiocDataPackage.sh "curatedbreastdata-2.30.0" diff --git a/recipes/bioconductor-curatedcrcdata/meta.yaml b/recipes/bioconductor-curatedcrcdata/meta.yaml index 9e1ade1a1bcd2..56546d4ac282f 100644 --- a/recipes/bioconductor-curatedcrcdata/meta.yaml +++ b/recipes/bioconductor-curatedcrcdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "curatedCRCData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c88686b133a9f30f4904dc4e706ef5c8 + md5: c36bf5dbc0970503f4137b55e8c65534 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedcrcdata", max_pin="x.x") }}' noarch: generic # Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-nlme run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-nlme - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedcrcdata/post-link.sh b/recipes/bioconductor-curatedcrcdata/post-link.sh index a684c9f7a3324..fd84280190a21 100644 --- a/recipes/bioconductor-curatedcrcdata/post-link.sh +++ b/recipes/bioconductor-curatedcrcdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedcrcdata-2.32.0" +installBiocDataPackage.sh "curatedcrcdata-2.34.0" diff --git a/recipes/bioconductor-curatedmetagenomicdata/meta.yaml b/recipes/bioconductor-curatedmetagenomicdata/meta.yaml index fd3c6cc2e1a5c..8f7bf4f49af2c 100644 --- a/recipes/bioconductor-curatedmetagenomicdata/meta.yaml +++ b/recipes/bioconductor-curatedmetagenomicdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.8.0" %} +{% set version = "3.10.0" %} {% set name = "curatedMetagenomicData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f24faacda7b263f1bcde098dbffa5f8f + md5: 39c08149fe4261d4961ff1235825ae97 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedmetagenomicdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, DT, knitr, readr, rmarkdown, scater, testthat, utils, uwot, vegan requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-mia >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-mia >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-dplyr - r-magrittr @@ -37,12 +38,12 @@ requirements: - r-tidyr - r-tidyselect run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-mia >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-mia >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-dplyr - r-magrittr @@ -53,7 +54,7 @@ requirements: - r-tidyr - r-tidyselect - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedmetagenomicdata/post-link.sh b/recipes/bioconductor-curatedmetagenomicdata/post-link.sh index 6e0440addbb55..1766abe724ad8 100644 --- a/recipes/bioconductor-curatedmetagenomicdata/post-link.sh +++ b/recipes/bioconductor-curatedmetagenomicdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedmetagenomicdata-3.8.0" +installBiocDataPackage.sh "curatedmetagenomicdata-3.10.0" diff --git a/recipes/bioconductor-curatedovariandata/meta.yaml b/recipes/bioconductor-curatedovariandata/meta.yaml index a204bc966f9f5..ae3f6134fef68 100644 --- a/recipes/bioconductor-curatedovariandata/meta.yaml +++ b/recipes/bioconductor-curatedovariandata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.1" %} {% set name = "curatedOvarianData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0cbda3a714637304ffcc38aa91588c86 + md5: 7651ff7abb11057b3ceec8f869e259d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedovariandata", max_pin="x.x") }}' noarch: generic # Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedovariandata/post-link.sh b/recipes/bioconductor-curatedovariandata/post-link.sh index b8688a68dcdc4..2dca151523690 100644 --- a/recipes/bioconductor-curatedovariandata/post-link.sh +++ b/recipes/bioconductor-curatedovariandata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedovariandata-1.38.0" +installBiocDataPackage.sh "curatedovariandata-1.40.1" diff --git a/recipes/bioconductor-curatedtbdata/meta.yaml b/recipes/bioconductor-curatedtbdata/meta.yaml index e1559e07a2936..86218926bfa5d 100644 --- a/recipes/bioconductor-curatedtbdata/meta.yaml +++ b/recipes/bioconductor-curatedtbdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "curatedTBData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d09277f807e04495c582052e25930d02 + md5: 190a770c4f5df45cf722b7ee287a2384 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedtbdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, DT, dplyr, HGNChelper, knitr, methods, rmarkdown, SummarizedExperiment, sva, testthat requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - r-base - r-rlang run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - r-base - r-rlang - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedtbdata/post-link.sh b/recipes/bioconductor-curatedtbdata/post-link.sh index e9fe0f3a58674..460b16dba5ca4 100644 --- a/recipes/bioconductor-curatedtbdata/post-link.sh +++ b/recipes/bioconductor-curatedtbdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedtbdata-1.6.0" +installBiocDataPackage.sh "curatedtbdata-1.8.0" diff --git a/recipes/bioconductor-curatedtcgadata/meta.yaml b/recipes/bioconductor-curatedtcgadata/meta.yaml index 30a3fed4b41ae..a2dfc71c781c2 100644 --- a/recipes/bioconductor-curatedtcgadata/meta.yaml +++ b/recipes/bioconductor-curatedtcgadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.2" %} +{% set version = "1.24.0" %} {% set name = "curatedTCGAData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 066107da416bfad28b75ee3488dbdad0 + md5: de450b3bbb137b63a1ca46ae81a96909 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedtcgadata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, RaggedExperiment, readr, rmarkdown, TCGAutils, testthat requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedtcgadata/post-link.sh b/recipes/bioconductor-curatedtcgadata/post-link.sh index 9431278b28ca6..151fe01e10b62 100644 --- a/recipes/bioconductor-curatedtcgadata/post-link.sh +++ b/recipes/bioconductor-curatedtcgadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedtcgadata-1.22.2" +installBiocDataPackage.sh "curatedtcgadata-1.24.0" diff --git a/recipes/bioconductor-customcmpdb/meta.yaml b/recipes/bioconductor-customcmpdb/meta.yaml index 94ee55331b883..b6f9d4baff3ab 100644 --- a/recipes/bioconductor-customcmpdb/meta.yaml +++ b/recipes/bioconductor-customcmpdb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "customCMPdb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a2da348c8192136738fff3c390a390b + md5: 1aa1425d87c45ac42f2c7ed808a7a583 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-customcmpdb", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - r-rappdirs - r-rsqlite - r-xml run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - r-rappdirs - r-rsqlite diff --git a/recipes/bioconductor-customprodb/meta.yaml b/recipes/bioconductor-customprodb/meta.yaml index 422fecfca8d82..a90f2ffde8365 100644 --- a/recipes/bioconductor-customprodb/meta.yaml +++ b/recipes/bioconductor-customprodb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.41.0" %} {% set name = "customProDB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 51e83c7af0198e0ac93b5aadb34d50d5 + md5: 08f0eb20ac48a7b8f1e27b45522dd029 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-customprodb", max_pin="x.x") }}' noarch: generic # Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-ahocorasicktrie - r-base - r-dbi @@ -41,18 +42,18 @@ requirements: - r-rsqlite - r-stringr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-ahocorasicktrie - r-base - r-dbi diff --git a/recipes/bioconductor-cyanofilter/meta.yaml b/recipes/bioconductor-cyanofilter/meta.yaml index 2aeab900d9dd4..35f0db1c71cb4 100644 --- a/recipes/bioconductor-cyanofilter/meta.yaml +++ b/recipes/bioconductor-cyanofilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "cyanoFilter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 368e6b94dab2f6f3e34e633dc2d6a14c + md5: a562257b012ddcf28b78c5cee7e85fa3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cyanofilter", max_pin="x.x") }}' noarch: generic # Suggests: magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowdensity >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowdensity >=1.36.0,<1.37.0' - r-base - r-cytometree - r-ggally - r-ggplot2 - r-mrfdepth run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowdensity >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowdensity >=1.36.0,<1.37.0' - r-base - r-cytometree - r-ggally diff --git a/recipes/bioconductor-cycle/meta.yaml b/recipes/bioconductor-cycle/meta.yaml index 860242e4bf1b7..f9388f490a65e 100644 --- a/recipes/bioconductor-cycle/meta.yaml +++ b/recipes/bioconductor-cycle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "cycle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 04088083f69f37fd4bf35ad28e0b57ae + md5: 8c659d2ae2fb2b31f4b6dd07d68873be build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cycle", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-mfuzz >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-mfuzz >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-mfuzz >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-mfuzz >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-cydar/meta.yaml b/recipes/bioconductor-cydar/meta.yaml index 9e2835f0bcff6..4f5ab55d02786 100644 --- a/recipes/bioconductor-cydar/meta.yaml +++ b/recipes/bioconductor-cydar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "cydar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7b8dbb3a9113d2bba4b2a9f656e8edb1 + md5: b804632cc0742b1e2f9910353a6ed75d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cydar", max_pin="x.x") }}' # Suggests: ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet, BiocStyle, flowStats # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-rcpp - r-shiny @@ -36,14 +37,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-rcpp - r-shiny diff --git a/recipes/bioconductor-cyp450cdf/meta.yaml b/recipes/bioconductor-cyp450cdf/meta.yaml index 24e5aa29562cf..278e2ac3086d0 100644 --- a/recipes/bioconductor-cyp450cdf/meta.yaml +++ b/recipes/bioconductor-cyp450cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "cyp450cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7923c4d24b7b654d0f59d52ed2258eb9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cyp450cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cytodx/meta.yaml b/recipes/bioconductor-cytodx/meta.yaml index b7755fcbf70b2..fa2f5ec95a63d 100644 --- a/recipes/bioconductor-cytodx/meta.yaml +++ b/recipes/bioconductor-cytodx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CytoDx" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 34c6cd6a96a62551f4ca24cb91b76842 + md5: 86d2f225be6ebdaecd3aa4960e443796 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytodx", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-doparallel - r-dplyr @@ -29,7 +30,7 @@ requirements: - r-rpart - r-rpart.plot run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-doparallel - r-dplyr diff --git a/recipes/bioconductor-cytofpower/meta.yaml b/recipes/bioconductor-cytofpower/meta.yaml index a2083e7d3ff5b..981d052fa8067 100644 --- a/recipes/bioconductor-cytofpower/meta.yaml +++ b/recipes/bioconductor-cytofpower/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "CyTOFpower" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b01cc449a6fe4426458624c5705bcec9 + md5: ea70d698bf8ba363250de04f634c5f74 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytofpower", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), BiocStyle, knitr requirements: host: - - 'bioconductor-cytoglmm >=1.8.0,<1.9.0' - - 'bioconductor-diffcyt >=1.20.0,<1.21.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-cytoglmm >=1.10.0,<1.11.0' + - 'bioconductor-diffcyt >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-dt @@ -37,9 +38,9 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-cytoglmm >=1.8.0,<1.9.0' - - 'bioconductor-diffcyt >=1.20.0,<1.21.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-cytoglmm >=1.10.0,<1.11.0' + - 'bioconductor-diffcyt >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-dt diff --git a/recipes/bioconductor-cytofqc/meta.yaml b/recipes/bioconductor-cytofqc/meta.yaml index d21510eafbdd4..47f974c4c82e4 100644 --- a/recipes/bioconductor-cytofqc/meta.yaml +++ b/recipes/bioconductor-cytofqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "cytofQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d0505813678c5c80055b22702fd6efc1 + md5: 7a4e866c0e57f639b41828c211aff31f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytofqc", max_pin="x.x") }}' noarch: generic # Suggests: gridExtra, knitr, RColorBrewer, testthat, uwot requirements: host: - - 'bioconductor-catalyst >=1.24.0,<1.25.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-catalyst >=1.26.0,<1.27.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-eztune @@ -37,11 +38,11 @@ requirements: - r-rmarkdown - r-ssc run: - - 'bioconductor-catalyst >=1.24.0,<1.25.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-catalyst >=1.26.0,<1.27.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-eztune diff --git a/recipes/bioconductor-cytoglmm/meta.yaml b/recipes/bioconductor-cytoglmm/meta.yaml index f4c4346d39a43..7c2e9656c33dc 100644 --- a/recipes/bioconductor-cytoglmm/meta.yaml +++ b/recipes/bioconductor-cytoglmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "CytoGLMM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c5784f488db9c90aee9aaef89bb2979f + md5: 3a4b95062a82da6afe217f20ef905460 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytoglmm", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-caret - r-cowplot @@ -44,7 +45,7 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-caret - r-cowplot diff --git a/recipes/bioconductor-cytokernel/meta.yaml b/recipes/bioconductor-cytokernel/meta.yaml index 07981eccb8167..e78587f65500f 100644 --- a/recipes/bioconductor-cytokernel/meta.yaml +++ b/recipes/bioconductor-cytokernel/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "cytoKernel" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5a4d7c512bf35c94d3ff2ba67915455 + md5: 2e1e2b8d2c545a69a0cec180964f2fd9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytokernel", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ashr - r-base - r-circlize @@ -35,10 +36,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ashr - r-base - r-circlize diff --git a/recipes/bioconductor-cytolib/meta.yaml b/recipes/bioconductor-cytolib/meta.yaml index fab17798770e4..9c473184d4d42 100644 --- a/recipes/bioconductor-cytolib/meta.yaml +++ b/recipes/bioconductor-cytolib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "cytolib" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9f90833841459092d549952e5d99124e + md5: f06a976c84ae2adf3c08d07cd90af7f4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytolib", max_pin="x.x") }}' # Suggests: knitr, rmarkdown # SystemRequirements: GNU make, C++11 requirements: host: - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-rprotobuflib >=2.12.0,<2.13.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' - r-base - - 'r-bh >=1.75.0.0' + - 'r-bh >=1.81.0.0' - libblas - liblapack run: - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-rprotobuflib >=2.12.0,<2.13.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' - r-base - - 'r-bh >=1.75.0.0' + - 'r-bh >=1.81.0.0' build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-cytomapper/meta.yaml b/recipes/bioconductor-cytomapper/meta.yaml index c120d00160aca..cd40bb5f75e8b 100644 --- a/recipes/bioconductor-cytomapper/meta.yaml +++ b/recipes/bioconductor-cytomapper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "cytomapper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a792c54688d69d44dbf91fd86d900a08 + md5: 140e57707c43aeb7bd3b2e48b634464a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytomapper", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat, shinytest requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggbeeswarm - r-ggplot2 @@ -43,15 +44,15 @@ requirements: - r-svgpanzoom - r-viridis run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggbeeswarm - r-ggplot2 diff --git a/recipes/bioconductor-cytomem/meta.yaml b/recipes/bioconductor-cytomem/meta.yaml index abdb5dec2f33b..5c3bb8333f7b3 100644 --- a/recipes/bioconductor-cytomem/meta.yaml +++ b/recipes/bioconductor-cytomem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "cytoMEM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5727668f7e144170c6b66ed00a1fce77 + md5: 4a407b89f327c4c88301e81f982598f9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytomem", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-gplots - r-matrixstats run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-gplots - r-matrixstats diff --git a/recipes/bioconductor-cytoml/meta.yaml b/recipes/bioconductor-cytoml/meta.yaml index fb7b3b6300c72..ee27b56fde053 100644 --- a/recipes/bioconductor-cytoml/meta.yaml +++ b/recipes/bioconductor-cytoml/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "CytoML" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5118f217fc4d383753ddb7c749b5c949 + md5: 4b0060416cdeef7876cb9aaeb81dbaf7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytoml", max_pin="x.x") }}' # Suggests: testthat, flowWorkspaceData , knitr, rmarkdown, parallel # SystemRequirements: xml2, GNU make, C++11 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cytolib >=2.12.0,<2.13.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-ggcyto >=1.28.0,<1.29.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-opencyto >=2.12.0,<2.13.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-rprotobuflib >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cytolib >=2.14.0,<2.15.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-ggcyto >=1.30.0,<1.31.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-opencyto >=2.14.0,<2.15.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' - r-base - 'r-bh >=1.62.0-1' - r-cpp11 @@ -45,17 +46,17 @@ requirements: - liblapack - libxml2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cytolib >=2.12.0,<2.13.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-ggcyto >=1.28.0,<1.29.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-opencyto >=2.12.0,<2.13.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-rprotobuflib >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cytolib >=2.14.0,<2.15.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-ggcyto >=1.30.0,<1.31.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-opencyto >=2.14.0,<2.15.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' - r-base - 'r-bh >=1.62.0-1' - r-cpp11 diff --git a/recipes/bioconductor-cytopipeline/meta.yaml b/recipes/bioconductor-cytopipeline/meta.yaml index 5fbad5f102509..7e23057f3914e 100644 --- a/recipes/bioconductor-cytopipeline/meta.yaml +++ b/recipes/bioconductor-cytopipeline/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.2" %} +{% set version = "1.2.0" %} {% set name = "CytoPipeline" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 03008ccf1f86b39cc48a5f9fa82ae3a2 + md5: a4ed3b88553c7115d7dce368a0fda5a5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytopipeline", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-flowai >=1.30.0,<1.31.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-ggcyto >=1.28.0,<1.29.0' - - 'bioconductor-peacoqc >=1.10.0,<1.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-flowai >=1.32.0,<1.33.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-ggcyto >=1.30.0,<1.31.0' + - 'bioconductor-peacoqc >=1.12.0,<1.13.0' - r-base - r-diagram - 'r-ggplot2 >=3.4.1' @@ -35,12 +36,12 @@ requirements: - r-scales - r-withr run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-flowai >=1.30.0,<1.31.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-ggcyto >=1.28.0,<1.29.0' - - 'bioconductor-peacoqc >=1.10.0,<1.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-flowai >=1.32.0,<1.33.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-ggcyto >=1.30.0,<1.31.0' + - 'bioconductor-peacoqc >=1.12.0,<1.13.0' - r-base - r-diagram - 'r-ggplot2 >=3.4.1' diff --git a/recipes/bioconductor-cytopipelinegui/build.sh b/recipes/bioconductor-cytopipelinegui/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cytopipelinegui/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cytopipelinegui/meta.yaml b/recipes/bioconductor-cytopipelinegui/meta.yaml new file mode 100644 index 0000000000000..de5a7ec5baba2 --- /dev/null +++ b/recipes/bioconductor-cytopipelinegui/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "CytoPipelineGUI" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fb6a6a7aad638be11919a144f3d9907a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytopipelinegui", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, patchwork +requirements: + host: + - 'bioconductor-cytopipeline >=1.2.0,<1.3.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - r-base + - r-ggplot2 + - r-plotly + - r-shiny + run: + - 'bioconductor-cytopipeline >=1.2.0,<1.3.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - r-base + - r-ggplot2 + - r-plotly + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=3) | file LICENSE' + summary: 'GUI''s for visualization of flow cytometry data analysis pipelines' + description: 'This package is the companion of the `CytoPipeline` package. It provides GUI''s (shiny apps) for the visualization of flow cytometry data analysis pipelines that are run with `CytoPipeline`. Two shiny applications are provided, i.e. an interactive flow frame assessment and comparison tool and an interactive scale transformations visualization and adjustment tool.' + license_file: LICENSE + diff --git a/recipes/bioconductor-cytoviewer/meta.yaml b/recipes/bioconductor-cytoviewer/meta.yaml index be640d04c0d65..dbf9da026b8dd 100644 --- a/recipes/bioconductor-cytoviewer/meta.yaml +++ b/recipes/bioconductor-cytoviewer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "cytoviewer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: def4b0774e3872eb4cca490bd369318e + md5: dc34f69f53490911e6f621d76db69f4c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytoviewer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat requirements: host: - - 'bioconductor-cytomapper >=1.12.0,<1.13.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-cytomapper >=1.14.0,<1.15.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-archive - r-base - r-colourpicker @@ -37,11 +38,11 @@ requirements: - r-svgpanzoom - r-viridis run: - - 'bioconductor-cytomapper >=1.12.0,<1.13.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-cytomapper >=1.14.0,<1.15.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-archive - r-base - r-colourpicker diff --git a/recipes/bioconductor-dada2/meta.yaml b/recipes/bioconductor-dada2/meta.yaml index 34e6608a6fe44..6e500493c1345 100644 --- a/recipes/bioconductor-dada2/meta.yaml +++ b/recipes/bioconductor-dada2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "dada2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8825d2a5c14a5d9ad3482743da42a215 + md5: 096baf34b4618af27b1b430945d3a189 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dada2", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-ggplot2 >=2.1.0' - 'r-rcpp >=0.12.0' @@ -34,11 +35,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-ggplot2 >=2.1.0' - 'r-rcpp >=0.12.0' diff --git a/recipes/bioconductor-daglogo/meta.yaml b/recipes/bioconductor-daglogo/meta.yaml index cba07b792c916..0e97dccda1777 100644 --- a/recipes/bioconductor-daglogo/meta.yaml +++ b/recipes/bioconductor-daglogo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "dagLogo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 143a623abf782e42e9c0ddf40f058e0d + md5: cb8662ee04599fa0076e344d2bf933d1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-daglogo", max_pin="x.x") }}' noarch: generic # Suggests: XML, grImport, grImport2, BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' - - 'bioconductor-uniprot.ws >=2.40.0,<2.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' + - 'bioconductor-uniprot.ws >=2.42.0,<2.43.0' - r-base - r-httr - r-pheatmap run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' - - 'bioconductor-uniprot.ws >=2.40.0,<2.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' + - 'bioconductor-uniprot.ws >=2.42.0,<2.43.0' - r-base - r-httr - r-pheatmap diff --git a/recipes/bioconductor-dama/meta.yaml b/recipes/bioconductor-dama/meta.yaml index 94240cd993003..6f827bb23d349 100644 --- a/recipes/bioconductor-dama/meta.yaml +++ b/recipes/bioconductor-dama/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "daMA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 491bcd2f0f98f6fae9a9914a1d9f39cd + md5: ec7e80e81b9d6eb5a76ce06c761bb7da build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dama", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-damefinder/meta.yaml b/recipes/bioconductor-damefinder/meta.yaml index 393440433602d..070f5d8dc6e1a 100644 --- a/recipes/bioconductor-damefinder/meta.yaml +++ b/recipes/bioconductor-damefinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "DAMEfinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90d7b5746b798073b831599c1f17dddc + md5: 0f99003a20995ebd0c15fce1a407765f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-damefinder", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-cowplot - r-ggplot2 @@ -41,18 +42,18 @@ requirements: - r-reshape2 - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-cowplot - r-ggplot2 diff --git a/recipes/bioconductor-damirseq/meta.yaml b/recipes/bioconductor-damirseq/meta.yaml index ddfdd6adad361..8f31010215ab8 100644 --- a/recipes/bioconductor-damirseq/meta.yaml +++ b/recipes/bioconductor-damirseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "DaMiRseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 40d2de748f89528f9be59dff14696cdb + md5: 64986e7db314ddba69d156b35f974680 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-damirseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-arm - r-base - r-caret @@ -49,12 +50,12 @@ requirements: - r-reshape2 - r-rsnns run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-arm - r-base - r-caret @@ -85,8 +86,7 @@ about: summary: 'Data Mining for RNA-seq data: normalization, feature selection and classification' description: 'The DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them for both binary and multi-class classification purposes. The package accepts any kind of data presented as a table of raw counts and allows including both continous and factorial variables that occur with the experimental setting. A series of functions enable the user to clean up the data by filtering genomic features and samples, to adjust data by identifying and removing the unwanted source of variation (i.e. batches and confounding factors) and to select the best predictors for modeling. Finally, a "stacking" ensemble learning technique is applied to build a robust classification model. Every step includes a checkpoint that the user may exploit to assess the effects of data management by looking at diagnostic plots, such as clustering and heatmaps, RLE boxplots, MDS or correlation plot.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - extra: container: - extended-base: True + extended-base: true diff --git a/recipes/bioconductor-dapar/meta.yaml b/recipes/bioconductor-dapar/meta.yaml index bcc1f3cc45b40..3e5c822b5adaa 100644 --- a/recipes/bioconductor-dapar/meta.yaml +++ b/recipes/bioconductor-dapar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.2" %} +{% set version = "1.34.2" %} {% set name = "DAPAR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,110 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 795af5225e1256f97f94864c8002aae6 + md5: 98c2672a3b694f6d1989cdd4f00cd8e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dapar", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, BiocStyle, AnnotationDbi, clusterProfiler, graph, diptest, cluster, vioplot, visNetwork, vsn, igraph, FactoMineR, factoextra, dendextend, parallel, doParallel, Mfuzz, apcluster, forcats, readxl, openxlsx, multcomp, purrr, tibble, knitr, norm, scales, tidyverse, cp4p, imp4p (>= 1.1),lme4, dplyr, limma, preprocessCore, stringr, tidyr, impute, gplots, grDevices, reshape2, graphics, stats, methods, ggplot2, RColorBrewer, Matrix, org.Sc.sgd.db +# Suggests: testthat, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dapardata >=1.30.0,<1.31.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-dapardata >=1.32.0,<1.33.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mfuzz >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' + - r-apcluster - r-base + - r-cluster + - r-cp4p + - r-dendextend + - r-diptest + - r-doparallel + - r-dplyr + - r-factoextra + - r-factominer + - r-forcats - r-foreach + - r-ggplot2 + - r-gplots - r-highcharter + - r-igraph + - r-imp4p + - r-knitr + - r-lme4 + - r-matrix + - r-multcomp + - r-norm + - r-openxlsx + - r-purrr + - r-rcolorbrewer + - r-readxl + - r-reshape2 + - r-scales + - r-stringr + - r-tibble + - r-tidyr + - r-tidyverse + - r-vioplot + - r-visnetwork run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dapardata >=1.30.0,<1.31.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-dapardata >=1.32.0,<1.33.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mfuzz >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' + - r-apcluster - r-base + - r-cluster + - r-cp4p + - r-dendextend + - r-diptest + - r-doparallel + - r-dplyr + - r-factoextra + - r-factominer + - r-forcats - r-foreach + - r-ggplot2 + - r-gplots - r-highcharter + - r-igraph + - r-imp4p + - r-knitr + - r-lme4 + - r-matrix + - r-multcomp + - r-norm + - r-openxlsx + - r-purrr + - r-rcolorbrewer + - r-readxl + - r-reshape2 + - r-scales + - r-stringr + - r-tibble + - r-tidyr + - r-tidyverse + - r-vioplot + - r-visnetwork test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dapardata/meta.yaml b/recipes/bioconductor-dapardata/meta.yaml index c7ff1c8be6f2d..a88aae6c229f6 100644 --- a/recipes/bioconductor-dapardata/meta.yaml +++ b/recipes/bioconductor-dapardata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "DAPARdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d730f1b7ef4aab628882f7b9355c7b5 + md5: 5906f180d2e824affe9f2850424c7612 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dapardata", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, DAPAR +# Suggests: knitr, DAPAR, BiocStyle requirements: host: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base run: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dapardata/post-link.sh b/recipes/bioconductor-dapardata/post-link.sh index 0aa7a2b9ed549..3788427c5fce2 100644 --- a/recipes/bioconductor-dapardata/post-link.sh +++ b/recipes/bioconductor-dapardata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dapardata-1.30.0" +installBiocDataPackage.sh "dapardata-1.32.0" diff --git a/recipes/bioconductor-dart/meta.yaml b/recipes/bioconductor-dart/meta.yaml index 16e9a3deaa689..a29f5a06cb466 100644 --- a/recipes/bioconductor-dart/meta.yaml +++ b/recipes/bioconductor-dart/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "DART" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54c28a2ba5064bfed75a4e9e631a65c7 + md5: cc7bd6015b08890ec53f8004091c3bb5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dart", max_pin="x.x") }}' noarch: generic # Suggests: breastCancerVDX, breastCancerMAINZ, Biobase requirements: diff --git a/recipes/bioconductor-data-packages/dataURLs.json b/recipes/bioconductor-data-packages/dataURLs.json index 2c6d28f61bbda..2b5d690d1d314 100644 --- a/recipes/bioconductor-data-packages/dataURLs.json +++ b/recipes/bioconductor-data-packages/dataURLs.json @@ -1 +1 @@ -{"ritandata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.15/data/experiment/src/contrib/RITANdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/RITANdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ritandata/bioconductor-ritandata_1.20.0_src_all.tar.gz"], "md5": "4a9a65c5312893ef3bf279efd32d53f8", "fn": "RITANdata_1.20.0.tar.gz"}, "bioplex-1.3.4": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BioPlex_1.3.4.tar.gz", "https://bioarchive.galaxyproject.org/BioPlex_1.3.4.tar.gz", 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"https://depot.galaxyproject.org/software/bioconductor-ahlrbasedbs/bioconductor-ahlrbasedbs_1.5.0_src_all.tar.gz"], "md5": "b1266d2bab652542d6f7289898c3e781", "fn": "AHLRBaseDbs_1.5.0.tar.gz"}, "ahmeshdbs-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/AHMeSHDbs_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/AHMeSHDbs_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahmeshdbs/bioconductor-ahmeshdbs_1.5.0_src_all.tar.gz"], "md5": "87c396d15191843ec3cdced73bf504f8", "fn": "AHMeSHDbs_1.5.0.tar.gz"}, "ahpathbankdbs-0.99.5": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/AHPathbankDbs_0.99.5.tar.gz", "https://bioarchive.galaxyproject.org/AHPathbankDbs_0.99.5.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahpathbankdbs/bioconductor-ahpathbankdbs_0.99.5_src_all.tar.gz", 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"WES.1KG.WUGSC_1.34.0.tar.gz"}, "wgsmapp-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/WGSmapp_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/WGSmapp_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wgsmapp/bioconductor-wgsmapp_1.14.0_src_all.tar.gz"], "md5": "dfc3f5a82d532551e2d6c21b11c99566", "fn": "WGSmapp_1.14.0.tar.gz"}, "xcoredata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/xcoredata_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/xcoredata_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xcoredata/bioconductor-xcoredata_1.6.0_src_all.tar.gz"], "md5": "214626bfcbb5d66445324f6e367142c7", "fn": "xcoredata_1.6.0.tar.gz"}, "xhybcasneuf-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/XhybCasneuf_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/XhybCasneuf_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xhybcasneuf/bioconductor-xhybcasneuf_1.40.0_src_all.tar.gz"], "md5": "f3e6306b5c05fb026e36e4c60656e25a", "fn": "XhybCasneuf_1.40.0.tar.gz"}, "yeastcc-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastCC_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastCC_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastcc/bioconductor-yeastcc_1.42.0_src_all.tar.gz"], "md5": "847d9bba73cb25f458f608c2cd6bf0e8", "fn": "yeastCC_1.42.0.tar.gz"}, "yeastexpdata-0.48.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastExpData_0.48.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastExpData_0.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastexpdata/bioconductor-yeastexpdata_0.48.0_src_all.tar.gz"], "md5": "7cd63808a957defe831bf3e9d3ef4789", "fn": "yeastExpData_0.48.0.tar.gz"}, "yeastgsdata-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastGSData_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastGSData_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastgsdata/bioconductor-yeastgsdata_0.40.0_src_all.tar.gz"], "md5": "bc455a9ecd3eb2652f887026841b3c69", "fn": "yeastGSData_0.40.0.tar.gz"}, "yeastnagalakshmi-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastNagalakshmi_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastNagalakshmi_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastnagalakshmi/bioconductor-yeastnagalakshmi_1.38.0_src_all.tar.gz"], "md5": "ea5068bf2b4053452f416c56ab32736a", "fn": "yeastNagalakshmi_1.38.0.tar.gz"}, "yeastrnaseq-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastRNASeq_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastRNASeq_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastrnaseq/bioconductor-yeastrnaseq_0.40.0_src_all.tar.gz"], "md5": "2344deacf993b96e1709ad96b710471f", "fn": "yeastRNASeq_0.40.0.tar.gz"}, "zebrafishrnaseq-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/zebrafishRNASeq_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafishRNASeq_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafishrnaseq/bioconductor-zebrafishrnaseq_1.22.0_src_all.tar.gz"], "md5": "c1fcbadec1b25e4b28483c015f7ab35c", "fn": "zebrafishRNASeq_1.22.0.tar.gz"}} \ No newline at end of file diff --git a/recipes/bioconductor-data-packages/meta.yaml b/recipes/bioconductor-data-packages/meta.yaml index e1e4b22d3f8b8..9a5e1a2092398 100644 --- a/recipes/bioconductor-data-packages/meta.yaml +++ b/recipes/bioconductor-data-packages/meta.yaml @@ -1,10 +1,12 @@ package: name: 'bioconductor-data-packages' - version: '20230718' + version: '20231203' source: build: - number: 1 + number: 0 noarch: generic + run_exports: + - {{ pin_subpackage("bioconductor-data-packages", max_pin=None) }} requirements: run: - r-base diff --git a/recipes/bioconductor-davidtiling/meta.yaml b/recipes/bioconductor-davidtiling/meta.yaml index c60799926ebfa..35f0720944fec 100644 --- a/recipes/bioconductor-davidtiling/meta.yaml +++ b/recipes/bioconductor-davidtiling/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "davidTiling" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa55aaed3cb0a0e29db8c538c636b447 + md5: dace46d6f640014aff544e0faf355b5e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-davidtiling", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-tilingarray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-tilingarray >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-tilingarray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-tilingarray >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-davidtiling/post-link.sh b/recipes/bioconductor-davidtiling/post-link.sh index 2c0cdbe1d7e3e..ebb07a26801fe 100644 --- a/recipes/bioconductor-davidtiling/post-link.sh +++ b/recipes/bioconductor-davidtiling/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "davidtiling-1.40.0" +installBiocDataPackage.sh "davidtiling-1.42.0" diff --git a/recipes/bioconductor-dcanr/meta.yaml b/recipes/bioconductor-dcanr/meta.yaml index d01daf020a69d..839e3b308764b 100644 --- a/recipes/bioconductor-dcanr/meta.yaml +++ b/recipes/bioconductor-dcanr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "dcanr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d2c15eccd56d9265e4b6d81fa4ab3653 + md5: 1a30832879c85ae9430a463d581ba978 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dcanr", max_pin="x.x") }}' noarch: generic # Suggests: EBcoexpress, testthat, EBarrays, GeneNet, mclust, minqa, SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle, edgeR requirements: diff --git a/recipes/bioconductor-dcats/build.sh b/recipes/bioconductor-dcats/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dcats/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dcats/meta.yaml b/recipes/bioconductor-dcats/meta.yaml new file mode 100644 index 0000000000000..121d93a21050b --- /dev/null +++ b/recipes/bioconductor-dcats/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "DCATS" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8a6002426027bd88d05a2b8759d5a12e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dcats", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat (>= 3.0.0), knitr, Seurat, SeuratObject, tidyverse, rmarkdown, BiocStyle +requirements: + host: + - r-aod + - r-base + - r-e1071 + - r-matrixstats + - r-mcmcpack + - r-robustbase + run: + - r-aod + - r-base + - r-e1071 + - r-matrixstats + - r-mcmcpack + - r-robustbase +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Differential Composition Analysis Transformed by a Similarity matrix' + description: 'Methods to detect the differential composition abundances between conditions in singel-cell RNA-seq experiments, with or without replicates. It aims to correct bias introduced by missclaisification and enable controlling of confounding covariates. To avoid the influence of proportion change from big cell types, DCATS can use either total cell number or specific reference group as normalization term.' + license_file: LICENSE + diff --git a/recipes/bioconductor-dce/meta.yaml b/recipes/bioconductor-dce/meta.yaml index d2b9af554e2c9..82addc1e3b3ab 100644 --- a/recipes/bioconductor-dce/meta.yaml +++ b/recipes/bioconductor-dce/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.7.0" %} +{% set version = "1.10.0" %} {% set name = "dce" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 43a65a2d1518138f7f6a6984e025fcde + md5: dbebdd246ea193f92c1a466a84617876 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dce", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, cowplot, ggplotify, dagitty, lmtest, sandwich, devtools, curatedTCGAData, TCGAutils, SummarizedExperiment, RcppParallel, docopt, CARNIVAL requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-epinem >=1.24.0,<1.25.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-mnem >=1.16.0,<1.17.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-epinem >=1.26.0,<1.27.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-mnem >=1.18.0,<1.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-assertthat - r-base - r-dplyr @@ -53,13 +54,13 @@ requirements: - r-tidygraph - r-tidyverse run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-epinem >=1.24.0,<1.25.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-mnem >=1.16.0,<1.17.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-epinem >=1.26.0,<1.27.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-mnem >=1.18.0,<1.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-assertthat - r-base - r-dplyr diff --git a/recipes/bioconductor-dcgsa/meta.yaml b/recipes/bioconductor-dcgsa/meta.yaml index 77f6314b8fb7d..81d2701989b49 100644 --- a/recipes/bioconductor-dcgsa/meta.yaml +++ b/recipes/bioconductor-dcgsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "dcGSA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4c250b2149d2ecfe5fa7b22d305b6753 + md5: f824cffdf3d7c4f41b44d2cc46b69998 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dcgsa", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-matrix run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-ddct/meta.yaml b/recipes/bioconductor-ddct/meta.yaml index 2d4d457b53232..88e86641ae0b3 100644 --- a/recipes/bioconductor-ddct/meta.yaml +++ b/recipes/bioconductor-ddct/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "ddCt" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e9800430fe0d1654a624db09b883e2c + md5: 560588380b356d55a4e11811ae9100e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ddct", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), RUnit requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-lattice - 'r-rcolorbrewer >=0.1-3' - r-xtable run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-lattice - 'r-rcolorbrewer >=0.1-3' diff --git a/recipes/bioconductor-ddpcrclust/meta.yaml b/recipes/bioconductor-ddpcrclust/meta.yaml index f01a2b33e6d6e..342aec460ad83 100644 --- a/recipes/bioconductor-ddpcrclust/meta.yaml +++ b/recipes/bioconductor-ddpcrclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ddPCRclust" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04448bd253195b441eabc6f2f17b208e + md5: 63c29b24786957fcb604e73a61066e47 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ddpcrclust", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowdensity >=1.34.0,<1.35.0' - - 'bioconductor-flowpeaks >=1.46.0,<1.47.0' - - 'bioconductor-samspectral >=1.54.0,<1.55.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowdensity >=1.36.0,<1.37.0' + - 'bioconductor-flowpeaks >=1.48.0,<1.49.0' + - 'bioconductor-samspectral >=1.56.0,<1.57.0' - r-base - r-clue - r-ggplot2 @@ -32,10 +33,10 @@ requirements: - r-plotrix - r-r.utils run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowdensity >=1.34.0,<1.35.0' - - 'bioconductor-flowpeaks >=1.46.0,<1.47.0' - - 'bioconductor-samspectral >=1.54.0,<1.55.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowdensity >=1.36.0,<1.37.0' + - 'bioconductor-flowpeaks >=1.48.0,<1.49.0' + - 'bioconductor-samspectral >=1.56.0,<1.57.0' - r-base - r-clue - r-ggplot2 diff --git a/recipes/bioconductor-dearseq/meta.yaml b/recipes/bioconductor-dearseq/meta.yaml index b67e37a6861c6..d73ece4475cbb 100644 --- a/recipes/bioconductor-dearseq/meta.yaml +++ b/recipes/bioconductor-dearseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "dearseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 544bd47d884e994f11d6b49f331a4915 + md5: 40f5669b310e7d2142836e3b1592bdd6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dearseq", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA, knitr, limma, readxl, rmarkdown, S4Vectors, SummarizedExperiment, testthat, covr requirements: diff --git a/recipes/bioconductor-debcam/meta.yaml b/recipes/bioconductor-debcam/meta.yaml index 14ea154da7e6e..0af1f12365332 100644 --- a/recipes/bioconductor-debcam/meta.yaml +++ b/recipes/bioconductor-debcam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "debCAM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 777e6f50d5b0121ba5cc208d1697512b + md5: 87d118edcaf90e70fd6aafc865ac5c6a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-debcam", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl # SystemRequirements: Java (>= 1.8) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-apcluster - r-base - r-corpcor @@ -36,9 +37,9 @@ requirements: - r-rjava - openjdk run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-apcluster - r-base - r-corpcor diff --git a/recipes/bioconductor-debrowser/meta.yaml b/recipes/bioconductor-debrowser/meta.yaml index 6c96afb5dbe75..ba6472bfcdadd 100644 --- a/recipes/bioconductor-debrowser/meta.yaml +++ b/recipes/bioconductor-debrowser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.2" %} +{% set version = "1.30.0" %} {% set name = "debrowser" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6deaca84c5d4d7f700e23ab0887b4567 + md5: dc51add531d95b1e7a924062aa773018 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-debrowser", max_pin="x.x") }}' noarch: generic # Suggests: testthat, rmarkdown, knitr requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-harman >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-harman >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-ashr - r-base - r-colourpicker @@ -58,24 +59,24 @@ requirements: - r-shinyjs - r-stringi run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-harman >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-harman >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-ashr - r-base - r-colourpicker diff --git a/recipes/bioconductor-decipher/meta.yaml b/recipes/bioconductor-decipher/meta.yaml index 4ce9ee8807ab5..257e0cf8b5364 100644 --- a/recipes/bioconductor-decipher/meta.yaml +++ b/recipes/bioconductor-decipher/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "DECIPHER" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9396595ebcedf5d570edb11acc6198e0 + md5: 0a32c782d61a604dc3594c684daa8c75 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-decipher", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-dbi - 'r-rsqlite >=1.1' - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-dbi - 'r-rsqlite >=1.1' diff --git a/recipes/bioconductor-decomptumor2sig/meta.yaml b/recipes/bioconductor-decomptumor2sig/meta.yaml index fc0d87e519d65..a220fbdc707c4 100644 --- a/recipes/bioconductor-decomptumor2sig/meta.yaml +++ b/recipes/bioconductor-decomptumor2sig/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "decompTumor2Sig" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6e5ef097fd6a7f21bc4d0aea7cb72a00 + md5: efd7bdadb25752241823124b560e9214 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-decomptumor2sig", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-ggplot2 @@ -41,16 +42,16 @@ requirements: - 'r-quadprog >=1.5-5' - r-readxl run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-deconrnaseq/meta.yaml b/recipes/bioconductor-deconrnaseq/meta.yaml index dc799c1ab8852..a32a24d5aab35 100644 --- a/recipes/bioconductor-deconrnaseq/meta.yaml +++ b/recipes/bioconductor-deconrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "DeconRNASeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fe6899279ea73a5b02aee2addc34f38d + md5: d38af67b8408b66b85fbb4061442b953 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deconrnaseq", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - r-base - r-ggplot2 - r-limsolve run: - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - r-base - r-ggplot2 - r-limsolve diff --git a/recipes/bioconductor-decontam/meta.yaml b/recipes/bioconductor-decontam/meta.yaml index c451e14479b93..92c3bba5ab045 100644 --- a/recipes/bioconductor-decontam/meta.yaml +++ b/recipes/bioconductor-decontam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "decontam" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 549a965f3aa9c02b7c4533c81acd2252 + md5: 0e6be1cbff9c4396692e39aadc0a5b9e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-decontam", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, phyloseq requirements: diff --git a/recipes/bioconductor-decontx/build.sh b/recipes/bioconductor-decontx/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-decontx/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-decontx/meta.yaml b/recipes/bioconductor-decontx/meta.yaml new file mode 100644 index 0000000000000..4a08a6867b10a --- /dev/null +++ b/recipes/bioconductor-decontx/meta.yaml @@ -0,0 +1,88 @@ +{% set version = "1.0.0" %} +{% set name = "decontX" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1e2f4af9204397b8104543dd954bb390 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-decontx", max_pin="x.x") }}' +# Suggests: BiocStyle, dplyr, knitr, rmarkdown, scran, SingleCellMultiModal, TENxPBMCData, testthat (>= 3.0.0) +# SystemRequirements: GNU make +requirements: + host: + - 'bioconductor-celda >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - 'r-bh >=1.66.0' + - r-dbscan + - r-ggplot2 + - 'r-matrix >=1.5.3' + - r-mcmcprecision + - r-patchwork + - r-plyr + - 'r-rcpp >=0.12.0' + - 'r-rcppeigen >=0.3.3.3.0' + - 'r-rcppparallel >=5.0.1' + - r-reshape2 + - 'r-rstan >=2.18.1' + - 'r-rstantools >=2.2.0' + - r-seurat + - 'r-stanheaders >=2.18.0' + - r-withr + - libblas + - liblapack + run: + - 'bioconductor-celda >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - 'r-bh >=1.66.0' + - r-dbscan + - r-ggplot2 + - 'r-matrix >=1.5.3' + - r-mcmcprecision + - r-patchwork + - r-plyr + - 'r-rcpp >=0.12.0' + - 'r-rcppeigen >=0.3.3.3.0' + - 'r-rcppparallel >=5.0.1' + - r-reshape2 + - 'r-rstan >=2.18.1' + - 'r-rstantools >=2.2.0' + - r-seurat + - 'r-stanheaders >=2.18.0' + - r-withr + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Decontamination of single cell genomics data' + description: 'This package contains implementation of DecontX (Yang et al. 2020), a decontamination algorithm for single-cell RNA-seq, and DecontPro (Yin et al. 2023), a decontamination algorithm for single cell protein expression data. DecontX is a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. DecontPro is a Bayesian method that estimates the level of contamination from ambient and background sources in CITE-seq ADT dataset and decontaminate the dataset.' + license_file: LICENSE + diff --git a/recipes/bioconductor-deconvr/meta.yaml b/recipes/bioconductor-deconvr/meta.yaml index ddfd91252440c..ea453fe8601db 100644 --- a/recipes/bioconductor-deconvr/meta.yaml +++ b/recipes/bioconductor-deconvr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "deconvR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 378b68def947127eaecc6e0f16231a81 + md5: 77963b41f8655665f3aac5e2cb1d529c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deconvr", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), roxygen2 (>= 7.1.2), doParallel (>= 1.0.16), parallel, knitr (>= 1.34), BiocStyle (>= 2.20.2), reshape2 (>= 1.4.4), ggplot2 (>= 3.3.5), rmarkdown, devtools (>= 2.4.2), sessioninfo (>= 1.1.1), covr, granulator, RefManageR requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-methylkit >=1.26.0,<1.27.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-methylkit >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - 'r-data.table >=1.14.0' @@ -41,12 +42,12 @@ requirements: - 'r-rsq >=2.2' - 'r-tidyr >=1.1.3' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-methylkit >=1.26.0,<1.27.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-methylkit >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - 'r-data.table >=1.14.0' diff --git a/recipes/bioconductor-decoupler/meta.yaml b/recipes/bioconductor-decoupler/meta.yaml index ff57fa682a15e..5694c36e329e4 100644 --- a/recipes/bioconductor-decoupler/meta.yaml +++ b/recipes/bioconductor-decoupler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "decoupleR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46b97475fd42e3633fb5c40d26c88d4e + md5: de2a391693476223ec54521aa77ba121 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-decoupler", max_pin="x.x") }}' noarch: generic # Suggests: glmnet (>= 4.1.0), GSVA, viper, fgsea (>= 1.15.4), AUCell, SummarizedExperiment, rpart, ranger, BiocStyle, covr, knitr, pkgdown, RefManageR, rmarkdown, roxygen2, sessioninfo, pheatmap, testthat, OmnipathR, Seurat, ggplot2, ggrepel, patchwork requirements: diff --git a/recipes/bioconductor-deepbluer/build_failure.linux-64.yaml b/recipes/bioconductor-deepbluer/build_failure.linux-64.yaml index 32a64afe45536..4cd5b4a0d4f6b 100644 --- a/recipes/bioconductor-deepbluer/build_failure.linux-64.yaml +++ b/recipes/bioconductor-deepbluer/build_failure.linux-64.yaml @@ -1,72 +1,72 @@ -recipe_sha: b09c118bdb9ad88319ef992ea639cfc1161541201e802900f905d1027c7fcdcc # The commit at which this recipe failed to build. +recipe_sha: 298dc02b6321425f565f394b84e67a916cb488fbfb52ae216e284b9f02ba71ce # The commit at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- - r-withr: 2.5.0-r43hc72bb7e_2 conda-forge - r-xfun: 0.39-r43ha503ecb_1 conda-forge - r-xml: 3.99_0.14-r43hc38eee6_2 conda-forge - r-yaml: 2.3.7-r43h57805ef_1 conda-forge - readline: 8.2-h8228510_1 conda-forge - sed: 4.8-he412f7d_0 conda-forge - setuptools: 68.0.0-pyhd8ed1ab_0 conda-forge sysroot_linux-64: 2.12-he073ed8_16 conda-forge - tk: 8.6.12-h27826a3_0 conda-forge - tktable: 2.10-hb7b940f_3 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h0c5db8f_5 conda-forge toml: 0.10.2-pyhd8ed1ab_0 conda-forge - tomlkit: 0.11.8-pyha770c72_0 conda-forge - tzdata: 2023c-h71feb2d_0 conda-forge - wheel: 0.40.0-pyhd8ed1ab_1 conda-forge + tomlkit: 0.12.3-pyha770c72_0 conda-forge + tzdata: 2023d-h0c530f3_0 conda-forge + wheel: 0.42.0-pyhd8ed1ab_0 conda-forge xmltodict: 0.13.0-pyhd8ed1ab_0 conda-forge xorg-kbproto: 1.0.7-h7f98852_1002 conda-forge - xorg-libice: 1.0.10-h7f98852_0 conda-forge - xorg-libsm: 1.2.3-hd9c2040_1000 conda-forge - xorg-libx11: 1.8.6-h8ee46fc_0 conda-forge + xorg-libice: 1.1.1-hd590300_0 conda-forge + xorg-libsm: 1.2.4-h7391055_0 conda-forge + xorg-libx11: 1.8.7-h8ee46fc_0 conda-forge xorg-libxau: 1.0.11-hd590300_0 conda-forge xorg-libxdmcp: 1.1.3-h7f98852_0 conda-forge xorg-libxext: 1.3.4-h0b41bf4_2 conda-forge xorg-libxrender: 0.9.11-hd590300_0 conda-forge - xorg-libxt: 1.3.0-hd590300_0 conda-forge + xorg-libxt: 1.3.0-hd590300_1 conda-forge xorg-renderproto: 0.11.1-h7f98852_1002 conda-forge xorg-xextproto: 7.3.0-h0b41bf4_1003 conda-forge xorg-xproto: 7.0.31-h7f98852_1007 conda-forge xz: 5.2.6-h166bdaf_0 conda-forge yaml: 0.2.5-h7f98852_2 conda-forge - yq: 3.2.2-pyhd8ed1ab_0 conda-forge + yq: 3.2.3-pyhd8ed1ab_0 conda-forge zlib: 1.2.13-hd590300_5 conda-forge - zstd: 1.5.2-hfc55251_7 conda-forge + zstd: 1.5.5-hfc55251_0 conda-forge Preparing transaction: ...working... done Verifying transaction: ...working... done - Executing transaction: ...working... done + Executing transaction: ...working... + To install TinyTeX with tinytex::install_tinytex() the system must have a functional Perl + installation with a File::Find module. Most end-user systems will already satisfy this + requirement; however, some minimal contexts (e.g., containers) may not. Perl is available + via Conda Forge as the package perl. See https://github.com/rstudio/tinytex/issues/419 + + + done [34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 533.1kB/s 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 756.0kB/s 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 1.8MB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.4MB/s 0.0s [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 1.3MB/s 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 4.1MB/s 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.0MB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.4MB/s 0.0s [?25h ## Package Plan ## - environment location: /opt/conda/conda-bld/bioconductor-deepbluer_1689835533309/_build_env + environment location: /opt/conda/conda-bld/bioconductor-deepbluer_1703295180448/_build_env Source cache directory is: /opt/conda/conda-bld/src_cache INFO:conda_build.source:Source cache directory is: /opt/conda/conda-bld/src_cache - Downloading source to cache: DeepBlueR_1.26.0_6b686d18b4.tar.gz - INFO:conda_build.source:Downloading source to cache: DeepBlueR_1.26.0_6b686d18b4.tar.gz - Downloading https://bioconductor.org/packages/3.17/bioc/src/contrib/DeepBlueR_1.26.0.tar.gz - INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.17/bioc/src/contrib/DeepBlueR_1.26.0.tar.gz + Downloading source to cache: DeepBlueR_1.27.0_2217f4325c.tar.gz + INFO:conda_build.source:Downloading source to cache: DeepBlueR_1.27.0_2217f4325c.tar.gz + Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/DeepBlueR_1.27.0.tar.gz + INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/DeepBlueR_1.27.0.tar.gz Success INFO:conda_build.source:Success Extracting download - source tree in: /opt/conda/conda-bld/bioconductor-deepbluer_1689835533309/work - export PREFIX=/opt/conda/conda-bld/bioconductor-deepbluer_1689835533309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ - export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-deepbluer_1689835533309/_build_env - export SRC_DIR=/opt/conda/conda-bld/bioconductor-deepbluer_1689835533309/work + source tree in: /opt/conda/conda-bld/bioconductor-deepbluer_1703295180448/work + export PREFIX=/opt/conda/conda-bld/bioconductor-deepbluer_1703295180448/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-deepbluer_1703295180448/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-deepbluer_1703295180448/work During startup - Warning message: Setting LC_TIME failed, using "C" - * installing to library /opt/conda/conda-bld/bioconductor-deepbluer_1689835533309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library + * installing to library /opt/conda/conda-bld/bioconductor-deepbluer_1703295180448/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library * installing *source* package DeepBlueR ... ** using staged installation ** R @@ -79,10 +79,10 @@ log: |2- "503" Error in xml.rpc(deepblue_options("url"), "list_column_types", user_key) : Problems + ERROR: lazy loading failed for package DeepBlueR Error: unable to load R code in package DeepBlueR Execution halted - ERROR: lazy loading failed for package DeepBlueR - * removing /opt/conda/conda-bld/bioconductor-deepbluer_1689835533309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/DeepBlueR + * removing /opt/conda/conda-bld/bioconductor-deepbluer_1703295180448/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/DeepBlueR Traceback (most recent call last): File "/opt/conda/bin/conda-mambabuild", line 10, in sys.exit(main()) @@ -100,5 +100,5 @@ log: |2- return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-deepbluer_1689835533309/work/conda_build.sh']' returned non-zero exit status 1. + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-deepbluer_1703295180448/work/conda_build.sh']' returned non-zero exit status 1. # Last 100 lines of the build log. diff --git a/recipes/bioconductor-deepbluer/meta.yaml b/recipes/bioconductor-deepbluer/meta.yaml index 973fe509bbb9a..05c2f44656ae9 100644 --- a/recipes/bioconductor-deepbluer/meta.yaml +++ b/recipes/bioconductor-deepbluer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.27.0" %} {% set name = "DeepBlueR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b686d18b4c2c51cad4976f4187303fa + md5: 2217f4325cc72c3e22c330fa3a8dd25b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deepbluer", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, LOLA, Gviz, gplots, ggplot2, tidyr, RColorBrewer, matrixStats requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-diffr @@ -38,9 +39,9 @@ requirements: - r-withr - r-xml run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-diffr diff --git a/recipes/bioconductor-deeppincs/meta.yaml b/recipes/bioconductor-deeppincs/meta.yaml index 9551fe7cc35c7..9e15f3e125853 100644 --- a/recipes/bioconductor-deeppincs/meta.yaml +++ b/recipes/bioconductor-deeppincs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "DeepPINCS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b2ad842adfd8cdc86a4e7fb8e1dad8d + md5: cc5fbdd874a89f88ffed9c215f1e3d74 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deeppincs", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-ttgsea >=1.8.0,<1.9.0' + - 'bioconductor-ttgsea >=1.10.0,<1.11.0' - r-base - r-catencoders - r-keras @@ -35,7 +36,7 @@ requirements: - r-tokenizers - r-webchem run: - - 'bioconductor-ttgsea >=1.8.0,<1.9.0' + - 'bioconductor-ttgsea >=1.10.0,<1.11.0' - r-base - r-catencoders - r-keras diff --git a/recipes/bioconductor-deepsnv/meta.yaml b/recipes/bioconductor-deepsnv/meta.yaml index e24a3b3c16087..66edfae750ac9 100644 --- a/recipes/bioconductor-deepsnv/meta.yaml +++ b/recipes/bioconductor-deepsnv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "deepSNV" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c1b8f9884aafbf5492ce90f19486c2ec + md5: 4df42adbe4997ad401a7d2505ee2b227 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deepsnv", max_pin="x.x") }}' # Suggests: RColorBrewer, knitr, rmarkdown # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-vgam - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-vgam build: diff --git a/recipes/bioconductor-deformats/meta.yaml b/recipes/bioconductor-deformats/meta.yaml index 58f77e127633a..e9aaba108780e 100644 --- a/recipes/bioconductor-deformats/meta.yaml +++ b/recipes/bioconductor-deformats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "DEFormats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61f1496fd145226998b44613f7b0e4b2 + md5: d4fd53366cc3ead5959b9af782ff6790 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deformats", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-data.table run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-data.table diff --git a/recipes/bioconductor-degnorm/meta.yaml b/recipes/bioconductor-degnorm/meta.yaml index 115a4a3d466b8..a0f2b8bb9bca8 100644 --- a/recipes/bioconductor-degnorm/meta.yaml +++ b/recipes/bioconductor-degnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "DegNorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1de83a750bfb953d4984c3fed01730c2 + md5: 45dbc8183e1e18f3027b7880d3b5ef5a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-degnorm", max_pin="x.x") }}' # Suggests: knitr,rmarkdown,formatR requirements: host: - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-doparallel @@ -40,12 +41,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-degraph/meta.yaml b/recipes/bioconductor-degraph/meta.yaml index bb3c122bcd32c..d8a23d376a3ec 100644 --- a/recipes/bioconductor-degraph/meta.yaml +++ b/recipes/bioconductor-degraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "DEGraph" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73c561cbb1e5f175b84a1f0837c002e8 + md5: c61fb687376b321b9a52dfd15375e0b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-degraph", max_pin="x.x") }}' noarch: generic # Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-ncigraph >=1.48.0,<1.49.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-ncigraph >=1.50.0,<1.51.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-lattice - r-mvtnorm @@ -33,11 +34,11 @@ requirements: - r-r.utils - r-rrcov run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-ncigraph >=1.48.0,<1.49.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-ncigraph >=1.50.0,<1.51.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-lattice - r-mvtnorm diff --git a/recipes/bioconductor-degreport/meta.yaml b/recipes/bioconductor-degreport/meta.yaml index 104ec171f847c..73f13f7830437 100644 --- a/recipes/bioconductor-degreport/meta.yaml +++ b/recipes/bioconductor-degreport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.4" %} {% set name = "DEGreport" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d7a33c4f6e46476e1130b27b0a34dc2 + md5: d7c43c419f87827c0a116e3ae905ead7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-degreport", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom - r-circlize - r-cluster - r-cowplot + - r-dendextend - r-dplyr - r-ggdendro - r-ggplot2 @@ -46,23 +48,25 @@ requirements: - r-reshape - r-rlang - r-scales + - r-stringi - r-stringr - r-tibble - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom - r-circlize - r-cluster - r-cowplot + - r-dendextend - r-dplyr - r-ggdendro - r-ggplot2 @@ -75,6 +79,7 @@ requirements: - r-reshape - r-rlang - r-scales + - r-stringi - r-stringr - r-tibble - r-tidyr diff --git a/recipes/bioconductor-degseq/meta.yaml b/recipes/bioconductor-degseq/meta.yaml index 1b1c385fc5d8f..1fd5c9056f400 100644 --- a/recipes/bioconductor-degseq/meta.yaml +++ b/recipes/bioconductor-degseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.1" %} {% set name = "DEGseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: befdaa80e6df3dba5b23aba158858b45 + md5: cc89e25cb7e9afc38b5fb2bba34722b5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-degseq", max_pin="x.x") }}' requirements: host: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - libblas - liblapack run: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-delayedarray/meta.yaml b/recipes/bioconductor-delayedarray/meta.yaml index b26889d89e854..164a7bfd3c0bc 100644 --- a/recipes/bioconductor-delayedarray/meta.yaml +++ b/recipes/bioconductor-delayedarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.26.6" %} +{% set version = "0.28.0" %} {% set name = "DelayedArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d15ca54caa5e28aa00c97dd61db886b + md5: 812e7575d6eaa61f5b68364cdf1da3d9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-delayedarray", max_pin="x.x") }}' # Suggests: BiocParallel, HDF5Array (>= 1.17.12), genefilter, SummarizedExperiment, airway, lobstr, DelayedMatrixStats, knitr, rmarkdown, BiocStyle, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4arrays >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4arrays >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sparsearray >=1.2.0,<1.3.0' - r-base - r-matrix - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4arrays >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4arrays >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sparsearray >=1.2.0,<1.3.0' - r-base - r-matrix build: diff --git a/recipes/bioconductor-delayeddataframe/meta.yaml b/recipes/bioconductor-delayeddataframe/meta.yaml index 6534ae371b8b5..986a848355d4e 100644 --- a/recipes/bioconductor-delayeddataframe/meta.yaml +++ b/recipes/bioconductor-delayeddataframe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "DelayedDataFrame" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 348557d31d23d725601581912e43e2ea + md5: dd12410d16a2e6cf7bb022d2aa334bf7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-delayeddataframe", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, knitr, rmarkdown, SeqArray, GDSArray +# Suggests: testthat, knitr, rmarkdown, BiocStyle, SeqArray, GDSArray requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-delayedmatrixstats/meta.yaml b/recipes/bioconductor-delayedmatrixstats/meta.yaml index 5bb1eb58c256d..f3b73711617f5 100644 --- a/recipes/bioconductor-delayedmatrixstats/meta.yaml +++ b/recipes/bioconductor-delayedmatrixstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "DelayedMatrixStats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 88739eb294c38fc717e77987455a1d58 + md5: 890845d8c80a2b64cd02b3ff7f1e504d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-delayedmatrixstats", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, knitr, rmarkdown, covr, BiocStyle, microbenchmark, profmem, HDF5Array +# Suggests: testthat, knitr, rmarkdown, BiocStyle, microbenchmark, profmem, HDF5Array, matrixStats (>= 1.0.0) requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' - r-base - 'r-matrix >=1.5-0' - - 'r-matrixstats >=1.0.0' run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' - r-base - 'r-matrix >=1.5-0' - - 'r-matrixstats >=1.0.0' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-delayedrandomarray/meta.yaml b/recipes/bioconductor-delayedrandomarray/meta.yaml index 435ccc7188e36..084a5e1dbc8b2 100644 --- a/recipes/bioconductor-delayedrandomarray/meta.yaml +++ b/recipes/bioconductor-delayedrandomarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "DelayedRandomArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d4147f1b05d871632f2549d95a775883 + md5: 2f583ab177fd333cf626827fc28a6faf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-delayedrandomarray", max_pin="x.x") }}' # Suggests: testthat, knitr, BiocStyle, rmarkdown, Matrix # SystemRequirements: C++11 requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - r-base - r-bh - r-dqrng @@ -29,7 +30,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - r-base - r-bh - r-dqrng diff --git a/recipes/bioconductor-delayedtensor/meta.yaml b/recipes/bioconductor-delayedtensor/meta.yaml index ed7c95961bdc5..be01c68df53e5 100644 --- a/recipes/bioconductor-delayedtensor/meta.yaml +++ b/recipes/bioconductor-delayedtensor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "DelayedTensor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4651a15b7f778aefab7307d6fd600631 + md5: ee3e89ac7a0b9f3ca79f744edfdc69b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-delayedtensor", max_pin="x.x") }}' noarch: generic # Suggests: markdown, rmarkdown, BiocStyle, knitr, testthat, magrittr, dplyr, reticulate requirements: host: - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedrandomarray >=1.8.0,<1.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedrandomarray >=1.10.0,<1.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - r-base - r-einsum - r-irlba - r-matrix - r-rtensor run: - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedrandomarray >=1.8.0,<1.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedrandomarray >=1.10.0,<1.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - r-base - r-einsum - r-irlba diff --git a/recipes/bioconductor-delocal/meta.yaml b/recipes/bioconductor-delocal/meta.yaml index 6dc88c6c7f306..f9361e910db48 100644 --- a/recipes/bioconductor-delocal/meta.yaml +++ b/recipes/bioconductor-delocal/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "DELocal" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f595f5306f040c92e53f70db5fb4d81 + md5: 40f2eac89260ff4692fb02047990d048 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-delocal", max_pin="x.x") }}' noarch: generic -# Suggests: biomaRt, knitr, PCRedux, rmarkdown, stringr +# Suggests: biomaRt, knitr, PCRedux, rmarkdown, stringr, BiocStyle requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 - r-matrixstats - r-reshape2 run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-deltacapturec/meta.yaml b/recipes/bioconductor-deltacapturec/meta.yaml index fc51052ee4e7c..16b711e2ce632 100644 --- a/recipes/bioconductor-deltacapturec/meta.yaml +++ b/recipes/bioconductor-deltacapturec/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "deltaCaptureC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ac0f8754bd5250993302876e3b443615 + md5: e70cf57b6d22164dd5712a3441b0a788 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deltacapturec", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-tictoc run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-tictoc diff --git a/recipes/bioconductor-deltagseg/meta.yaml b/recipes/bioconductor-deltagseg/meta.yaml index d4b20475cbb57..a0a6ce76a69a8 100644 --- a/recipes/bioconductor-deltagseg/meta.yaml +++ b/recipes/bioconductor-deltagseg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "deltaGseg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84ea9181363b1231227685b65a28ca13 + md5: e92ca25a67a9250f26c6263043c60ee2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deltagseg", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: diff --git a/recipes/bioconductor-demand/meta.yaml b/recipes/bioconductor-demand/meta.yaml index 36e5b90b870e2..b56d0286db48a 100644 --- a/recipes/bioconductor-demand/meta.yaml +++ b/recipes/bioconductor-demand/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "DeMAND" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dbc37106827433bc654a90a4ac7e6701 + md5: ccb354bddebbebda6c42453810f10e70 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-demand", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-demuxmix/meta.yaml b/recipes/bioconductor-demuxmix/meta.yaml index 2c905657b4e60..252585cebc11f 100644 --- a/recipes/bioconductor-demuxmix/meta.yaml +++ b/recipes/bioconductor-demuxmix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "demuxmix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 146120afb774a862ecfb93ec5fb970b0 + md5: 9bbdcc634e542fe151a50a2511206140 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-demuxmix", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, cowplot, DropletUtils, knitr, reshape2, rmarkdown, testthat (>= 3.0.0) requirements: diff --git a/recipes/bioconductor-demuxsnp/build.sh b/recipes/bioconductor-demuxsnp/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-demuxsnp/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-demuxsnp/meta.yaml b/recipes/bioconductor-demuxsnp/meta.yaml new file mode 100644 index 0000000000000..ad5982ba15810 --- /dev/null +++ b/recipes/bioconductor-demuxsnp/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.0.0" %} +{% set name = "demuxSNP" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 66a0ed302acbc18c7a106d99bf645133 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-demuxsnp", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, Seurat, ComplexHeatmap, viridisLite, ggpubr, dittoSeq, EnsDb.Hsapiens.v86, BiocStyle, RefManageR, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-demuxmix >=1.4.0,<1.5.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - r-base + - r-class + - r-combinat + - r-matrix + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-demuxmix >=1.4.0,<1.5.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - r-base + - r-class + - r-combinat + - r-matrix +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'scRNAseq demultiplexing using cell hashing and SNPs' + description: 'This package assists in demultiplexing scRNAseq data using both cell hashing and SNPs data. The SNP profile of each group os learned using high confidence assignments from the cell hashing data. Cells which cannot be assigned with high confidence from the cell hashing data are assigned to their most similar group based on their SNPs. We also provide some helper function to optimise SNP selection, create training data and merge SNP data into the SingleCellExperiment framework.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-densvis/meta.yaml b/recipes/bioconductor-densvis/meta.yaml index aaa52a0863d1a..936a9b9557490 100644 --- a/recipes/bioconductor-densvis/meta.yaml +++ b/recipes/bioconductor-densvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.2" %} +{% set version = "1.12.0" %} {% set name = "densvis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a6a87938d3267e5f4ba279e1c0c91533 + md5: cf3ee330c8c9f0b396feb398e342cf8d build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: knitr, rmarkdown, BiocStyle, ggplot2, Rtsne, uwot, testthat + run_exports: '{{ pin_subpackage("bioconductor-densvis", max_pin="x.x") }}' +# Suggests: knitr, rmarkdown, BiocStyle, ggplot2, uwot, testthat requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' - r-assertthat - r-base - r-irlba - r-rcpp - r-reticulate + - r-rtsne - libblas - liblapack run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' - r-assertthat - r-base - r-irlba - r-rcpp - r-reticulate + - r-rtsne build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-dep/meta.yaml b/recipes/bioconductor-dep/meta.yaml index a44133258ced4..6f0664c7a0333 100644 --- a/recipes/bioconductor-dep/meta.yaml +++ b/recipes/bioconductor-dep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "DEP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://{{ name|lower }}ot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d020fdba2ecaec00e6f17559a2a7454 + md5: 2bfaf5d5bfd3f05c7a7a80742bd43f7c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dep", max_pin="x.x") }}' noarch: generic # Suggests: testthat, enrichR, knitr, BiocStyle requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-assertthat - r-base - r-circlize @@ -46,11 +47,11 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-assertthat - r-base - r-circlize diff --git a/recipes/bioconductor-depecher/meta.yaml b/recipes/bioconductor-depecher/meta.yaml index 32b81b60fc458..74da60263ebdb 100644 --- a/recipes/bioconductor-depecher/meta.yaml +++ b/recipes/bioconductor-depecher/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "DepecheR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b560cc798d7fb32413c75317b73e45d9 + md5: 201fe937f16e843f49fbe35a4ae1ebb6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-depecher", max_pin="x.x") }}' # Suggests: uwot, testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-mixomics >=6.24.0,<6.25.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' - r-base - 'r-beanplot >=1.2' + - 'r-collapse >=1.9.2' - 'r-dosnow >=1.0.16' - 'r-dplyr >=0.7.8' - 'r-fnn >=1.1.3' @@ -41,9 +43,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-mixomics >=6.24.0,<6.25.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' - r-base - 'r-beanplot >=1.2' + - 'r-collapse >=1.9.2' - 'r-dosnow >=1.0.16' - 'r-dplyr >=0.7.8' - 'r-fnn >=1.1.3' diff --git a/recipes/bioconductor-depinfer/meta.yaml b/recipes/bioconductor-depinfer/meta.yaml index e735db3795146..94dc1dcdf83ca 100644 --- a/recipes/bioconductor-depinfer/meta.yaml +++ b/recipes/bioconductor-depinfer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "DepInfeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dcf243eeb7152508a9beb10faa48f249 + md5: d673a7cc6ac21a4d899238878c09533f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-depinfer", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, tibble, ggplot2, missForest, pheatmap, RColorBrewer, ggrepel, BiocStyle, ggbeeswarm requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-glmnet - r-matrixstats run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-glmnet - r-matrixstats diff --git a/recipes/bioconductor-depmap/meta.yaml b/recipes/bioconductor-depmap/meta.yaml index 515f8263f9737..f38b98fd584e6 100644 --- a/recipes/bioconductor-depmap/meta.yaml +++ b/recipes/bioconductor-depmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "depmap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d4405c4714a46efd721be9905eddc21f + md5: 7f00d05c7f899e622293767baa04e120 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-depmap", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, viridis, gridExtra, ggplot2, readr, tibble, stringr, tidyr requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - r-dplyr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - r-dplyr - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-depmap/post-link.sh b/recipes/bioconductor-depmap/post-link.sh index 1f90ee9ff67c0..a1ee9c05ab0be 100644 --- a/recipes/bioconductor-depmap/post-link.sh +++ b/recipes/bioconductor-depmap/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "depmap-1.14.0" +installBiocDataPackage.sh "depmap-1.16.0" diff --git a/recipes/bioconductor-deqms/meta.yaml b/recipes/bioconductor-deqms/meta.yaml index b1f046d308f58..7fee72622c3bd 100644 --- a/recipes/bioconductor-deqms/meta.yaml +++ b/recipes/bioconductor-deqms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "DEqMS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 58542439f1c16afe6974fd4ee95852c4 + md5: bc308e6f683ca1bf0dcdb703274575ac build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deqms", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle,knitr,rmarkdown,markdown,plyr,reshape2,farms,utils,ggrepel,ExperimentHub,LSD requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-matrixstats run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-matrixstats diff --git a/recipes/bioconductor-derfinder/meta.yaml b/recipes/bioconductor-derfinder/meta.yaml index 2c8eafb1cfd89..5f1ca01fd980f 100644 --- a/recipes/bioconductor-derfinder/meta.yaml +++ b/recipes/bioconductor-derfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "derfinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,49 +11,50 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ba0d27535c6e19834607cc8aabc4de9f + md5: a3ef629c180b64b0776c880164603c7b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-derfinder", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 2.5.19), sessioninfo, derfinderData (>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitr (>= 1.6), limma, RefManageR, rmarkdown (>= 0.3.3), testthat (>= 2.1.0), TxDb.Hsapiens.UCSC.hg19.knownGene, covr requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-derfinderhelper >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-derfinderhelper >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-hmisc run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-derfinderhelper >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-derfinderhelper >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-hmisc test: @@ -63,7 +64,11 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach' - description: 'This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.' + description: | + This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. + Two implementations of the DER Finder approach are included in this package: (1) single base-level + F-statistics and (2) DER identification at the expressed regions-level. + The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks. extra: identifiers: - biotools:derfinder diff --git a/recipes/bioconductor-derfinderdata/meta.yaml b/recipes/bioconductor-derfinderdata/meta.yaml index c52d8fcd7b912..ab731b2b7adf4 100644 --- a/recipes/bioconductor-derfinderdata/meta.yaml +++ b/recipes/bioconductor-derfinderdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "derfinderData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7787e049bcee25cb354773f1fd2cf27 + md5: 032efff51d29eae3fc1a5e032c0f3c40 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-derfinderdata", max_pin="x.x") }}' noarch: generic # Suggests: sessioninfo, knitr (>= 1.6), RefManageR, rmarkdown (>= 0.3.3), BiocStyle requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-derfinderdata/post-link.sh b/recipes/bioconductor-derfinderdata/post-link.sh index cfddf0ccc3eeb..07fd8f6c6666d 100644 --- a/recipes/bioconductor-derfinderdata/post-link.sh +++ b/recipes/bioconductor-derfinderdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "derfinderdata-2.18.0" +installBiocDataPackage.sh "derfinderdata-2.20.0" diff --git a/recipes/bioconductor-derfinderhelper/meta.yaml b/recipes/bioconductor-derfinderhelper/meta.yaml index 5b4c926b08b6d..d23d5cb1f7b01 100644 --- a/recipes/bioconductor-derfinderhelper/meta.yaml +++ b/recipes/bioconductor-derfinderhelper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "derfinderHelper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 85b9dc14c66f5aa287e9673f955f65da + md5: 2544077112525d7f25f34270ed365423 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-derfinderhelper", max_pin="x.x") }}' noarch: generic # Suggests: sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19), RefManageR, rmarkdown (>= 0.3.3), testthat, covr requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-derfinderplot/meta.yaml b/recipes/bioconductor-derfinderplot/meta.yaml index 77fbfe9a49ff5..2890878efb489 100644 --- a/recipes/bioconductor-derfinderplot/meta.yaml +++ b/recipes/bioconductor-derfinderplot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "derfinderPlot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9c60bba2ab936a7c037c3d6311a6b18d + md5: c3dbd553554f3b043b8f03e4b05a964a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-derfinderplot", max_pin="x.x") }}' noarch: generic # Suggests: biovizBase (>= 1.27.2), bumphunter (>= 1.7.6), derfinderData (>= 0.99.0), sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19), org.Hs.eg.db, RefManageR, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, covr requirements: host: - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-plyr @@ -36,14 +37,14 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-plyr diff --git a/recipes/bioconductor-descan2/meta.yaml b/recipes/bioconductor-descan2/meta.yaml index 8bfd045281a86..655f19ab5b6b3 100644 --- a/recipes/bioconductor-descan2/meta.yaml +++ b/recipes/bioconductor-descan2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "DEScan2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5c5a508823352ccf16d9af41b273a9a5 + md5: 476f052d4a86e27d332812852fd7e0c1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-descan2", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-glue @@ -40,17 +41,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-glue diff --git a/recipes/bioconductor-deseq2/meta.yaml b/recipes/bioconductor-deseq2/meta.yaml index bd256801fe5c6..fbad8ff890c69 100644 --- a/recipes/bioconductor-deseq2/meta.yaml +++ b/recipes/bioconductor-deseq2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.2" %} +{% set version = "1.42.0" %} {% set name = "DESeq2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8869279f9f3cd28d15e65ea75f8d8aab + md5: 5eb89526ce9fd4da98b1a5e0b5ba0bf3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deseq2", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, pasilla (>= 0.2.10), glmGamPoi, BiocManager requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - - r-ggplot2 + - 'r-ggplot2 >=3.4.0' - r-locfit - r-matrixstats - 'r-rcpp >=0.11.0' @@ -36,15 +38,16 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - - r-ggplot2 + - 'r-ggplot2 >=3.4.0' - r-locfit - r-matrixstats - 'r-rcpp >=0.11.0' diff --git a/recipes/bioconductor-desingle/meta.yaml b/recipes/bioconductor-desingle/meta.yaml index bde60c8322a09..2f3cbbd1c30a4 100644 --- a/recipes/bioconductor-desingle/meta.yaml +++ b/recipes/bioconductor-desingle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "DEsingle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee4807f0e64627ced9f59afee0b77b5b + md5: 6969e960919434ccd6e5b9bdd926aece build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-desingle", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, SingleCellExperiment requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - 'r-bbmle >=1.0.18' - 'r-gamlss >=4.4-0' @@ -31,7 +32,7 @@ requirements: - 'r-pscl >=1.4.9' - 'r-vgam >=1.0-2' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - 'r-bbmle >=1.0.18' - 'r-gamlss >=4.4-0' diff --git a/recipes/bioconductor-desousa2013/meta.yaml b/recipes/bioconductor-desousa2013/meta.yaml index 4e0410693b971..ffb817248a4d9 100644 --- a/recipes/bioconductor-desousa2013/meta.yaml +++ b/recipes/bioconductor-desousa2013/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "DeSousa2013" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a12b8cbbcf6b3ccc758dacd1ef01852 + md5: 41a3ca5cba40653eb4be04203aaf60ac build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-desousa2013", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-frma >=1.52.0,<1.53.0' - - 'bioconductor-frmatools >=1.52.0,<1.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-frma >=1.54.0,<1.55.0' + - 'bioconductor-frmatools >=1.54.0,<1.55.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - 'bioconductor-hgu133plus2frmavecs >=1.5.0,<1.6.0' - - 'bioconductor-siggenes >=1.74.0,<1.75.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-cluster - r-gplots @@ -38,16 +39,16 @@ requirements: - r-rocr - r-survival run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-frma >=1.52.0,<1.53.0' - - 'bioconductor-frmatools >=1.52.0,<1.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-frma >=1.54.0,<1.55.0' + - 'bioconductor-frmatools >=1.54.0,<1.55.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - 'bioconductor-hgu133plus2frmavecs >=1.5.0,<1.6.0' - - 'bioconductor-siggenes >=1.74.0,<1.75.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-cluster - r-gplots @@ -56,7 +57,7 @@ requirements: - r-rocr - r-survival - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' build: - {{ cdt('mesa-libgl-devel') }} # [linux] - {{ cdt('mesa-dri-drivers') }} # [linux] diff --git a/recipes/bioconductor-desousa2013/post-link.sh b/recipes/bioconductor-desousa2013/post-link.sh index acd6ef56f68c2..4c31f29da3892 100644 --- a/recipes/bioconductor-desousa2013/post-link.sh +++ b/recipes/bioconductor-desousa2013/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "desousa2013-1.36.0" +installBiocDataPackage.sh "desousa2013-1.38.0" diff --git a/recipes/bioconductor-despace/meta.yaml b/recipes/bioconductor-despace/meta.yaml index 1628764112915..6ad56c3815333 100644 --- a/recipes/bioconductor-despace/meta.yaml +++ b/recipes/bioconductor-despace/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "DESpace" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ebe4a43a2479a091a19a012ae6db464c + md5: 436915bded5ec94da6e412ccdff80e8e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-despace", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle, ExperimentHub, concaveman, spatialLIBD, purrr, scuttle, utils requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-cowplot @@ -41,13 +42,13 @@ requirements: - r-patchwork - r-scales run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-cowplot diff --git a/recipes/bioconductor-destiny/meta.yaml b/recipes/bioconductor-destiny/meta.yaml index d92ce04f87d79..4bb1c1f0f7225 100644 --- a/recipes/bioconductor-destiny/meta.yaml +++ b/recipes/bioconductor-destiny/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.14.0" %} +{% set version = "3.16.0" %} {% set name = "destiny" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 251c5635adf088e2ee70626a60e1489d + md5: b86a5cbd268832cb7a6da5999e50393b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-destiny", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, igraph, testthat, FNN, tidyverse, gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq, org.Mm.eg.db, scran, repr # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot.multistats - r-ggplot2 @@ -47,11 +48,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot.multistats - r-ggplot2 diff --git a/recipes/bioconductor-desubs/meta.yaml b/recipes/bioconductor-desubs/meta.yaml index 5840dfa722811..98b6a9306f8b5 100644 --- a/recipes/bioconductor-desubs/meta.yaml +++ b/recipes/bioconductor-desubs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "DEsubs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e37c127e2b3fdfe0613d43ef5c2e949c + md5: 1e2b74c85e35888eab89ac39a363c32c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-desubs", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, rmarkdown requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-ebseq >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-circlize - r-ggplot2 @@ -37,12 +38,12 @@ requirements: - r-nbpseq - r-pheatmap run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-ebseq >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-circlize - r-ggplot2 diff --git a/recipes/bioconductor-dewseq/meta.yaml b/recipes/bioconductor-dewseq/meta.yaml index dc3676bb2df17..035c2b2dbe9ed 100644 --- a/recipes/bioconductor-dewseq/meta.yaml +++ b/recipes/bioconductor-dewseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.2" %} {% set name = "DEWSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02180a59d83e6a2ef88b2bea89104832 + md5: 4164c3c7d4967586861e0c2d40815ec5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dewseq", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, testthat, BiocStyle, IHW +# Suggests: knitr, rmarkdown, tidyverse, testthat, BiocStyle, IHW requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-data.table >=1.11.8' - r-r.utils run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-data.table >=1.11.8' - r-r.utils diff --git a/recipes/bioconductor-dexma/meta.yaml b/recipes/bioconductor-dexma/meta.yaml index 555a80d3f5b3e..f828df78731c2 100644 --- a/recipes/bioconductor-dexma/meta.yaml +++ b/recipes/bioconductor-dexma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.6" %} {% set name = "DExMA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8155bdaa13020bf598c9357286d290cb + md5: 7397f231c7a241e6bfb258ca064ff8b7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dexma", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, qpdf, BiocGenerics, RUnit requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dexmadata >=1.8.0,<1.9.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-dexmadata >=1.10.0,<1.11.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-bnstruct - r-pheatmap @@ -36,13 +37,13 @@ requirements: - r-scales - r-swamp run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dexmadata >=1.8.0,<1.9.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-dexmadata >=1.10.0,<1.11.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-bnstruct - r-pheatmap diff --git a/recipes/bioconductor-dexmadata/meta.yaml b/recipes/bioconductor-dexmadata/meta.yaml index 7c093e1e7363b..418aaacbbfa95 100644 --- a/recipes/bioconductor-dexmadata/meta.yaml +++ b/recipes/bioconductor-dexmadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "DExMAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bc2fd62dd24eeaee294a624610b75918 + md5: 3d2a9cc7d0044ffc23e572f4c5cc4426 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dexmadata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dexmadata/post-link.sh b/recipes/bioconductor-dexmadata/post-link.sh index 166930720a76a..deb9a0366746c 100644 --- a/recipes/bioconductor-dexmadata/post-link.sh +++ b/recipes/bioconductor-dexmadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dexmadata-1.8.0" +installBiocDataPackage.sh "dexmadata-1.10.0" diff --git a/recipes/bioconductor-dexseq/build.sh b/recipes/bioconductor-dexseq/build.sh index c1d13421f5f1e..a9c2ad544d4dc 100644 --- a/recipes/bioconductor-dexseq/build.sh +++ b/recipes/bioconductor-dexseq/build.sh @@ -8,4 +8,11 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . \ No newline at end of file + +$R CMD INSTALL --build . +python_path=$PREFIX/lib/R/library/DEXSeq/python_scripts +echo python3 ${python_path}/dexseq_prepare_annotation.py '"$@"' > $PREFIX/bin/dexseq_prepare_annotation.py +chmod +x $PREFIX/bin/dexseq_prepare_annotation.py + +echo python3 ${python_path}/dexseq_count.py '"$@"' > $PREFIX/bin/dexseq_count.py +chmod +x $PREFIX/bin/dexseq_count.py diff --git a/recipes/bioconductor-dexseq/meta.yaml b/recipes/bioconductor-dexseq/meta.yaml index 0a42a1c1397a8..29b4cbc81fbe4 100644 --- a/recipes/bioconductor-dexseq/meta.yaml +++ b/recipes/bioconductor-dexseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "DEXSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,48 +11,49 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 83652c928d49e5ea8c284a5b5d37a46a + md5: 8e5876f927b0b0cdfc4a402bfb4fb3d6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dexseq", max_pin="x.x") }}' noarch: generic -# Suggests: GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown, testthat, pasillaBamSubset, GenomicAlignments, roxygen2 +# Suggests: GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown, testthat, pasillaBamSubset, GenomicAlignments, roxygen2, glmGamPoi requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-hwriter - r-rcolorbrewer - r-statmod - r-stringr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-hwriter - r-rcolorbrewer diff --git a/recipes/bioconductor-dfp/meta.yaml b/recipes/bioconductor-dfp/meta.yaml index 6fbaa70b6753c..846c1dbfc78a7 100644 --- a/recipes/bioconductor-dfp/meta.yaml +++ b/recipes/bioconductor-dfp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "DFP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8f6a4937ae9aaadca48470a41911245 + md5: 5eb14fe67a6dd0599cd24c3473eec349 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dfp", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-dialignr/meta.yaml b/recipes/bioconductor-dialignr/meta.yaml index 4aa8508dc2b67..b0ad1e11855dc 100644 --- a/recipes/bioconductor-dialignr/meta.yaml +++ b/recipes/bioconductor-dialignr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "DIAlignR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 64265ce3d538110aac22ed20a151c9b3 + md5: b67387fec7e8a9e5de5189fecd7077aa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dialignr", max_pin="x.x") }}' # Suggests: knitr, akima, lattice, scales, gridExtra, latticeExtra, rmarkdown, BiocStyle, BiocParallel, testthat (>= 2.1.0) # SystemRequirements: C++14 requirements: host: - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-ape - r-base - r-bit64 @@ -44,7 +45,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-ape - r-base - r-bit64 diff --git a/recipes/bioconductor-diffbind/meta.yaml b/recipes/bioconductor-diffbind/meta.yaml index b1b7a2f20e370..57d109de6119d 100644 --- a/recipes/bioconductor-diffbind/meta.yaml +++ b/recipes/bioconductor-diffbind/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.10.0" %} +{% set version = "3.12.0" %} {% set name = "DiffBind" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9cdbcead719d0c3d268ff9184c2a146e + md5: aa7c15e33713ad0ced01a5b6442e2d3d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diffbind", max_pin="x.x") }}' # Suggests: BiocStyle, testthat, xtable, rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid # SystemRequirements: GNU make requirements: host: - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-greylistchip >=1.32.0,<1.33.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-systempiper >=2.6.0,<2.7.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-greylistchip >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-systempiper >=2.8.0,<2.9.0' - r-amap - r-ashr - r-base @@ -48,19 +49,19 @@ requirements: - libblas - liblapack run: - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-greylistchip >=1.32.0,<1.33.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-systempiper >=2.6.0,<2.7.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-greylistchip >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-systempiper >=2.8.0,<2.9.0' - r-amap - r-ashr - r-base diff --git a/recipes/bioconductor-diffcoexp/meta.yaml b/recipes/bioconductor-diffcoexp/meta.yaml index 5e7d4bebf284e..aa9d59c7e2550 100644 --- a/recipes/bioconductor-diffcoexp/meta.yaml +++ b/recipes/bioconductor-diffcoexp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "diffcoexp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 161074b1baaa04dfba989eb96d6931ac + md5: 0985f656837da53f557041125f7583a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diffcoexp", max_pin="x.x") }}' noarch: generic -# Suggests: GEOquery +# Suggests: GEOquery, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-diffcorr - r-igraph - r-psych - r-wgcna run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-diffcorr - r-igraph diff --git a/recipes/bioconductor-diffcyt/meta.yaml b/recipes/bioconductor-diffcyt/meta.yaml index e99566efd27fe..cd7e975c7fa60 100644 --- a/recipes/bioconductor-diffcyt/meta.yaml +++ b/recipes/bioconductor-diffcyt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "diffcyt" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4fc1208b2b23cb07450a1b1f9250594b + md5: 8118267e493c2646533a9730a876d340 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diffcyt", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowsom >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowsom >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-dplyr @@ -37,13 +38,13 @@ requirements: - r-reshape2 - r-tidyr run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowsom >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowsom >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-dplyr diff --git a/recipes/bioconductor-differentialregulation/meta.yaml b/recipes/bioconductor-differentialregulation/meta.yaml index eff49e2146e20..a4577cc53de1e 100644 --- a/recipes/bioconductor-differentialregulation/meta.yaml +++ b/recipes/bioconductor-differentialregulation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.2" %} +{% set version = "2.0.2" %} {% set name = "DifferentialRegulation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37854686cce5bc0d3bdf3b839ad04d69 + md5: 875793d502c3e521b4faa3eba0d1c2e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-differentialregulation", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, BiocStyle -# SystemRequirements: C++11 +# SystemRequirements: C++17 requirements: host: - - 'bioconductor-bandits >=1.16.0,<1.17.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-bandits >=1.18.0,<1.19.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-base - r-data.table - r-doparallel - r-dorng - r-foreach - r-ggplot2 + - r-gridextra - r-mass - r-matrix - r-rcpp @@ -38,16 +40,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-bandits >=1.16.0,<1.17.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-bandits >=1.18.0,<1.19.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-base - r-data.table - r-doparallel - r-dorng - r-foreach - r-ggplot2 + - r-gridextra - r-mass - r-matrix - r-rcpp diff --git a/recipes/bioconductor-diffgeneanalysis/meta.yaml b/recipes/bioconductor-diffgeneanalysis/meta.yaml index 26231b27f9c7b..2ddba971b2d64 100644 --- a/recipes/bioconductor-diffgeneanalysis/meta.yaml +++ b/recipes/bioconductor-diffgeneanalysis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.82.0" %} +{% set version = "1.84.0" %} {% set name = "diffGeneAnalysis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3dd06a23dac4ee41a326424187d4082b + md5: aa3d8c4ce3b83b8a6f02e87384dd649f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diffgeneanalysis", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-diffhic/meta.yaml b/recipes/bioconductor-diffhic/meta.yaml index 19abc926ef125..a3b151ea656d1 100644 --- a/recipes/bioconductor-diffhic/meta.yaml +++ b/recipes/bioconductor-diffhic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "diffHic" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,56 +11,57 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a1e279c2d1f02340a6cbcc771e64ce3 + md5: ba97084f7b4e4510514df43be6eb9bf8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diffhic", max_pin="x.x") }}' # Suggests: BSgenome.Ecoli.NCBI.20080805, Matrix, testthat # SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-locfit - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-locfit - r-rcpp diff --git a/recipes/bioconductor-difflogo/meta.yaml b/recipes/bioconductor-difflogo/meta.yaml index 7655cc38189e1..7021a22253322 100644 --- a/recipes/bioconductor-difflogo/meta.yaml +++ b/recipes/bioconductor-difflogo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "DiffLogo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37d13c84d12b18ac6a302bd4ed9672fe + md5: f122cc5f6153c8dc4fabe92b33d1e608 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-difflogo", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, seqLogo, MotifDb requirements: diff --git a/recipes/bioconductor-diffloopdata/meta.yaml b/recipes/bioconductor-diffloopdata/meta.yaml index fa1e401e6f017..5578e9031bc30 100644 --- a/recipes/bioconductor-diffloopdata/meta.yaml +++ b/recipes/bioconductor-diffloopdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "diffloopdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8e004a82f024eb82c188415e8ca65563 + md5: 748ee71ae44999ca2c568619ad5a47eb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diffloopdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-diffloopdata/post-link.sh b/recipes/bioconductor-diffloopdata/post-link.sh index 73218bbd38264..51e96d69fdede 100644 --- a/recipes/bioconductor-diffloopdata/post-link.sh +++ b/recipes/bioconductor-diffloopdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "diffloopdata-1.28.0" +installBiocDataPackage.sh "diffloopdata-1.30.0" diff --git a/recipes/bioconductor-diffustats/meta.yaml b/recipes/bioconductor-diffustats/meta.yaml index e61fddfc151de..0a7ea0001788f 100644 --- a/recipes/bioconductor-diffustats/meta.yaml +++ b/recipes/bioconductor-diffustats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "diffuStats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aafc3aa67189fbbb04b4ac8ea2df5280 + md5: 7c47ae0431034f3de807ad1fa3684530 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diffustats", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata, BiocStyle, reshape2, utils # SystemRequirements: GNU make requirements: diff --git a/recipes/bioconductor-diffutr/meta.yaml b/recipes/bioconductor-diffutr/meta.yaml index 59d6828c1d6dc..e43e853baf8f8 100644 --- a/recipes/bioconductor-diffutr/meta.yaml +++ b/recipes/bioconductor-diffutr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "diffUTR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7c06f1c637e763f2dd8ac0209145fa2 + md5: 10b4af48c1a3f5e823c67cf569dcf1c2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diffutr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-dexseq >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -41,18 +42,18 @@ requirements: - r-stringi - r-viridislite run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-dexseq >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-diggit/meta.yaml b/recipes/bioconductor-diggit/meta.yaml index 4c5fcd80a3b97..43b921f1c6b65 100644 --- a/recipes/bioconductor-diggit/meta.yaml +++ b/recipes/bioconductor-diggit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "diggit" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 51bae1ffaac56dfb95c2a3a0bdc769ec + md5: 8685d9b55ebfad0b44d6ca96d6fb4ab0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diggit", max_pin="x.x") }}' noarch: generic # Suggests: diggitdata requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base - r-ks run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base - r-ks test: diff --git a/recipes/bioconductor-diggitdata/meta.yaml b/recipes/bioconductor-diggitdata/meta.yaml index e50de6a3e7821..b4c6cdf57ec45 100644 --- a/recipes/bioconductor-diggitdata/meta.yaml +++ b/recipes/bioconductor-diggitdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "diggitdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d68dbde08e8d4b936a15a73a23a48830 + md5: 48dc6a1a35dae2169279a2766e3b56de build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diggitdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-diggitdata/post-link.sh b/recipes/bioconductor-diggitdata/post-link.sh index d1dfc6fddbbe7..3d3e3107cca47 100644 --- a/recipes/bioconductor-diggitdata/post-link.sh +++ b/recipes/bioconductor-diggitdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "diggitdata-1.32.0" +installBiocDataPackage.sh "diggitdata-1.34.0" diff --git a/recipes/bioconductor-dino/meta.yaml b/recipes/bioconductor-dino/meta.yaml index e7d9e88c73391..f3775ab4fc288 100644 --- a/recipes/bioconductor-dino/meta.yaml +++ b/recipes/bioconductor-dino/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "Dino" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0c8e15f69998933ef26099e60db42b92 + md5: cf084f6d83c8245a5c4969849a7e3e82 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dino", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), knitr, rmarkdown, BiocStyle, devtools, ggplot2, gridExtra, ggpubr, grid, magick, hexbin requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-matrixstats - r-seurat run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-matrixstats diff --git a/recipes/bioconductor-dir.expiry/meta.yaml b/recipes/bioconductor-dir.expiry/meta.yaml index e916f0fbdac8d..77e5aabe1d30e 100644 --- a/recipes/bioconductor-dir.expiry/meta.yaml +++ b/recipes/bioconductor-dir.expiry/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "dir.expiry" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 21f10f90c60b2b127529b1b1028d5756 + md5: ddefb728416ca4283805e19a898e9245 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dir.expiry", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat, BiocStyle requirements: diff --git a/recipes/bioconductor-director/meta.yaml b/recipes/bioconductor-director/meta.yaml index d3f2403c8d18c..8cd98393738e0 100644 --- a/recipes/bioconductor-director/meta.yaml +++ b/recipes/bioconductor-director/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "Director" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 41504b173dd3af18b1ee7ba53979e0e5 + md5: 7c6c9d1a4762ffbdf723111273ee0899 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-director", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-dirichletmultinomial/meta.yaml b/recipes/bioconductor-dirichletmultinomial/meta.yaml index 39b57980f9af4..c522f169f7852 100644 --- a/recipes/bioconductor-dirichletmultinomial/meta.yaml +++ b/recipes/bioconductor-dirichletmultinomial/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "DirichletMultinomial" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 645e54be0954e16b383584892733e45d + md5: 8527c543b1ada9640d2f434fb516ff4e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dirichletmultinomial", max_pin="x.x") }}' # Suggests: lattice, parallel, MASS, RColorBrewer, xtable # SystemRequirements: gsl requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - libblas - liblapack - gsl run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - gsl build: diff --git a/recipes/bioconductor-discordant/meta.yaml b/recipes/bioconductor-discordant/meta.yaml index 35fbc9e4ae863..8a2f3fd4b1593 100644 --- a/recipes/bioconductor-discordant/meta.yaml +++ b/recipes/bioconductor-discordant/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "discordant" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8e0656f834cd221da58ba523968b30bc + md5: 78ce10a5d9777c9db9b72fec29688bee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-discordant", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-biwt - r-dplyr @@ -30,7 +31,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-biwt - r-dplyr diff --git a/recipes/bioconductor-discorhythm/meta.yaml b/recipes/bioconductor-discorhythm/meta.yaml index a66ba2d3d9725..f66f116d7b1fa 100644 --- a/recipes/bioconductor-discorhythm/meta.yaml +++ b/recipes/bioconductor-discorhythm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "DiscoRhythm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c96324132931c93539174ad49ee1b914 + md5: c502bfa871cb7e3aa322684117a70b2f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-discorhythm", max_pin="x.x") }}' noarch: generic # Suggests: testthat # SystemRequirements: To generate html reports pandoc (http://pandoc.org/installing.html) is required. requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom - r-data.table @@ -55,10 +56,10 @@ requirements: - r-zip - pandoc run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom - r-data.table diff --git a/recipes/bioconductor-distinct/build_failure.linux-64.yaml b/recipes/bioconductor-distinct/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..b4346b41f3fe8 --- /dev/null +++ b/recipes/bioconductor-distinct/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 4cdee96b11c599d7d86852005b1fcdb8fc168a77b8c4cd0973697dbfc2af519f # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + compiler error +log: |2- + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/Archive/distinct/distinct_1.14.0.tar.gz + INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/Archive/distinct/distinct_1.14.0.tar.gz + Success + INFO:conda_build.source:Success + Extracting download + source tree in: /opt/conda/conda-bld/bioconductor-distinct_1703301470415/work + export PREFIX=/opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-distinct_1703301470415/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-distinct_1703301470415/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-distinct-1.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-distinct-1.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-distinct-1.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-distinct-1.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library + * installing *source* package distinct ... + ** using staged installation + ** libs + using C compiler: x86_64-conda-linux-gnu-c (conda-forge gcc 12.3.0-3) 12.3.0 + using C11 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rfast/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1700316003380/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c Perm.cpp -o Perm.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rfast/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1700316003380/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c Perm_covariates.cpp -o Perm_covariates.o + In file included from /opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/Rfast/include/Rfast/templates.h:10, + from /opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/Rfast/include/Rfast/matrix.hpp:14, + from /opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/Rfast/include/Rfast.h:5, + from Perm_covariates.cpp:2: + /opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/Rfast/include/Rfast/parallel.h:7:10: fatal error: RcppParallel.h: No such file or directory + 7 | #include + | ^~~~~~~~~~~~~~~~ + compilation terminated. + make: *** [/opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/etc/Makeconf:200: Perm_covariates.o] Error 1 + ERROR: compilation failed for package distinct + * removing /opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/distinct + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build + utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, + File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-distinct_1703301470415/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-distinct/build_failure.osx-64.yaml b/recipes/bioconductor-distinct/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..be50a664177f3 --- /dev/null +++ b/recipes/bioconductor-distinct/build_failure.osx-64.yaml @@ -0,0 +1,38 @@ +recipe_sha: 4cdee96b11c599d7d86852005b1fcdb8fc168a77b8c4cd0973697dbfc2af519f # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + parallel.h:7:10: fatal error: 'RcppParallel.h' file not found +category: |- + compiler error +log: |- + 12:17:08 BIOCONDA INFO (ERR) In file included from Perm_covariates.cpp:2: + 12:17:08 BIOCONDA INFO (ERR) In file included from /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/Rfast/include/Rfast.h:5: + 12:17:08 BIOCONDA INFO (ERR) In file included from /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/Rfast/include/Rfast/matrix.hpp:14: + 12:17:08 BIOCONDA INFO (ERR) In file included from /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/Rfast/include/Rfast/templates.h:10: + 12:17:08 BIOCONDA INFO (ERR) /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/Rfast/include/Rfast/parallel.h:7:10: fatal error: 'RcppParallel.h' file not found + 12:17:08 BIOCONDA INFO (ERR) #include + 12:17:08 BIOCONDA INFO (ERR) ^~~~~~~~~~~~~~~~ + 12:17:08 BIOCONDA INFO (ERR) 1 error generated. + 12:17:08 BIOCONDA INFO (ERR) make: *** [/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/etc/Makeconf:200: Perm_covariates.o] Error 1 + 12:17:08 BIOCONDA INFO (ERR) ERROR: compilation failed for package ‘distinct’ + 12:17:08 BIOCONDA INFO (ERR) * removing ‘/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/distinct’ + 12:17:09 BIOCONDA INFO (ERR) Traceback (most recent call last): + 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in + 12:17:09 BIOCONDA INFO (ERR) sys.exit(main()) + 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + 12:17:09 BIOCONDA INFO (ERR) call_conda_build(action, config) + 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + 12:17:09 BIOCONDA INFO (ERR) result = api.build( + 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + 12:17:09 BIOCONDA INFO (ERR) return build_tree( + 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + 12:17:09 BIOCONDA INFO (ERR) packages_from_this = build(metadata, stats, + 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build + 12:17:09 BIOCONDA INFO (ERR) utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, + 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + 12:17:09 BIOCONDA INFO (ERR) return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + 12:17:09 BIOCONDA INFO (ERR) raise subprocess.CalledProcessError(proc.returncode, _args) + 12:17:09 BIOCONDA INFO (ERR) subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/work/conda_build.sh']' returned non-zero exit status 1. + 12:17:18 BIOCONDA ERROR COMMAND FAILED (exited with 1): /opt/mambaforge/envs/bioconda/bin/conda mambabuild --override-channels --no-anaconda-upload -c conda-forge -c bioconda -c defaults -e /opt/mambaforge/envs/bioconda/conda_build_config.yaml -e /opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml recipes/bioconductor-distinct/meta.yaml + diff --git a/recipes/bioconductor-distinct/meta.yaml b/recipes/bioconductor-distinct/meta.yaml index 5d70c56cc8d36..94fd0a58dc596 100644 --- a/recipes/bioconductor-distinct/meta.yaml +++ b/recipes/bioconductor-distinct/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.2" %} +{% set version = "1.14.0" %} {% set name = "distinct" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 952be7f89ed08259c89941b312132b35 + md5: b4817384f7f8fad6e30ee01270e31d10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-distinct", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, UpSetR, BiocStyle # SystemRequirements: C++11 requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-dorng @@ -37,10 +38,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-dorng diff --git a/recipes/bioconductor-dittoseq/meta.yaml b/recipes/bioconductor-dittoseq/meta.yaml index da1c9a0e79891..2c331373afe40 100644 --- a/recipes/bioconductor-dittoseq/meta.yaml +++ b/recipes/bioconductor-dittoseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "dittoSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7b2089286b90a1e519b82194f205784c + md5: 6d7e63c0018a57726033bb5862dccf7e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dittoseq", max_pin="x.x") }}' noarch: generic # Suggests: plotly, testthat, Seurat (>= 2.2), DESeq2, edgeR, ggplot.multistats, knitr, rmarkdown, BiocStyle, scRNAseq, ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-colorspace >=1.4' - r-cowplot @@ -34,9 +35,9 @@ requirements: - r-pheatmap - r-reshape2 run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-colorspace >=1.4' - r-cowplot diff --git a/recipes/bioconductor-divergence/meta.yaml b/recipes/bioconductor-divergence/meta.yaml index 8405572604541..a322557c552a1 100644 --- a/recipes/bioconductor-divergence/meta.yaml +++ b/recipes/bioconductor-divergence/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "divergence" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0d386fade56d1aefb877693d2d468aca + md5: 0ead0047c69549361f0f86d7207aee2b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-divergence", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-dks/meta.yaml b/recipes/bioconductor-dks/meta.yaml index 54475c9ca8d0f..ea476c6b5f0f4 100644 --- a/recipes/bioconductor-dks/meta.yaml +++ b/recipes/bioconductor-dks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "dks" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bda53a4f0f6a746a4f0ade7ecbc9d728 + md5: f15cb2d88222e2936dc9460d69a924ad build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dks", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-dlbcl/meta.yaml b/recipes/bioconductor-dlbcl/meta.yaml index 826b1990b2a5f..5324572ce48c0 100644 --- a/recipes/bioconductor-dlbcl/meta.yaml +++ b/recipes/bioconductor-dlbcl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.1" %} {% set name = "DLBCL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f22495affaad1066fbe54791486ebd53 + md5: a2906f8e35b0457c1cd8052d2457d40b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dlbcl", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dlbcl/post-link.sh b/recipes/bioconductor-dlbcl/post-link.sh index 4a3925603037e..c17921df4bc39 100644 --- a/recipes/bioconductor-dlbcl/post-link.sh +++ b/recipes/bioconductor-dlbcl/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dlbcl-1.40.0" +installBiocDataPackage.sh "dlbcl-1.42.1" diff --git a/recipes/bioconductor-dmchmm/meta.yaml b/recipes/bioconductor-dmchmm/meta.yaml index 3fbd3d1cd7b03..440303fd576f2 100644 --- a/recipes/bioconductor-dmchmm/meta.yaml +++ b/recipes/bioconductor-dmchmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "DMCHMM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1bd9934bf164aae70e6b1eacadbcdae4 + md5: 4a4e52e12df4e699e0e20d13828f25f0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dmchmm", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-calibrate - r-fdrtool - r-multcomp run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-calibrate - r-fdrtool diff --git a/recipes/bioconductor-dmelsgi/meta.yaml b/recipes/bioconductor-dmelsgi/meta.yaml index 64e1775ca9de6..6dabf001c9956 100644 --- a/recipes/bioconductor-dmelsgi/meta.yaml +++ b/recipes/bioconductor-dmelsgi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "DmelSGI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 611e89ab1359a4e0283b61e75205878f + md5: c13b3a8f881ca54d5e8ddf52ebe8b86a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dmelsgi", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, EBImage, RColorBrewer, RNAinteractMAPK, hwriter, xtable, beeswarm requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-abind - r-base - r-gplots @@ -30,8 +31,8 @@ requirements: - r-knitr - r-tsp run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-abind - r-base - r-gplots @@ -39,7 +40,7 @@ requirements: - r-knitr - r-tsp - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dmelsgi/post-link.sh b/recipes/bioconductor-dmelsgi/post-link.sh index 517c5d22c9e6c..9666ced12ef5f 100644 --- a/recipes/bioconductor-dmelsgi/post-link.sh +++ b/recipes/bioconductor-dmelsgi/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dmelsgi-1.32.0" +installBiocDataPackage.sh "dmelsgi-1.34.0" diff --git a/recipes/bioconductor-dmrcaller/meta.yaml b/recipes/bioconductor-dmrcaller/meta.yaml index 334e3141ab264..877d463affcbd 100644 --- a/recipes/bioconductor-dmrcaller/meta.yaml +++ b/recipes/bioconductor-dmrcaller/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "DMRcaller" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 721451b67d2e53e1d2a76142208c18cb + md5: 1c5b37620b4950eb63e32c3063235e8e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dmrcaller", max_pin="x.x") }}' # Suggests: knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-betareg - r-rcpp @@ -30,9 +31,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-betareg - r-rcpp diff --git a/recipes/bioconductor-dmrcatedata/meta.yaml b/recipes/bioconductor-dmrcatedata/meta.yaml index cff320dcd2e33..06d80da935efd 100644 --- a/recipes/bioconductor-dmrcatedata/meta.yaml +++ b/recipes/bioconductor-dmrcatedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "DMRcatedata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c2d0addb7984dadb9a3c0012dcd8c719 + md5: ac938c6259121c4a60ca3c8c5bfdf724 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dmrcatedata", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-plyr - r-readxl run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-plyr - r-readxl - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dmrcatedata/post-link.sh b/recipes/bioconductor-dmrcatedata/post-link.sh index eabb638ec0fc9..d4ad6b968cb0a 100644 --- a/recipes/bioconductor-dmrcatedata/post-link.sh +++ b/recipes/bioconductor-dmrcatedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dmrcatedata-2.18.0" +installBiocDataPackage.sh "dmrcatedata-2.20.0" diff --git a/recipes/bioconductor-dmrscan/meta.yaml b/recipes/bioconductor-dmrscan/meta.yaml index 53143408153e9..0b03fd4a53375 100644 --- a/recipes/bioconductor-dmrscan/meta.yaml +++ b/recipes/bioconductor-dmrscan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "DMRScan" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e05e55e05878903f9d35e30c7bbf3a37 + md5: 698b81baf921ef394adedb8d8ff7ba7f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dmrscan", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, BiocManager requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-mass - r-matrix - r-mvtnorm - r-rcpproll run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-mass - r-matrix diff --git a/recipes/bioconductor-dmrseq/meta.yaml b/recipes/bioconductor-dmrseq/meta.yaml index efaa67d94c3ec..505c49b1d0fb8 100644 --- a/recipes/bioconductor-dmrseq/meta.yaml +++ b/recipes/bioconductor-dmrseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "dmrseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 30fbe6664a5ed95ed8cd32e6726fd218 + md5: a8181423ea50609ae16545b9f8bb1895 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dmrseq", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, BiocStyle +# Suggests: knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-annotatr >=1.26.0,<1.27.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-annotatr >=1.28.0,<1.29.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-locfit @@ -40,17 +41,17 @@ requirements: - r-outliers - r-rcolorbrewer run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-annotatr >=1.26.0,<1.27.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-annotatr >=1.28.0,<1.29.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-locfit diff --git a/recipes/bioconductor-dnabarcodecompatibility/meta.yaml b/recipes/bioconductor-dnabarcodecompatibility/meta.yaml index d8cb8b9e6de09..bc74f779dfa5a 100644 --- a/recipes/bioconductor-dnabarcodecompatibility/meta.yaml +++ b/recipes/bioconductor-dnabarcodecompatibility/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "DNABarcodeCompatibility" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 481a9ea651c4ff63152c214b3250677e + md5: b1e2988c254cf089a2f887abf139b7bf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dnabarcodecompatibility", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-dnabarcodes >=1.30.0,<1.31.0' + - 'bioconductor-dnabarcodes >=1.32.0,<1.33.0' - r-base - r-dplyr - r-numbers @@ -29,7 +30,7 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-dnabarcodes >=1.30.0,<1.31.0' + - 'bioconductor-dnabarcodes >=1.32.0,<1.33.0' - r-base - r-dplyr - r-numbers diff --git a/recipes/bioconductor-dnabarcodes/meta.yaml b/recipes/bioconductor-dnabarcodes/meta.yaml index bb47078fe041c..53c9caad94d27 100644 --- a/recipes/bioconductor-dnabarcodes/meta.yaml +++ b/recipes/bioconductor-dnabarcodes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "DNABarcodes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7922c9dbc0b216fca9de9a18afef465a + md5: 6047e393e89e644fbf9aa4aa5a9faa64 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dnabarcodes", max_pin="x.x") }}' # Suggests: knitr, BiocStyle, rmarkdown requirements: host: diff --git a/recipes/bioconductor-dnacopy/meta.yaml b/recipes/bioconductor-dnacopy/meta.yaml index f788a79e19267..11f96aa6d76d5 100644 --- a/recipes/bioconductor-dnacopy/meta.yaml +++ b/recipes/bioconductor-dnacopy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.1" %} +{% set version = "1.76.0" %} {% set name = "DNAcopy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 41ab8f2ec3f9ee0a4b63eb57e97cdeef + md5: 1b80859f79a39def302664f11b91a98f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dnacopy", max_pin="x.x") }}' requirements: host: - r-base @@ -34,7 +35,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'DNA copy number data analysis' + summary: 'DNA Copy Number Data Analysis' description: 'Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: diff --git a/recipes/bioconductor-dnafusion/meta.yaml b/recipes/bioconductor-dnafusion/meta.yaml index 38aeb1d4e0dcc..03be682d7e794 100644 --- a/recipes/bioconductor-dnafusion/meta.yaml +++ b/recipes/bioconductor-dnafusion/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "DNAfusion" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: edd9b9e868337162ddb38fa5eca32876 + md5: b7ef2bb10bea5334d6d159208c284c16 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dnafusion", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, sessioninfo, BiocStyle requirements: host: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base test: commands: diff --git a/recipes/bioconductor-dnashaper/meta.yaml b/recipes/bioconductor-dnashaper/meta.yaml index 05df265da888d..06c57e6991e97 100644 --- a/recipes/bioconductor-dnashaper/meta.yaml +++ b/recipes/bioconductor-dnashaper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "DNAshapeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 92308b5f9b7b9ed27d5663313d92f2a2 + md5: f2b90849d52bce75d88a4970f08c2544 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dnashaper", max_pin="x.x") }}' # Suggests: AnnotationHub, knitr, rmarkdown, testthat, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19, caret requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-fields - 'r-rcpp >=0.12.1' - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-fields - 'r-rcpp >=0.12.1' diff --git a/recipes/bioconductor-dnazoodata/meta.yaml b/recipes/bioconductor-dnazoodata/meta.yaml index 07a9c8399ec46..6ac0f55444cfb 100644 --- a/recipes/bioconductor-dnazoodata/meta.yaml +++ b/recipes/bioconductor-dnazoodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "DNAZooData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 76d7687720d175ca13a1057c22b68b1e + md5: 06c4b9dbbaddc3dd4dcdc51e34150aa7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dnazoodata", max_pin="x.x") }}' noarch: generic # Suggests: dplyr, testthat, methods, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-hicexperiment >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rjson run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-hicexperiment >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rjson - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dnazoodata/post-link.sh b/recipes/bioconductor-dnazoodata/post-link.sh index 99f71e297f7d8..34b10c2512e29 100644 --- a/recipes/bioconductor-dnazoodata/post-link.sh +++ b/recipes/bioconductor-dnazoodata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dnazoodata-1.0.0" +installBiocDataPackage.sh "dnazoodata-1.2.0" diff --git a/recipes/bioconductor-do.db/meta.yaml b/recipes/bioconductor-do.db/meta.yaml index b8fcca5ca4089..5c3b17b44eba8 100644 --- a/recipes/bioconductor-do.db/meta.yaml +++ b/recipes/bioconductor-do.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.9" %} {% set name = "DO.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 63dda6d46d2fe40c52a2e79260a7fb9d build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-do.db", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dominoeffect/meta.yaml b/recipes/bioconductor-dominoeffect/meta.yaml index 71dd0a84aba94..eb625150b9ecb 100644 --- a/recipes/bioconductor-dominoeffect/meta.yaml +++ b/recipes/bioconductor-dominoeffect/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "DominoEffect" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f620b081e95046b62ef0c8f9081f26e3 + md5: 2e92d099e31b5feaf035b8eb5ad92376 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dominoeffect", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table test: diff --git a/recipes/bioconductor-donapllp2013/meta.yaml b/recipes/bioconductor-donapllp2013/meta.yaml index e2e5d42e94204..abdd5e739d806 100644 --- a/recipes/bioconductor-donapllp2013/meta.yaml +++ b/recipes/bioconductor-donapllp2013/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "DonaPLLP2013" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1ef96235e9049d31e27f5e5fff17d1ec + md5: d8dc37afefc52856d520540b07faf545 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-donapllp2013", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-base run: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-donapllp2013/post-link.sh b/recipes/bioconductor-donapllp2013/post-link.sh index 091fa30e9113d..5921a0116e213 100644 --- a/recipes/bioconductor-donapllp2013/post-link.sh +++ b/recipes/bioconductor-donapllp2013/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "donapllp2013-1.38.0" +installBiocDataPackage.sh "donapllp2013-1.40.0" diff --git a/recipes/bioconductor-doppelgangr/meta.yaml b/recipes/bioconductor-doppelgangr/meta.yaml index fa878f48b7983..8038472db593b 100644 --- a/recipes/bioconductor-doppelgangr/meta.yaml +++ b/recipes/bioconductor-doppelgangr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "doppelgangR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 294c75b10f9555eca7ba92b5d903c3b0 + md5: c50eff7bb5871b545a8199a9b1c4667b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-doppelgangr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-digest - r-mnormt run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-digest - r-mnormt diff --git a/recipes/bioconductor-dorothea/meta.yaml b/recipes/bioconductor-dorothea/meta.yaml index 827105752b8d7..e6eda607d7e68 100644 --- a/recipes/bioconductor-dorothea/meta.yaml +++ b/recipes/bioconductor-dorothea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "dorothea" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 068a6de9744d9d5c7085dfe910968e17 + md5: d1ad1213db5d54f1fc6ef8d195b9bbc0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dorothea", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, BiocStyle, OmnipathR, viper, knitr, pheatmap, pkgdown, rmarkdown, Seurat, SingleCellExperiment, SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils requirements: host: - - 'bioconductor-bcellviper >=1.36.0,<1.37.0' - - 'bioconductor-decoupler >=2.6.0,<2.7.0' + - 'bioconductor-bcellviper >=1.38.0,<1.39.0' + - 'bioconductor-decoupler >=2.8.0,<2.9.0' - r-base - r-dplyr - r-magrittr run: - - 'bioconductor-bcellviper >=1.36.0,<1.37.0' - - 'bioconductor-decoupler >=2.6.0,<2.7.0' + - 'bioconductor-bcellviper >=1.38.0,<1.39.0' + - 'bioconductor-decoupler >=2.8.0,<2.9.0' - r-base - r-dplyr - r-magrittr - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dorothea/post-link.sh b/recipes/bioconductor-dorothea/post-link.sh index ed11f25157cc9..b77af7c38dc2e 100644 --- a/recipes/bioconductor-dorothea/post-link.sh +++ b/recipes/bioconductor-dorothea/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dorothea-1.12.0" +installBiocDataPackage.sh "dorothea-1.14.0" diff --git a/recipes/bioconductor-doscheda/meta.yaml b/recipes/bioconductor-doscheda/meta.yaml index 4b32f2f293aaf..896c4140c8007 100644 --- a/recipes/bioconductor-doscheda/meta.yaml +++ b/recipes/bioconductor-doscheda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "Doscheda" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8fc89a023bcd59d4fabf8d485b7826d1 + md5: 3eee0480f798b00860daaf2cb88325ca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-doscheda", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-calibrate - r-corrgram @@ -41,9 +42,9 @@ requirements: - r-shinydashboard - r-stringr run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-calibrate - r-corrgram diff --git a/recipes/bioconductor-dose/meta.yaml b/recipes/bioconductor-dose/meta.yaml index 2598bc88fb879..0d10dde0a81d3 100644 --- a/recipes/bioconductor-dose/meta.yaml +++ b/recipes/bioconductor-dose/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.26.1" %} +{% set version = "3.28.1" %} {% set name = "DOSE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1dad84a44c7ce259b0538d452cb7aaf9 + md5: 11096edb2862c8a442f53435082e40b6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dose", max_pin="x.x") }}' noarch: generic -# Suggests: prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, rmarkdown, org.Hs.eg.db, testthat +# Suggests: prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, rmarkdown, org.Hs.eg.db, MPO.db, HPO.db, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - 'bioconductor-hdo.db >=0.99.0,<0.100.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-ggplot2 - r-reshape2 + - r-yulab.utils run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - 'bioconductor-hdo.db >=0.99.0,<0.100.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-ggplot2 - r-reshape2 + - r-yulab.utils test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-doser/meta.yaml b/recipes/bioconductor-doser/meta.yaml index 9e43fae39943c..7b6a6fdc3f312 100644 --- a/recipes/bioconductor-doser/meta.yaml +++ b/recipes/bioconductor-doser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "doseR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 23b8b183287c77bfae54e16a488988d8 + md5: 20251942acb7343859507c138bc2b902 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-doser", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-digest - r-lme4 @@ -31,9 +32,9 @@ requirements: - r-mclust - r-runit run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-digest - r-lme4 diff --git a/recipes/bioconductor-doubletrouble/meta.yaml b/recipes/bioconductor-doubletrouble/meta.yaml index 7536d4a2b14e1..a6b8eb760d0b6 100644 --- a/recipes/bioconductor-doubletrouble/meta.yaml +++ b/recipes/bioconductor-doubletrouble/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.1" %} {% set name = "doubletrouble" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3900ef117b25b1aad217a9953deb4a46 + md5: e494ee8650e6c8a13c7149c68683bea8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-doubletrouble", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), knitr, feature, BiocStyle, rmarkdown, covr, sessioninfo requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-msa2dist >=1.4.0,<1.5.0' - - 'bioconductor-syntenet >=1.2.0,<1.3.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-msa2dist >=1.6.0,<1.7.0' + - 'bioconductor-syntenet >=1.4.0,<1.5.0' - r-base - r-ggplot2 - r-mclust + - r-rlang run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-msa2dist >=1.4.0,<1.5.0' - - 'bioconductor-syntenet >=1.2.0,<1.3.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-msa2dist >=1.6.0,<1.7.0' + - 'bioconductor-syntenet >=1.4.0,<1.5.0' - r-base - r-ggplot2 - r-mclust + - r-rlang test: commands: - '$R -e "library(''{{ name }}'')"' @@ -43,6 +50,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Identification and classification of duplicated genes' - description: 'doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are: i. whole-genome duplication (WGD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). If users want a simpler classification scheme, duplicates can also be classified into WGD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.' + description: 'doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-drawproteins/meta.yaml b/recipes/bioconductor-drawproteins/meta.yaml index cb3cac5120abe..54bccf2331977 100644 --- a/recipes/bioconductor-drawproteins/meta.yaml +++ b/recipes/bioconductor-drawproteins/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "drawProteins" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 309e0805cb162bc9e22e8ad73dd775a9 + md5: 67cbf634b37851946e9cc3885cdda6c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drawproteins", max_pin="x.x") }}' noarch: generic # Suggests: covr, testthat, knitr, rmarkdown, BiocStyle requirements: diff --git a/recipes/bioconductor-dreamlet/build.sh b/recipes/bioconductor-dreamlet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dreamlet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dreamlet/build_failure.linux-64.yaml b/recipes/bioconductor-dreamlet/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0e452d24e3b59 --- /dev/null +++ b/recipes/bioconductor-dreamlet/build_failure.linux-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 9267c92fbfbee2b151933e110f05e516a8f84863f222f244128a2f63b327fcf7 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + nothing provides requested r-mashr >=0.2.52 +category: |- + dependency issue diff --git a/recipes/bioconductor-dreamlet/build_failure.osx-64.yaml b/recipes/bioconductor-dreamlet/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..0e452d24e3b59 --- /dev/null +++ b/recipes/bioconductor-dreamlet/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 9267c92fbfbee2b151933e110f05e516a8f84863f222f244128a2f63b327fcf7 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + nothing provides requested r-mashr >=0.2.52 +category: |- + dependency issue diff --git a/recipes/bioconductor-dreamlet/meta.yaml b/recipes/bioconductor-dreamlet/meta.yaml new file mode 100644 index 0000000000000..14eba535c39a1 --- /dev/null +++ b/recipes/bioconductor-dreamlet/meta.yaml @@ -0,0 +1,106 @@ +{% set version = "1.0.0" %} +{% set name = "dreamlet" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 34ea1ec9e44c635699ed9cf8deed29cd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dreamlet", max_pin="x.x") }}' +# Suggests: BiocStyle, knitr, pander, rmarkdown, muscat, ExperimentHub, RUnit, scater, scuttle +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variancepartition >=1.32.0,<1.33.0' + - 'bioconductor-zenith >=1.4.0,<1.5.0' + - r-ashr + - r-base + - r-data.table + - r-dplyr + - r-ggplot2 + - r-ggrepel + - r-gtools + - 'r-lme4 >=1.1-33' + - 'r-mashr >=0.2.52' + - r-mass + - r-matrix + - r-purrr + - r-rcpp + - r-rdpack + - r-reshape2 + - r-scattermore + - r-tidyr + - libblas + - liblapack + run: + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variancepartition >=1.32.0,<1.33.0' + - 'bioconductor-zenith >=1.4.0,<1.5.0' + - r-ashr + - r-base + - r-data.table + - r-dplyr + - r-ggplot2 + - r-ggrepel + - r-gtools + - 'r-lme4 >=1.1-33' + - 'r-mashr >=0.2.52' + - r-mass + - r-matrix + - r-purrr + - r-rcpp + - r-rdpack + - r-reshape2 + - r-scattermore + - r-tidyr + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Cohort-scale differential expression analysis of single cell data using linear (mixed) models' + description: 'Recent advances in single cell/nucleus transcriptomic technology has enabled collection of cohort-scale datasets to study cell type specific gene expression differences associated disease state, stimulus, and genetic regulation. The scale of these data, complex study designs, and low read count per cell mean that characterizing cell type specific molecular mechanisms requires a user-frieldly, purpose-build analytical framework. We have developed the dreamlet package that applies a pseudobulk approach and fits a regression model for each gene and cell cluster to test differential expression across individuals associated with a trait of interest. Use of precision-weighted linear mixed models enables accounting for repeated measures study designs, high dimensional batch effects, and varying sequencing depth or observed cells per biosample.' + diff --git a/recipes/bioconductor-dresscheck/meta.yaml b/recipes/bioconductor-dresscheck/meta.yaml index 9f7499d0e8bbb..5c21bedf99cda 100644 --- a/recipes/bioconductor-dresscheck/meta.yaml +++ b/recipes/bioconductor-dresscheck/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "dressCheck" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 27fc1d1485335601b86ab54b8380f1dc + md5: d6fb25eaad39c714024ed855c8c9c87d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dresscheck", max_pin="x.x") }}' noarch: generic # Suggests: survival, chron requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dresscheck/post-link.sh b/recipes/bioconductor-dresscheck/post-link.sh index 6bb9b9ee996f5..307a736efcaa5 100644 --- a/recipes/bioconductor-dresscheck/post-link.sh +++ b/recipes/bioconductor-dresscheck/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dresscheck-0.38.0" +installBiocDataPackage.sh "dresscheck-0.40.0" diff --git a/recipes/bioconductor-drimseq/meta.yaml b/recipes/bioconductor-drimseq/meta.yaml index 036fb1329f664..0900c40f993b6 100644 --- a/recipes/bioconductor-drimseq/meta.yaml +++ b/recipes/bioconductor-drimseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "DRIMSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7145a27da005c65bda5885bf2de31976 + md5: fae7a1b0945b2942ef3f633d68a74fd2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drimseq", max_pin="x.x") }}' noarch: generic # Suggests: PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-mass - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-mass diff --git a/recipes/bioconductor-drivernet/meta.yaml b/recipes/bioconductor-drivernet/meta.yaml index aa29c546732e6..6b233cd48cc6b 100644 --- a/recipes/bioconductor-drivernet/meta.yaml +++ b/recipes/bioconductor-drivernet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "DriverNet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c9d229b232a5ee18771af476f9477584 + md5: 78b923b016f6bd8097c1edc43ca0cca4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drivernet", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-droplettestfiles/meta.yaml b/recipes/bioconductor-droplettestfiles/meta.yaml index daca202c76a27..505870f109933 100644 --- a/recipes/bioconductor-droplettestfiles/meta.yaml +++ b/recipes/bioconductor-droplettestfiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "DropletTestFiles" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: addd41a9a235a4216b4c7067879203d6 + md5: 5a3a3f0d0901c90c6a2b173b976c4868 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-droplettestfiles", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, DropletUtils requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-droplettestfiles/post-link.sh b/recipes/bioconductor-droplettestfiles/post-link.sh index 0d1ccdac66b6c..968fbe466a2dc 100644 --- a/recipes/bioconductor-droplettestfiles/post-link.sh +++ b/recipes/bioconductor-droplettestfiles/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "droplettestfiles-1.10.0" +installBiocDataPackage.sh "droplettestfiles-1.12.0" diff --git a/recipes/bioconductor-dropletutils/meta.yaml b/recipes/bioconductor-dropletutils/meta.yaml index 063be886c2025..211af9c8e5c59 100644 --- a/recipes/bioconductor-dropletutils/meta.yaml +++ b/recipes/bioconductor-dropletutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "DropletUtils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0633d05d7dde6fe7e7c28eba4c5862db + md5: f1fe907e6269e652adc4607fdb335c41 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dropletutils", max_pin="x.x") }}' # Suggests: testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles # SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-dqrng @@ -45,21 +46,21 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-dqrng diff --git a/recipes/bioconductor-drosgenome1.db/meta.yaml b/recipes/bioconductor-drosgenome1.db/meta.yaml index 99ab030ba9492..8fc4379c2d8c6 100644 --- a/recipes/bioconductor-drosgenome1.db/meta.yaml +++ b/recipes/bioconductor-drosgenome1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "drosgenome1.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6432e2ae22cf58524278a559097bdf3a build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drosgenome1.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drosgenome1cdf/meta.yaml b/recipes/bioconductor-drosgenome1cdf/meta.yaml index 240ef113c68af..a6ce8e5c2a650 100644 --- a/recipes/bioconductor-drosgenome1cdf/meta.yaml +++ b/recipes/bioconductor-drosgenome1cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "drosgenome1cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e12983f2148c10ef1faa50f810b6eee3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drosgenome1cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drosgenome1probe/meta.yaml b/recipes/bioconductor-drosgenome1probe/meta.yaml index e944121e7679f..ec78a4874ba4f 100644 --- a/recipes/bioconductor-drosgenome1probe/meta.yaml +++ b/recipes/bioconductor-drosgenome1probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "drosgenome1probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1f12abdfeee65e8a6554f57507d86fb3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drosgenome1probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drosophila2.db/meta.yaml b/recipes/bioconductor-drosophila2.db/meta.yaml index aa6cda347819e..93fbb18884cc1 100644 --- a/recipes/bioconductor-drosophila2.db/meta.yaml +++ b/recipes/bioconductor-drosophila2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "drosophila2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c01d0d1b5e17c3b36ad801b44da72b96 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drosophila2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drosophila2cdf/meta.yaml b/recipes/bioconductor-drosophila2cdf/meta.yaml index f3aa808424b36..1b1e175abbed9 100644 --- a/recipes/bioconductor-drosophila2cdf/meta.yaml +++ b/recipes/bioconductor-drosophila2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "drosophila2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3323e723c133ff2b6188e22bebf3e20a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drosophila2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drosophila2probe/meta.yaml b/recipes/bioconductor-drosophila2probe/meta.yaml index b12a4cb086c88..15be4b2d9a764 100644 --- a/recipes/bioconductor-drosophila2probe/meta.yaml +++ b/recipes/bioconductor-drosophila2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "drosophila2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ba0251902ea0a5f0db61105bdcdc3530 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drosophila2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drugtargetinteractions/meta.yaml b/recipes/bioconductor-drugtargetinteractions/meta.yaml index 0e37c7539a4e0..27b696b08cd54 100644 --- a/recipes/bioconductor-drugtargetinteractions/meta.yaml +++ b/recipes/bioconductor-drugtargetinteractions/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.1" %} {% set name = "drugTargetInteractions" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9fdf995df89dbce9197ad2577325b409 + md5: c1a702c085df262e0a697b6687ea3ee4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drugtargetinteractions", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, knitr, rmarkdown, ggplot2, reshape2, DT, EnsDb.Hsapiens.v86 requirements: host: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-uniprot.ws >=2.40.0,<2.41.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-uniprot.ws >=2.42.0,<2.43.0' - r-base - r-dplyr - r-rappdirs - r-rsqlite run: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-uniprot.ws >=2.40.0,<2.41.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-uniprot.ws >=2.42.0,<2.43.0' - r-base - r-dplyr - r-rappdirs diff --git a/recipes/bioconductor-drugvsdisease/meta.yaml b/recipes/bioconductor-drugvsdisease/meta.yaml index 5a94487874b41..1189be641777b 100644 --- a/recipes/bioconductor-drugvsdisease/meta.yaml +++ b/recipes/bioconductor-drugvsdisease/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.42.0" %} +{% set version = "2.44.0" %} {% set name = "DrugVsDisease" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cea656c739b76d8bc0c44206d3419ae0 + md5: cfb6f4111b0003213278308c1672e49c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drugvsdisease", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-arrayexpress >=1.60.0,<1.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-cmap2data >=1.36.0,<1.37.0' - - 'bioconductor-drugvsdiseasedata >=1.36.0,<1.37.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-arrayexpress >=1.62.0,<1.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-cmap2data >=1.38.0,<1.39.0' + - 'bioconductor-drugvsdiseasedata >=1.38.0,<1.39.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - 'bioconductor-hgu133a2.db >=3.13.0,<3.14.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-runit - r-xtable run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-arrayexpress >=1.60.0,<1.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-cmap2data >=1.36.0,<1.37.0' - - 'bioconductor-drugvsdiseasedata >=1.36.0,<1.37.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-arrayexpress >=1.62.0,<1.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-cmap2data >=1.38.0,<1.39.0' + - 'bioconductor-drugvsdiseasedata >=1.38.0,<1.39.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - 'bioconductor-hgu133a2.db >=3.13.0,<3.14.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-runit - r-xtable diff --git a/recipes/bioconductor-drugvsdiseasedata/meta.yaml b/recipes/bioconductor-drugvsdiseasedata/meta.yaml index d780758c2d4db..ddef5ea5e9960 100644 --- a/recipes/bioconductor-drugvsdiseasedata/meta.yaml +++ b/recipes/bioconductor-drugvsdiseasedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "DrugVsDiseasedata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 64c011debe7f2f876d073b7383502db0 + md5: 40b800653aab57e822a18afe5bd1a2e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drugvsdiseasedata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drugvsdiseasedata/post-link.sh b/recipes/bioconductor-drugvsdiseasedata/post-link.sh index 1bea3948414ee..f2a69117547ff 100644 --- a/recipes/bioconductor-drugvsdiseasedata/post-link.sh +++ b/recipes/bioconductor-drugvsdiseasedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "drugvsdiseasedata-1.36.0" +installBiocDataPackage.sh "drugvsdiseasedata-1.38.0" diff --git a/recipes/bioconductor-dstruct/meta.yaml b/recipes/bioconductor-dstruct/meta.yaml index ed2b313366a99..6324f6b91a238 100644 --- a/recipes/bioconductor-dstruct/meta.yaml +++ b/recipes/bioconductor-dstruct/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "dStruct" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de647acd70d0a19a5b1bdf9758a8389c + md5: 294cd694534f0d82a92aaabeea86836f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dstruct", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) +# Suggests: BiocStyle, knitr, rmarkdown, tidyverse, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-purrr @@ -30,8 +31,8 @@ requirements: - r-rlang - r-zoo run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-purrr @@ -45,6 +46,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Identifying differentially reactive regions from RNA structurome profiling data' - description: 'dStruct identifies differentially reactive regions from RNA structurome profiling data. dStruct is compatible with a broad range of structurome profiling technologies, e.g., SHAPE-MaP, DMS-MaPseq, Structure-Seq, SHAPE-Seq, etc. See Choudhary et al, Genome Biology, 2019 for the underlying method.' + description: 'dStruct identifies differentially reactive regions from RNA structurome profiling data. dStruct is compatible with a broad range of structurome profiling technologies, e.g., SHAPE-MaP, DMS-MaPseq, Structure-Seq, SHAPE-Seq, etc. See Choudhary et al., Genome Biology, 2019 for the underlying method.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-dta/meta.yaml b/recipes/bioconductor-dta/meta.yaml index a5da04f2395dc..8ce1f64afc9a8 100644 --- a/recipes/bioconductor-dta/meta.yaml +++ b/recipes/bioconductor-dta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "DTA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d4f0fb0b0ca75c66def75c8a31f6867 + md5: 58705aacdbf08c61d4713273dbd9bc6f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dta", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-dune/meta.yaml b/recipes/bioconductor-dune/meta.yaml index 41c46b2937b8e..5b2e50d6b815b 100644 --- a/recipes/bioconductor-dune/meta.yaml +++ b/recipes/bioconductor-dune/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "Dune" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3842b818ceba7018c1cfa4b89a41347d + md5: afc7d133de0af7ccdc64a9a7a3722ccb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dune", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-aricode - r-base - r-dplyr @@ -33,8 +34,8 @@ requirements: - r-rcolorbrewer - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-aricode - r-base - r-dplyr diff --git a/recipes/bioconductor-duoclustering2018/meta.yaml b/recipes/bioconductor-duoclustering2018/meta.yaml index 1fda672436ba2..4d5c22819da1a 100644 --- a/recipes/bioconductor-duoclustering2018/meta.yaml +++ b/recipes/bioconductor-duoclustering2018/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "DuoClustering2018" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 697a0b8aecfb07cb6034d7626001f262 + md5: a2761f4db56025af2eaf8240392d01a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-duoclustering2018", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, iSEE, scater, SingleCellExperiment, SummarizedExperiment, plyr requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - r-dplyr - r-ggplot2 @@ -33,7 +34,7 @@ requirements: - r-tidyr - r-viridis run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - r-dplyr - r-ggplot2 @@ -45,7 +46,7 @@ requirements: - r-tidyr - r-viridis - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-duoclustering2018/post-link.sh b/recipes/bioconductor-duoclustering2018/post-link.sh index 1b85c5cdaacd6..25113c1241a25 100644 --- a/recipes/bioconductor-duoclustering2018/post-link.sh +++ b/recipes/bioconductor-duoclustering2018/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "duoclustering2018-1.18.0" +installBiocDataPackage.sh "duoclustering2018-1.20.0" diff --git a/recipes/bioconductor-dupradar/meta.yaml b/recipes/bioconductor-dupradar/meta.yaml index 6fc83d6d9e27d..c628243cfea17 100644 --- a/recipes/bioconductor-dupradar/meta.yaml +++ b/recipes/bioconductor-dupradar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "dupRadar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 25020f4fc2033e3cb25d8fbc428219a6 + md5: 306ba6ddb1786eb7ec5e6cb4bc15562e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dupradar", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, AnnotationHub requirements: host: - - 'bioconductor-rsubread >=2.14.0,<2.15.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' - r-base - r-kernsmooth run: - - 'bioconductor-rsubread >=2.14.0,<2.15.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' - r-base - r-kernsmooth test: diff --git a/recipes/bioconductor-dvddata/meta.yaml b/recipes/bioconductor-dvddata/meta.yaml index 5f230dac04d9c..2ab2b9dc07a65 100644 --- a/recipes/bioconductor-dvddata/meta.yaml +++ b/recipes/bioconductor-dvddata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "DvDdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c21d1ca3b1808272b1d90004201512b2 + md5: d07387219229c006ba96b9ab43ddf4ff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dvddata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dvddata/post-link.sh b/recipes/bioconductor-dvddata/post-link.sh index d1a8b4afcd138..650d586b47f90 100644 --- a/recipes/bioconductor-dvddata/post-link.sh +++ b/recipes/bioconductor-dvddata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dvddata-1.36.0" +installBiocDataPackage.sh "dvddata-1.38.0" diff --git a/recipes/bioconductor-dyebias/meta.yaml b/recipes/bioconductor-dyebias/meta.yaml index b95f864f1361d..fbbc05f23ec24 100644 --- a/recipes/bioconductor-dyebias/meta.yaml +++ b/recipes/bioconductor-dyebias/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "dyebias" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3103ff75b1717ba43653c272fec9c73f + md5: 2b3e10379a29b0cb931514e06fe7259f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dyebias", max_pin="x.x") }}' noarch: generic # Suggests: limma, convert, GEOquery, dyebiasexamples, methods requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base test: commands: diff --git a/recipes/bioconductor-dyebiasexamples/meta.yaml b/recipes/bioconductor-dyebiasexamples/meta.yaml index 587748a9d2149..060513470d522 100644 --- a/recipes/bioconductor-dyebiasexamples/meta.yaml +++ b/recipes/bioconductor-dyebiasexamples/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "dyebiasexamples" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8ba42215153001f0334b098938eacf9c + md5: b73aa6c0c98150b2bccba7802dda8c86 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dyebiasexamples", max_pin="x.x") }}' noarch: generic # Suggests: dyebias, convert, Biobase requirements: host: - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dyebiasexamples/post-link.sh b/recipes/bioconductor-dyebiasexamples/post-link.sh index b8db735360a71..15ba43db540e5 100644 --- a/recipes/bioconductor-dyebiasexamples/post-link.sh +++ b/recipes/bioconductor-dyebiasexamples/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dyebiasexamples-1.40.0" +installBiocDataPackage.sh "dyebiasexamples-1.42.0" diff --git a/recipes/bioconductor-dyndoc/meta.yaml b/recipes/bioconductor-dyndoc/meta.yaml index fe9c210847aff..e987221cef2d7 100644 --- a/recipes/bioconductor-dyndoc/meta.yaml +++ b/recipes/bioconductor-dyndoc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "DynDoc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec7f41041d851001acdf1c2c0b3b3626 + md5: 1d5ea2c0b36289466bdb8095b39634fd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dyndoc", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-easier/meta.yaml b/recipes/bioconductor-easier/meta.yaml index 2cedf31d5992c..340d682ef186c 100644 --- a/recipes/bioconductor-easier/meta.yaml +++ b/recipes/bioconductor-easier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.3" %} +{% set version = "1.8.0" %} {% set name = "easier" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 722dd22a32a8bc541b0ead14b639594d + md5: 65f72a669a157fdf57501fb32d1c0333 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-easier", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment, viper requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-decoupler >=2.6.0,<2.7.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dorothea >=1.12.0,<1.13.0' - - 'bioconductor-easierdata >=1.6.0,<1.7.0' - - 'bioconductor-progeny >=1.22.0,<1.23.0' - - 'bioconductor-quantiseqr >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-decoupler >=2.8.0,<2.9.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dorothea >=1.14.0,<1.15.0' + - 'bioconductor-easierdata >=1.8.0,<1.9.0' + - 'bioconductor-progeny >=1.24.0,<1.25.0' + - 'bioconductor-quantiseqr >=1.10.0,<1.11.0' - r-base - r-coin - r-dplyr @@ -43,13 +44,13 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-decoupler >=2.6.0,<2.7.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dorothea >=1.12.0,<1.13.0' - - 'bioconductor-easierdata >=1.6.0,<1.7.0' - - 'bioconductor-progeny >=1.22.0,<1.23.0' - - 'bioconductor-quantiseqr >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-decoupler >=2.8.0,<2.9.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dorothea >=1.14.0,<1.15.0' + - 'bioconductor-easierdata >=1.8.0,<1.9.0' + - 'bioconductor-progeny >=1.24.0,<1.25.0' + - 'bioconductor-quantiseqr >=1.10.0,<1.11.0' - r-base - r-coin - r-dplyr diff --git a/recipes/bioconductor-easierdata/meta.yaml b/recipes/bioconductor-easierdata/meta.yaml index 7c385d3a4d023..b7b3eb87fc60f 100644 --- a/recipes/bioconductor-easierdata/meta.yaml +++ b/recipes/bioconductor-easierdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "easierData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8cdf9119aa80107e2d8d6853c2a6fde + md5: 5092649863b833021ff8593731571183 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-easierdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-easierdata/post-link.sh b/recipes/bioconductor-easierdata/post-link.sh index f734c14187602..c4e73343e9661 100644 --- a/recipes/bioconductor-easierdata/post-link.sh +++ b/recipes/bioconductor-easierdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "easierdata-1.6.0" +installBiocDataPackage.sh "easierdata-1.8.0" diff --git a/recipes/bioconductor-easylift/build.sh b/recipes/bioconductor-easylift/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-easylift/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-easylift/meta.yaml b/recipes/bioconductor-easylift/meta.yaml new file mode 100644 index 0000000000000..61eabc651b5e0 --- /dev/null +++ b/recipes/bioconductor-easylift/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "easylift" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 86d8c0188c35ab56732fd5cc55475e8c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-easylift", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat (>= 3.0.0), IRanges, knitr, BiocStyle, rmarkdown +requirements: + host: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - r-base + - r-r.utils + run: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - r-base + - r-r.utils +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'An R package to perform genomic liftover' + description: 'The easylift package provides a convenient tool for genomic liftover operations between different genome assemblies. It seamlessly works with Bioconductor''s GRanges objects and chain files from the UCSC Genome Browser, allowing for straightforward handling of genomic ranges across various genome versions. One noteworthy feature of easylift is its integration with the BiocFileCache package. This integration automates the management and caching of chain files necessary for liftover operations. Users no longer need to manually specify chain file paths in their function calls, reducing the complexity of the liftover process.' + license_file: LICENSE + diff --git a/recipes/bioconductor-easyreporting/meta.yaml b/recipes/bioconductor-easyreporting/meta.yaml index 5f278d52db552..aa88366c1a868 100644 --- a/recipes/bioconductor-easyreporting/meta.yaml +++ b/recipes/bioconductor-easyreporting/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "easyreporting" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fa8f5e752448cad38c4a14242247ad60 + md5: cffad8bbd7df1cd9ac54b4605a0c555e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-easyreporting", max_pin="x.x") }}' noarch: generic # Suggests: distill, BiocStyle, knitr, readxl, edgeR, limma, EDASeq, statmod requirements: diff --git a/recipes/bioconductor-easyrnaseq/meta.yaml b/recipes/bioconductor-easyrnaseq/meta.yaml index 18fe1382616eb..4f704725ab89e 100644 --- a/recipes/bioconductor-easyrnaseq/meta.yaml +++ b/recipes/bioconductor-easyrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.36.0" %} +{% set version = "2.38.0" %} {% set name = "easyRNASeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,53 +11,54 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e5ce1f716e811ef9d2a9aad791b33253 + md5: c763a083ce852695593a183ff7f9edcb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-easyrnaseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 2.18.0), BSgenome (>= 1.58.0), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.32) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomeintervals >=1.56.0,<1.57.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomeintervals >=1.58.0,<1.59.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-locfit - 'r-lsd >=4.1-0' - 'r-rappdirs >=0.3.1' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomeintervals >=1.56.0,<1.57.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomeintervals >=1.58.0,<1.59.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-locfit - 'r-lsd >=4.1-0' diff --git a/recipes/bioconductor-eatonetalchipseq/meta.yaml b/recipes/bioconductor-eatonetalchipseq/meta.yaml index 8841323159b09..54fe87b9b4f10 100644 --- a/recipes/bioconductor-eatonetalchipseq/meta.yaml +++ b/recipes/bioconductor-eatonetalchipseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "EatonEtAlChIPseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fa5225647fa5b852a38635bb2ba759ef + md5: e7695c3761d5f3d41dec21b0c8b50947 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-eatonetalchipseq", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-eatonetalchipseq/post-link.sh b/recipes/bioconductor-eatonetalchipseq/post-link.sh index d230394725d2d..346813c7b54e0 100644 --- a/recipes/bioconductor-eatonetalchipseq/post-link.sh +++ b/recipes/bioconductor-eatonetalchipseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "eatonetalchipseq-0.38.0" +installBiocDataPackage.sh "eatonetalchipseq-0.40.0" diff --git a/recipes/bioconductor-ebarrays/meta.yaml b/recipes/bioconductor-ebarrays/meta.yaml index ab564f3bdf108..c4b790998b5de 100644 --- a/recipes/bioconductor-ebarrays/meta.yaml +++ b/recipes/bioconductor-ebarrays/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.64.0" %} +{% set version = "2.66.0" %} {% set name = "EBarrays" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 877a76dfa9d767cfc95b8073ddf7e45e + md5: d273e2e9411207653d4e079e14484026 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ebarrays", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-cluster - r-lattice - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-cluster - r-lattice diff --git a/recipes/bioconductor-ebcoexpress/meta.yaml b/recipes/bioconductor-ebcoexpress/meta.yaml index fce53590dbdff..f22be4d02c7b7 100644 --- a/recipes/bioconductor-ebcoexpress/meta.yaml +++ b/recipes/bioconductor-ebcoexpress/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "EBcoexpress" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a279447b6ebe095682a46c302d2759f3 + md5: 66fa4257fbd0222064b30f6c15e74ab1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ebcoexpress", max_pin="x.x") }}' # Suggests: graph, igraph, colorspace requirements: host: - - 'bioconductor-ebarrays >=2.64.0,<2.65.0' + - 'bioconductor-ebarrays >=2.66.0,<2.67.0' - r-base - r-mclust - r-minqa - libblas - liblapack run: - - 'bioconductor-ebarrays >=2.64.0,<2.65.0' + - 'bioconductor-ebarrays >=2.66.0,<2.67.0' - r-base - r-mclust - r-minqa diff --git a/recipes/bioconductor-ebimage/meta.yaml b/recipes/bioconductor-ebimage/meta.yaml index 4eb7975ed1018..e8b8c950d28d8 100644 --- a/recipes/bioconductor-ebimage/meta.yaml +++ b/recipes/bioconductor-ebimage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.42.0" %} +{% set version = "4.44.0" %} {% set name = "EBImage" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9cd9c206c813cac474584a16c247946b + md5: 22e920a81ab633cdbf753daf3e128d64 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ebimage", max_pin="x.x") }}' # Suggests: BiocStyle, digest, knitr, rmarkdown, shiny requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-abind - r-base - 'r-fftwtools >=0.9-7' @@ -34,7 +35,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-abind - r-base - 'r-fftwtools >=0.9-7' diff --git a/recipes/bioconductor-ebsea/meta.yaml b/recipes/bioconductor-ebsea/meta.yaml index db931d1204df1..d16b40144208f 100644 --- a/recipes/bioconductor-ebsea/meta.yaml +++ b/recipes/bioconductor-ebsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "EBSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a127e02c2d643195ec73bfa7668f9301 + md5: d016b1e83c4b885565a573db1b134fbd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ebsea", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-empiricalbrownsmethod >=1.28.0,<1.29.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-empiricalbrownsmethod >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-empiricalbrownsmethod >=1.28.0,<1.29.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-empiricalbrownsmethod >=1.30.0,<1.31.0' - r-base test: commands: diff --git a/recipes/bioconductor-ebseq/meta.yaml b/recipes/bioconductor-ebseq/meta.yaml index 6254ef104cf0e..056e0f895151f 100644 --- a/recipes/bioconductor-ebseq/meta.yaml +++ b/recipes/bioconductor-ebseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "2.0.0" %} {% set name = "EBSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1fa9347689a45799ec669c47880beec7 + md5: e64aabb38197aba0ee5985a1558cce60 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ - noarch: generic + run_exports: '{{ pin_subpackage("bioconductor-ebseq", max_pin="x.x") }}' +# SystemRequirements: c++11 requirements: host: - r-base + - r-bh - r-blockmodeling - r-gplots + - 'r-rcpp >=0.12.11' + - 'r-rcppeigen >=0.3.2.9.0' - r-testthat + - libblas + - liblapack run: - r-base + - r-bh - r-blockmodeling - r-gplots + - 'r-rcpp >=0.12.11' + - 'r-rcppeigen >=0.3.2.9.0' - r-testthat + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ebseqhmm/meta.yaml b/recipes/bioconductor-ebseqhmm/meta.yaml index 6995a1ad16d64..54ba10633450f 100644 --- a/recipes/bioconductor-ebseqhmm/meta.yaml +++ b/recipes/bioconductor-ebseqhmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.35.0" %} {% set name = "EBSeqHMM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c727c482e89c11143c38785c3fa9570 + md5: d63f173eea402bf0e63ed7018c66d4d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ebseqhmm", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ebseq >=1.40.0,<1.41.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' - r-base run: - - 'bioconductor-ebseq >=1.40.0,<1.41.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' - r-base test: commands: diff --git a/recipes/bioconductor-ecoli2.db/meta.yaml b/recipes/bioconductor-ecoli2.db/meta.yaml index a8c18503deeef..50e6af2815625 100644 --- a/recipes/bioconductor-ecoli2.db/meta.yaml +++ b/recipes/bioconductor-ecoli2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "ecoli2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 110d6549b1d105fdff31ab8f45b08d65 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecoli2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.eck12.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.eck12.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.eck12.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.eck12.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecoli2cdf/meta.yaml b/recipes/bioconductor-ecoli2cdf/meta.yaml index abb629a424e72..12b93a0ff9c58 100644 --- a/recipes/bioconductor-ecoli2cdf/meta.yaml +++ b/recipes/bioconductor-ecoli2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ecoli2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b5cd1f05322ce494132ff649de9806c6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecoli2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecoli2probe/meta.yaml b/recipes/bioconductor-ecoli2probe/meta.yaml index f1c2ebe9bc3c1..1d0e8f7b2081f 100644 --- a/recipes/bioconductor-ecoli2probe/meta.yaml +++ b/recipes/bioconductor-ecoli2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ecoli2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 061fcb782ee9da3aa5108881677a4531 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecoli2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecoliasv2cdf/meta.yaml b/recipes/bioconductor-ecoliasv2cdf/meta.yaml index 5ca8789b939ab..dda890ce3dddf 100644 --- a/recipes/bioconductor-ecoliasv2cdf/meta.yaml +++ b/recipes/bioconductor-ecoliasv2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ecoliasv2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d7771ca1648b26a6af5bfb7582c6c778 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecoliasv2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecoliasv2probe/meta.yaml b/recipes/bioconductor-ecoliasv2probe/meta.yaml index 9d840d05475b1..189c801a32b21 100644 --- a/recipes/bioconductor-ecoliasv2probe/meta.yaml +++ b/recipes/bioconductor-ecoliasv2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ecoliasv2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b3e4332266184576279c3a478f286dc9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecoliasv2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecolicdf/meta.yaml b/recipes/bioconductor-ecolicdf/meta.yaml index 57e2bf50c9017..ae5dec1242d25 100644 --- a/recipes/bioconductor-ecolicdf/meta.yaml +++ b/recipes/bioconductor-ecolicdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ecolicdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4e664c1ac41a8ab68ef22f8a889b916c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecolicdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecolik12.db0/meta.yaml b/recipes/bioconductor-ecolik12.db0/meta.yaml index af7c68888e039..5fe013dc64149 100644 --- a/recipes/bioconductor-ecolik12.db0/meta.yaml +++ b/recipes/bioconductor-ecolik12.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "ecoliK12.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: acf1faa22de4e8b535baf0d7403acbe0 + md5: dd303204595a25bc730695462e930247 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecolik12.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecolik12.db0/post-link.sh b/recipes/bioconductor-ecolik12.db0/post-link.sh index 3ac028b892847..1ea1a96c05c6f 100644 --- a/recipes/bioconductor-ecolik12.db0/post-link.sh +++ b/recipes/bioconductor-ecolik12.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ecolik12.db0-3.17.0" +installBiocDataPackage.sh "ecolik12.db0-3.18.0" diff --git a/recipes/bioconductor-ecolileucine/meta.yaml b/recipes/bioconductor-ecolileucine/meta.yaml index 8292b62611e44..d735e051bbdef 100644 --- a/recipes/bioconductor-ecolileucine/meta.yaml +++ b/recipes/bioconductor-ecolileucine/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "ecoliLeucine" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f29571bdbf113fe17eb2a91638acf1a + md5: 30af71114480d851f4dad806e7f8e0d1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecolileucine", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - 'bioconductor-ecolicdf >=2.18.0,<2.19.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - 'bioconductor-ecolicdf >=2.18.0,<2.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecolileucine/post-link.sh b/recipes/bioconductor-ecolileucine/post-link.sh index c8c483bd70916..069ee49494795 100644 --- a/recipes/bioconductor-ecolileucine/post-link.sh +++ b/recipes/bioconductor-ecolileucine/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ecolileucine-1.40.0" +installBiocDataPackage.sh "ecolileucine-1.42.0" diff --git a/recipes/bioconductor-ecoliprobe/meta.yaml b/recipes/bioconductor-ecoliprobe/meta.yaml index d5bea7a7e2d95..fc9b2941ec792 100644 --- a/recipes/bioconductor-ecoliprobe/meta.yaml +++ b/recipes/bioconductor-ecoliprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ecoliprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 09586f9907bdbc43ba5ea4ce07c1f756 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecoliprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecolisakai.db0/meta.yaml b/recipes/bioconductor-ecolisakai.db0/meta.yaml index 4673684e174f2..f4a33593ee350 100644 --- a/recipes/bioconductor-ecolisakai.db0/meta.yaml +++ b/recipes/bioconductor-ecolisakai.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "ecoliSakai.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f49e4fe2806f14f78db0de22d37a7e7 + md5: 2afd28e9062d869d37e3d65dbe410bcb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecolisakai.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecolisakai.db0/post-link.sh b/recipes/bioconductor-ecolisakai.db0/post-link.sh index 818939129b685..5a26a1ced0260 100644 --- a/recipes/bioconductor-ecolisakai.db0/post-link.sh +++ b/recipes/bioconductor-ecolisakai.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ecolisakai.db0-3.17.0" +installBiocDataPackage.sh "ecolisakai.db0-3.18.0" diff --git a/recipes/bioconductor-ecolitk/meta.yaml b/recipes/bioconductor-ecolitk/meta.yaml index 512663e7315e7..eb82d060744b5 100644 --- a/recipes/bioconductor-ecolitk/meta.yaml +++ b/recipes/bioconductor-ecolitk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "ecolitk" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8867acb9dd27e581f696ec0afd77be79 + md5: 58667dc1f403986935c98a97f2e0b9e2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecolitk", max_pin="x.x") }}' noarch: generic # Suggests: ecoliLeucine, ecolicdf, graph, multtest, affy requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-edaseq/meta.yaml b/recipes/bioconductor-edaseq/meta.yaml index d9ee0fb7067a8..4e0352c7939f4 100644 --- a/recipes/bioconductor-edaseq/meta.yaml +++ b/recipes/bioconductor-edaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "EDASeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1bedbd7d1b319ddeb8eff7fc5d2d9bb7 + md5: b2d28fdad31e8c56f68873b599ffc235 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-edaseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat, DESeq2, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-aroma.light >=3.30.0,<3.31.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-aroma.light >=3.32.0,<3.33.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-biocmanager run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-aroma.light >=3.30.0,<3.31.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-aroma.light >=3.32.0,<3.33.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-biocmanager test: diff --git a/recipes/bioconductor-edge/meta.yaml b/recipes/bioconductor-edge/meta.yaml index 2b0e02ce3cdcb..fc6de808fba13 100644 --- a/recipes/bioconductor-edge/meta.yaml +++ b/recipes/bioconductor-edge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "edge" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ce7aff708078e2ddba0b00c919a67429 + md5: 89d1683b6b4f9723b4c4fcef6972d543 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-edge", max_pin="x.x") }}' # Suggests: testthat, knitr, ggplot2, reshape2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-snm >=1.48.0,<1.49.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-snm >=1.50.0,<1.51.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-mass - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-snm >=1.48.0,<1.49.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-snm >=1.50.0,<1.51.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-mass build: diff --git a/recipes/bioconductor-edger/meta.yaml b/recipes/bioconductor-edger/meta.yaml index 5a3493060c73a..0884137cf6b49 100644 --- a/recipes/bioconductor-edger/meta.yaml +++ b/recipes/bioconductor-edger/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.42.4" %} +{% set version = "4.0.2" %} {% set name = "edgeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad81660fe783c10b69e06fdab6130dc8 + md5: 0ba48556be0c95b929db5bbed32923f3 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: jsonlite, readr, rhdf5, splines, statmod, Biobase, AnnotationDbi, SummarizedExperiment, org.Hs.eg.db, Matrix, SeuratObject + run_exports: '{{ pin_subpackage("bioconductor-edger", max_pin="x.x") }}' +# Suggests: jsonlite, readr, rhdf5, splines, knitr, AnnotationDbi, Biobase, BiocStyle, SummarizedExperiment, org.Hs.eg.db, Matrix, SeuratObject requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-locfit - r-rcpp - libblas - liblapack run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-locfit - r-rcpp diff --git a/recipes/bioconductor-edirquery/meta.yaml b/recipes/bioconductor-edirquery/meta.yaml index eeb40850533ac..2adef6a882208 100644 --- a/recipes/bioconductor-edirquery/meta.yaml +++ b/recipes/bioconductor-edirquery/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "EDIRquery" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ef6b7ba141cd7778c7d5bf31d138af2 + md5: ff19937af17cf0a7a874b986192d6b1c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-edirquery", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' - r-base - 'r-readr >=2.1.2' - 'r-tibble >=3.1.6' - 'r-tictoc >=1.0.1' run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' - r-base - 'r-readr >=2.1.2' - 'r-tibble >=3.1.6' diff --git a/recipes/bioconductor-eds/meta.yaml b/recipes/bioconductor-eds/meta.yaml index fc15dbcda7029..de545d756c8e0 100644 --- a/recipes/bioconductor-eds/meta.yaml +++ b/recipes/bioconductor-eds/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "eds" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0250c849115fe963572ba6669f5377a3 + md5: 5992ff2692afb665a65bc9755175de5c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-eds", max_pin="x.x") }}' # Suggests: knitr, tximportData, testthat (>= 3.0.0) # SystemRequirements: C++11 requirements: diff --git a/recipes/bioconductor-egad/meta.yaml b/recipes/bioconductor-egad/meta.yaml index 9413400986988..d7cb742f73393 100644 --- a/recipes/bioconductor-egad/meta.yaml +++ b/recipes/bioconductor-egad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "EGAD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f46e429f7ee3c80517e8fa46e1819e18 + md5: 9a76ae26d942a1e8b8c8764b80c69927 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-egad", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown, markdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-gplots - r-igraph @@ -34,10 +35,10 @@ requirements: - r-rcurl - r-zoo run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-gplots - r-igraph diff --git a/recipes/bioconductor-egseadata/meta.yaml b/recipes/bioconductor-egseadata/meta.yaml index bf8e5346a6f45..aab5bfb3fdc69 100644 --- a/recipes/bioconductor-egseadata/meta.yaml +++ b/recipes/bioconductor-egseadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "EGSEAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1ccaaafd4866fa1cf07e06b6370739a3 + md5: 838b30ae6caf7c3cbb854e0404b52cda build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-egseadata", max_pin="x.x") }}' noarch: generic # Suggests: EGSEA requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-egseadata/post-link.sh b/recipes/bioconductor-egseadata/post-link.sh index d17c19a3933ce..4969b6b51c98a 100644 --- a/recipes/bioconductor-egseadata/post-link.sh +++ b/recipes/bioconductor-egseadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "egseadata-1.28.0" +installBiocDataPackage.sh "egseadata-1.30.0" diff --git a/recipes/bioconductor-eir/meta.yaml b/recipes/bioconductor-eir/meta.yaml index 6a9d27cf785b5..882112a2aaeb1 100644 --- a/recipes/bioconductor-eir/meta.yaml +++ b/recipes/bioconductor-eir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "eiR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 23f3e513756302dbc768aa836d474f0f + md5: 71e5c96821411e053b417fb15618e1cb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-eir", max_pin="x.x") }}' # Suggests: BiocStyle, knitcitations, knitr, knitrBootstrap,rmarkdown,RSQLite requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - r-dbi - r-digest @@ -33,8 +34,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - r-dbi - r-digest diff --git a/recipes/bioconductor-eisar/meta.yaml b/recipes/bioconductor-eisar/meta.yaml index c06ab9d062533..5daa7b7fcd320 100644 --- a/recipes/bioconductor-eisar/meta.yaml +++ b/recipes/bioconductor-eisar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "eisaR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3338687a24a33d16373c1033c2150c7f + md5: 0a81a6727f2514ce8e2836cc170bdb19 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-eisar", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie, Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38, ensembldb, AnnotationDbi, GenomicFeatures, rtracklayer requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-elmer.data/meta.yaml b/recipes/bioconductor-elmer.data/meta.yaml index 7d864ee0ec783..46a704674c673 100644 --- a/recipes/bioconductor-elmer.data/meta.yaml +++ b/recipes/bioconductor-elmer.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "ELMER.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4bb614a1bd1fd96f91af883bad29c914 + md5: 565ea1aa52f3f61d16b7560859ed7a3a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-elmer.data", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, dplyr, devtools, DT, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-elmer.data/post-link.sh b/recipes/bioconductor-elmer.data/post-link.sh index e9acc598f0002..f070b978224f7 100644 --- a/recipes/bioconductor-elmer.data/post-link.sh +++ b/recipes/bioconductor-elmer.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "elmer.data-2.24.0" +installBiocDataPackage.sh "elmer.data-2.26.0" diff --git a/recipes/bioconductor-elmer/meta.yaml b/recipes/bioconductor-elmer/meta.yaml index f306c2e69897e..680af36125772 100644 --- a/recipes/bioconductor-elmer/meta.yaml +++ b/recipes/bioconductor-elmer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.1" %} +{% set version = "2.26.0" %} {% set name = "ELMER" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d6a247672fe62e4bedb7b72a56af020e + md5: 528e6779b95faafbb8ff2e32e0b28ca5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-elmer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr, sesameData requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-elmer.data >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgabiolinks >=2.28.0,<2.29.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-elmer.data >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgabiolinks >=2.30.0,<2.31.0' - r-base - r-circlize - r-doparallel @@ -62,20 +63,20 @@ requirements: - r-tidyr - r-xml2 run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-elmer.data >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgabiolinks >=2.28.0,<2.29.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-elmer.data >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgabiolinks >=2.30.0,<2.31.0' - r-base - r-circlize - r-doparallel diff --git a/recipes/bioconductor-emdomics/meta.yaml b/recipes/bioconductor-emdomics/meta.yaml index d592a8cc531b5..f0657e63a91b6 100644 --- a/recipes/bioconductor-emdomics/meta.yaml +++ b/recipes/bioconductor-emdomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "EMDomics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 23c951e5766c53a07cc1946335b4e06c + md5: 3ac097828648747f0be1ed4d956ecfa7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-emdomics", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-cdft - r-emdist - r-ggplot2 - r-matrixstats run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-cdft - r-emdist diff --git a/recipes/bioconductor-empiricalbrownsmethod/meta.yaml b/recipes/bioconductor-empiricalbrownsmethod/meta.yaml index 04d10e3cba9a4..e73e26279321b 100644 --- a/recipes/bioconductor-empiricalbrownsmethod/meta.yaml +++ b/recipes/bioconductor-empiricalbrownsmethod/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "EmpiricalBrownsMethod" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c7c4a27f1986e21a7bf4a447305fb916 + md5: cde2165928019f9c13982d640a1303c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-empiricalbrownsmethod", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-emtdata/meta.yaml b/recipes/bioconductor-emtdata/meta.yaml index c94df7781a194..7dbe179742d90 100644 --- a/recipes/bioconductor-emtdata/meta.yaml +++ b/recipes/bioconductor-emtdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "emtdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e4c17e43c1d50287179f7fb2f594d6c3 + md5: 4f861584cce979edd6d7bdce3624e916 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-emtdata", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), stringr, plyr, prettydoc, BiocStyle, Homo.sapiens, RColorBrewer, rmarkdown, BiocFileCache, knitr requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-emtdata/post-link.sh b/recipes/bioconductor-emtdata/post-link.sh index 414a9037e8614..93baa8560da53 100644 --- a/recipes/bioconductor-emtdata/post-link.sh +++ b/recipes/bioconductor-emtdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "emtdata-1.8.0" +installBiocDataPackage.sh "emtdata-1.10.0" diff --git a/recipes/bioconductor-encodexplorerdata/meta.yaml b/recipes/bioconductor-encodexplorerdata/meta.yaml index 4777d7613ad5e..5eb72ebf61053 100644 --- a/recipes/bioconductor-encodexplorerdata/meta.yaml +++ b/recipes/bioconductor-encodexplorerdata/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.5" %} {% set name = "ENCODExplorerData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c6d9b491548529db0739b79c98adacd7 build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-encodexplorerdata", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationHub, RUnit, BiocGenerics, knitr, curl, httr requirements: @@ -31,7 +32,7 @@ requirements: - r-jsonlite - r-rcurl - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-enhancedvolcano/meta.yaml b/recipes/bioconductor-enhancedvolcano/meta.yaml index 6940df17b140d..717cd7a75281d 100644 --- a/recipes/bioconductor-enhancedvolcano/meta.yaml +++ b/recipes/bioconductor-enhancedvolcano/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "EnhancedVolcano" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 32e59ff1c6981c80fcfef699efbe2798 + md5: b8224be72afe86d3d951a6a8fdc6788e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enhancedvolcano", max_pin="x.x") }}' noarch: generic # Suggests: ggalt, ggrastr, RUnit, BiocGenerics, knitr, DESeq2, pasilla, airway, org.Hs.eg.db, gridExtra, magrittr, rmarkdown requirements: diff --git a/recipes/bioconductor-enhancerhomologsearch/meta.yaml b/recipes/bioconductor-enhancerhomologsearch/meta.yaml index 8ce3dff69f64b..2d0d66cd9e7d2 100644 --- a/recipes/bioconductor-enhancerhomologsearch/meta.yaml +++ b/recipes/bioconductor-enhancerhomologsearch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.2" %} {% set name = "enhancerHomologSearch" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 72963b28ae430436bea374d01e6158da - patches: - - infinity.patch + md5: ce4ad762be83b367c02fc926bf67c383 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enhancerhomologsearch", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, MotifDb, testthat, TFBSTools requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-httr - r-jsonlite @@ -41,17 +40,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-httr - r-jsonlite diff --git a/recipes/bioconductor-enmcb/meta.yaml b/recipes/bioconductor-enmcb/meta.yaml index bcf851b6a4481..137714b151321 100644 --- a/recipes/bioconductor-enmcb/meta.yaml +++ b/recipes/bioconductor-enmcb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "EnMCB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dc2bd872fb5b7e28ec799d122512d7ab + md5: f9fee363d9285ffdf2895062fc0cf26b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enmcb", max_pin="x.x") }}' noarch: generic # Suggests: SummarizedExperiment, testthat, Biobase, survminer, affycoretools, knitr, plotROC, limma, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-boot - r-e1071 @@ -35,7 +36,7 @@ requirements: - r-survivalroc - r-survivalsvm run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-boot - r-e1071 diff --git a/recipes/bioconductor-enmix/meta.yaml b/recipes/bioconductor-enmix/meta.yaml index 7d2844fd82aa5..d38d91df9f69a 100644 --- a/recipes/bioconductor-enmix/meta.yaml +++ b/recipes/bioconductor-enmix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.01" %} +{% set version = "1.38.01" %} {% set name = "ENmix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,56 +11,57 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 581b13b091573a2925d86004487ed0c3 + md5: 3ac8861e8c3ad067b1baa266958227cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enmix", max_pin="x.x") }}' noarch: generic # Suggests: minfiData, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-dynamictreecut - r-foreach - r-gplots - r-gtools + - r-irlba - r-matrixstats - r-quadprog - r-rpmm run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-dynamictreecut - r-foreach - r-gplots - r-gtools + - r-irlba - r-matrixstats - r-quadprog - r-rpmm diff --git a/recipes/bioconductor-enrichedheatmap/build_failure.osx-64.yaml b/recipes/bioconductor-enrichedheatmap/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..a339ea97f8532 --- /dev/null +++ b/recipes/bioconductor-enrichedheatmap/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 9a6c8d621c8da5f9299d5af966645abebfcfa7fd1cab2bbd703ca5e6f763fec7 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + 11:47:03 BIOCONDA INFO (ERR) dyld[20647]: Library not loaded: '@rpath/libtapi.dylib' 11:47:03 BIOCONDA INFO (ERR) Referenced from: '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-609-h0fd476b_15/bin/x86_64-apple-darwin13.4.0-ld' 11:47:03 BIOCONDA INFO (ERR) Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-609-h0fd476b_15/bin/../lib/libtapi.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-609-h0fd476b_15/bin/../lib/libtapi.dylib' (no such file), '/usr/local/lib/libtapi.dylib' (no such file), '/usr/lib/libtapi.dylib' (no such file) 11:47:03 BIOCONDA INFO (ERR) clang-15: error: unable to execute command: Abort trap: 6 11:47:03 BIOCONDA INFO (ERR) clang-15: error: linker command failed due to signal (use -v to see invocation) +category: |- + compiler error diff --git a/recipes/bioconductor-enrichedheatmap/meta.yaml b/recipes/bioconductor-enrichedheatmap/meta.yaml index e7ffabb3dd518..87efa37d244c1 100644 --- a/recipes/bioconductor-enrichedheatmap/meta.yaml +++ b/recipes/bioconductor-enrichedheatmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "EnrichedHeatmap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3adcecb7cb7b60fb2dd0266052d697b + md5: 269aeb6d749072508069805663216dc4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enrichedheatmap", max_pin="x.x") }}' # Suggests: testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter, RColorBrewer requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-circlize >=0.4.5' - r-getoptlong @@ -32,9 +33,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-circlize >=0.4.5' - r-getoptlong diff --git a/recipes/bioconductor-enrichmentbrowser/meta.yaml b/recipes/bioconductor-enrichmentbrowser/meta.yaml index e2505a9c37c89..b55ecad92a7c4 100644 --- a/recipes/bioconductor-enrichmentbrowser/meta.yaml +++ b/recipes/bioconductor-enrichmentbrowser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.1" %} +{% set version = "2.32.0" %} {% set name = "EnrichmentBrowser" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,52 +11,53 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c543e0cbb1ba98aa022dbfaf08c537ee + md5: fa4ec5a19513178896d60057a26ec6ce build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enrichmentbrowser", max_pin="x.x") }}' noarch: generic # Suggests: ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools, airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr, rmarkdown, statmod requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-safe >=3.40.0,<3.41.0' - - 'bioconductor-spia >=2.52.0,<2.53.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-safe >=3.42.0,<3.43.0' + - 'bioconductor-spia >=2.54.0,<2.55.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biocmanager - r-hwriter run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-safe >=3.40.0,<3.41.0' - - 'bioconductor-spia >=2.52.0,<2.53.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-safe >=3.42.0,<3.43.0' + - 'bioconductor-spia >=2.54.0,<2.55.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biocmanager - r-hwriter diff --git a/recipes/bioconductor-enrichplot/meta.yaml b/recipes/bioconductor-enrichplot/meta.yaml index 57d62b1537dd7..60ac7b0cc9d3b 100644 --- a/recipes/bioconductor-enrichplot/meta.yaml +++ b/recipes/bioconductor-enrichplot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "enrichplot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d76d773c796cc76d486af2e796b6dca3 + md5: 4accfec43292c11ec0165092f3266ac2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enrichplot", max_pin="x.x") }}' noarch: generic -# Suggests: clusterProfiler, dplyr, europepmc, ggupset, knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, AnnotationDbi, ggplotify, ggridges, grDevices, gridExtra, ggrepel (>= 0.9.0), ggstar, treeio, scales, tidytree, ggtreeExtra, tidydr +# Suggests: clusterProfiler, dplyr, europepmc, ggupset, knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, AnnotationDbi, ggplotify, ggridges, grDevices, gridExtra, ggrepel (>= 0.9.0), ggstar, scales, ggtreeExtra, tidydr requirements: host: - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'r-aplot >=0.1.4' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'r-aplot >=0.2.1' - r-base + - 'r-ggfun >=0.1.3' - r-ggnewscale - r-ggplot2 - r-ggraph @@ -38,13 +40,14 @@ requirements: - r-rlang - r-scatterpie - r-shadowtext - - 'r-yulab.utils >=0.0.4' + - 'r-yulab.utils >=0.0.8' run: - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'r-aplot >=0.1.4' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'r-aplot >=0.2.1' - r-base + - 'r-ggfun >=0.1.3' - r-ggnewscale - r-ggplot2 - r-ggraph @@ -57,7 +60,7 @@ requirements: - r-rlang - r-scatterpie - r-shadowtext - - 'r-yulab.utils >=0.0.4' + - 'r-yulab.utils >=0.0.8' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-enrichtf/build_failure.linux-64.yaml b/recipes/bioconductor-enrichtf/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0885f7bb52630 --- /dev/null +++ b/recipes/bioconductor-enrichtf/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 1c991de1bbfe0824a102700e267a7f4665d9ce725d1b2ee87b87e8ec4ccbd588 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/linux-64 + pkgs/main/noarch + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.5s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/linux-64 100% + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.6s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/linux-64 100% + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/linux-64 + [] 1.7s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.8s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/noarch + pkgs/r/noarch + [] 1.9s + conda-forge/linux-64 + conda-forge/noarch + pkgs/r/linux-64 [2K[1A[2K[1A[2K[1A[2K[0G[] 2.0s + conda-forge/linux-64 + conda-forge/noarch 100% + pkgs/r/linux-64 [2K[1A[2K[1A[2K[1A[2K[0G[] 2.1s + conda-forge/linux-64 + pkgs/r/linux-64 [2K[1A[2K[1A[2K[0Gconda-forge/noarch + pkgs/r/linux-64 + [] 2.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.9s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.9s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.9s + conda-forge/linux-64 [2K[1A[2K[0G[] 5.0s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.1s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.2s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.3s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.4s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.5s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.6s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.7s + [2K[1A[2K[0Gconda-forge/linux-64 + [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.1MB/s 0.0s + opt/conda/conda-bld/noarch 1.4kB @ 28.7MB/s 0.0s + [?25hTraceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3089, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2879, in test + environ.create_env(metadata.config.test_prefix, actions, config=metadata.config, + File "/opt/conda/lib/python3.8/site-packages/conda_build/environ.py", line 1052, in create_env + display_actions(actions, index) + File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in display_actions + actions['LINK'] = [index[d] for d in actions['LINK']] + File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in + actions['LINK'] = [index[d] for d in actions['LINK']] + KeyError: Dist(channel='conda-forge', dist_name='python-3.12.1-hab00c5b_0_cpython', name='python', fmt='.conda', version='3.12.1', build_string='hab00c5b_0_cpython', build_number=0, base_url=None, platform=None) +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-enrichtf/meta.yaml b/recipes/bioconductor-enrichtf/meta.yaml index 497ae6659c32d..942370c55322c 100644 --- a/recipes/bioconductor-enrichtf/meta.yaml +++ b/recipes/bioconductor-enrichtf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "enrichTF" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3b22db2a149bf9e4cbe916173849722 + md5: a88296c9418e41a8e66fccc276925471 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enrichtf", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, webshot requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-pipeframe >=1.16.0,<1.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-pipeframe >=1.18.0,<1.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-ggplot2 - r-ggpubr @@ -41,18 +42,18 @@ requirements: - r-r.utils - r-rmarkdown run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-pipeframe >=1.16.0,<1.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-pipeframe >=1.18.0,<1.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-ggplot2 - r-ggpubr diff --git a/recipes/bioconductor-enrichviewnet/build.sh b/recipes/bioconductor-enrichviewnet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-enrichviewnet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-enrichviewnet/meta.yaml b/recipes/bioconductor-enrichviewnet/meta.yaml new file mode 100644 index 0000000000000..853b3336dc8e7 --- /dev/null +++ b/recipes/bioconductor-enrichviewnet/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.0.0" %} +{% set name = "enrichViewNet" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5b2eb51ee4f57abd3b77da182e7e5d1a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enrichviewnet", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - r-base + - r-gprofiler2 + - r-jsonlite + - r-strex + - r-stringr + run: + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - r-base + - r-gprofiler2 + - r-jsonlite + - r-strex + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'From functional enrichment results to biological networks' + description: 'This package enables the visualization of functional enrichment results as network graphs. First the package enables the visualization of enrichment results, in a format corresponding to the one generated by gprofiler2, as a customizable Cytoscape network. In those networks, both gene datasets (GO terms/pathways/protein complexes) and genes associated to the datasets are represented as nodes. While the edges connect each gene to its dataset(s). The package also provides the option to create enrichment maps from functional enrichment results. Enrichment maps enable the visualization of enriched terms into a network with edges connecting overlapping genes.' + diff --git a/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml b/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml index 035e577d1b943..e9d78eb695b76 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml +++ b/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Hsapiens.v75" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6c896475252903972bfc6c0eb0d8f334 build: - number: 14 + number: 15 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ensdb.hsapiens.v75", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml b/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml index 4c52d38262581..1ba0892011aad 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml +++ b/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Hsapiens.v79" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 16b5629805c07649b2aa501d34fcc588 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ensdb.hsapiens.v79", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml b/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml index a94e97097dfe1..f91361ab9fb38 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml +++ b/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Hsapiens.v86" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0c9e52512ff6dbbbdb754c4d41149939 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ensdb.hsapiens.v86", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml b/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml index 14ba8a094c45b..53552d68e3b42 100644 --- a/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml +++ b/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Mmusculus.v75" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 081bf6f90ff77031b634b4fe32e00be8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ensdb.mmusculus.v75", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml b/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml index 1035f94d66e52..b07f2e2eb5bd1 100644 --- a/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml +++ b/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Mmusculus.v79" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 28bbab743b0d2d550dbfa0bcd3274fad build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ensdb.mmusculus.v79", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml b/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml index ac9b5f465e9cf..a89441fa23d47 100644 --- a/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml +++ b/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Rnorvegicus.v75" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 40ff53b41aa6fad0d5bd15f9c6f3bad8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ensdb.rnorvegicus.v75", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml b/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml index 711cbb93749c5..5646d093a9d17 100644 --- a/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml +++ b/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Rnorvegicus.v79" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7d305bd0d1a073bd8c60063ae210a7a9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ensdb.rnorvegicus.v79", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensembldb/meta.yaml b/recipes/bioconductor-ensembldb/meta.yaml index 137ffef63ab7e..c421d63cd8558 100644 --- a/recipes/bioconductor-ensembldb/meta.yaml +++ b/recipes/bioconductor-ensembldb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "ensembldb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,47 +11,48 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4d1be7f0e9d2ff9e4c473b891eec62de + md5: 0ad7a33ad9592f54e39d647195aa4c91 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ensembldb", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), rmarkdown, AnnotationHub requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-curl - r-dbi - 'r-rsqlite >=1.1' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-curl - r-dbi diff --git a/recipes/bioconductor-ensemblvep/meta.yaml b/recipes/bioconductor-ensemblvep/meta.yaml index 0d0f14c7c5142..537285ab0b96e 100644 --- a/recipes/bioconductor-ensemblvep/meta.yaml +++ b/recipes/bioconductor-ensemblvep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "ensemblVEP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad5be46f89b6fb698603bf2caa25bc19 + md5: 378569d68f5d4973a7b16eb7cc2b9327 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ensemblvep", max_pin="x.x") }}' noarch: generic # Suggests: RUnit # SystemRequirements: Ensembl VEP (API version 105) and the Perl modules DBI and DBD::mysql must be installed. See the package README and Ensembl installation instructions: http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-epialleler/build.sh b/recipes/bioconductor-epialleler/build.sh index 5ea71a1203cac..c1d13421f5f1e 100644 --- a/recipes/bioconductor-epialleler/build.sh +++ b/recipes/bioconductor-epialleler/build.sh @@ -8,4 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-epialleler/meta.yaml b/recipes/bioconductor-epialleler/meta.yaml index ab584ae6edd1f..c3950d568d811 100644 --- a/recipes/bioconductor-epialleler/meta.yaml +++ b/recipes/bioconductor-epialleler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "epialleleR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,43 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e242bf8aa9a114b4eeebd2e7cd57c096 + md5: cbe73c32dc61dac41266279db72e4bee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epialleler", max_pin="x.x") }}' # Suggests: RUnit, knitr, rmarkdown, ggplot2, ggstance, gridExtra # SystemRequirements: C++17, GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bh - r-data.table - r-rcpp - - r-stringi - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bh - r-data.table - r-rcpp - - r-stringi build: - {{ compiler('c') }} - {{ compiler('cxx') }} @@ -58,6 +57,6 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'Fast, Epiallele-Aware Methylation Reporter' - description: 'Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls hypermethylated epiallele frequencies at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Other functionality includes extracting methylation patterns, computing the empirical cumulative distribution function for per-read beta values, and testing the significance of the association between epiallele methylation status and base frequencies at particular genomic positions (SNPs).' + summary: 'Fast, Epiallele-Aware Methylation Caller and Reporter' + description: 'Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls and reports cytosine methylation as well as frequencies of hypermethylated epialleles at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Among other things, this package can also extract methylation patterns and assess allele specificity of methylation.' diff --git a/recipes/bioconductor-epidecoder/meta.yaml b/recipes/bioconductor-epidecoder/meta.yaml index bd29b9981ab70..c322d6f121c8b 100644 --- a/recipes/bioconductor-epidecoder/meta.yaml +++ b/recipes/bioconductor-epidecoder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "epidecodeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 06413f62d44e93ed0fa687a6d81e00ff + md5: 409ed7c959818b7400944e1d20653f68 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epidecoder", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-dplyr - r-envstats @@ -31,9 +32,9 @@ requirements: - r-ggpubr - r-rstatix run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-dplyr - r-envstats diff --git a/recipes/bioconductor-epidish/meta.yaml b/recipes/bioconductor-epidish/meta.yaml index ecb9046de608f..5ae9b8411ac2a 100644 --- a/recipes/bioconductor-epidish/meta.yaml +++ b/recipes/bioconductor-epidish/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "EpiDISH" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: facabe437e4fd3e9c6e8a7545bfc2c55 + md5: db7b5d2165fad653dabc1bfd8faeab83 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epidish", max_pin="x.x") }}' noarch: generic # Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat requirements: diff --git a/recipes/bioconductor-epigenomix/meta.yaml b/recipes/bioconductor-epigenomix/meta.yaml index cf59745b01a7e..44a46bcbbb2a0 100644 --- a/recipes/bioconductor-epigenomix/meta.yaml +++ b/recipes/bioconductor-epigenomix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "epigenomix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3bf32e589c4fc3ea302d75a821ce29e1 + md5: eef6318b8b342675c1fdd4c99ed541e8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epigenomix", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-mcmcpack run: - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-mcmcpack test: diff --git a/recipes/bioconductor-epigrahmm/meta.yaml b/recipes/bioconductor-epigrahmm/meta.yaml index ccf466c267dbc..6ac28075e8219 100644 --- a/recipes/bioconductor-epigrahmm/meta.yaml +++ b/recipes/bioconductor-epigrahmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.2" %} +{% set version = "1.10.0" %} {% set name = "epigraHMM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a095bb8f775608ebfc7ca1a8ea4e165e + md5: 1c86fa9edec93550acae520d84420b88 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epigrahmm", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, BiocStyle, BSgenome.Rnorvegicus.UCSC.rn4, gcapc, chromstaRData # SystemRequirements: GNU make requirements: host: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-greylistchip >=1.32.0,<1.33.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-greylistchip >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-ggplot2 @@ -48,19 +49,19 @@ requirements: - libblas - liblapack run: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-greylistchip >=1.32.0,<1.33.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-greylistchip >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-epimix.data/meta.yaml b/recipes/bioconductor-epimix.data/meta.yaml index 508d3fb34bbbc..38d41a4d5a840 100644 --- a/recipes/bioconductor-epimix.data/meta.yaml +++ b/recipes/bioconductor-epimix.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.2" %} +{% set version = "1.4.0" %} {% set name = "EpiMix.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3234766b0bc549ab200604206a9ba5b8 + md5: 52c386f6828945121acfca44eabb7827 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epimix.data", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-epimix.data/post-link.sh b/recipes/bioconductor-epimix.data/post-link.sh index 0bd1b17c93d35..62d257d916df8 100644 --- a/recipes/bioconductor-epimix.data/post-link.sh +++ b/recipes/bioconductor-epimix.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "epimix.data-1.2.2" +installBiocDataPackage.sh "epimix.data-1.4.0" diff --git a/recipes/bioconductor-epimix/meta.yaml b/recipes/bioconductor-epimix/meta.yaml index 6630fa2901172..2f933593dc46b 100644 --- a/recipes/bioconductor-epimix/meta.yaml +++ b/recipes/bioconductor-epimix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.1.2" %} +{% set version = "1.4.0" %} {% set name = "EpiMix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f068a8ea3b2cd23bac159f19320d455 + md5: d86305c56618b7f327d0068e09ad6558 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epimix", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, clusterProfiler, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics +# Suggests: BiocStyle, clusterProfiler, GEOquery, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, multiMiR, miRBaseConverter requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-elmer.data >=2.24.0,<2.25.0' - - 'bioconductor-epimix.data >=1.2.0,<1.3.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-elmer.data >=2.26.0,<2.27.0' + - 'bioconductor-epimix.data >=1.4.0,<1.5.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-doparallel @@ -55,22 +55,21 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-elmer.data >=2.24.0,<2.25.0' - - 'bioconductor-epimix.data >=1.2.0,<1.3.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-elmer.data >=2.26.0,<2.27.0' + - 'bioconductor-epimix.data >=1.4.0,<1.5.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-epimutacions/meta.yaml b/recipes/bioconductor-epimutacions/meta.yaml index 2009149f65299..dec1d85892e1b 100644 --- a/recipes/bioconductor-epimutacions/meta.yaml +++ b/recipes/bioconductor-epimutacions/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.1" %} {% set name = "epimutacions" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: df7b334f2a1aa9a8ad23679c25578eda + md5: 73fdaf9db5e5d035601282d6e5d832fd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epimutacions", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra, methods, grDevices requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-epimutacionsdata >=1.4.0,<1.5.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-epimutacionsdata >=1.6.0,<1.7.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-ggplot2 - r-ggrepel @@ -59,32 +60,32 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-epimutacionsdata >=1.4.0,<1.5.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-epimutacionsdata >=1.6.0,<1.7.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-epimutacionsdata/meta.yaml b/recipes/bioconductor-epimutacionsdata/meta.yaml index 9fe6ecbb04437..761c0fbdf4067 100644 --- a/recipes/bioconductor-epimutacionsdata/meta.yaml +++ b/recipes/bioconductor-epimutacionsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "epimutacionsData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 162b5aaa6a5f6df2528dce4285efdea4 + md5: e2681ab8096fd0f2b7e5d8ed68928280 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epimutacionsdata", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, BiocStyle, knitr, ExperimentHub, minfi requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-epimutacionsdata/post-link.sh b/recipes/bioconductor-epimutacionsdata/post-link.sh index 0989eb175b6ad..04b4600843e28 100644 --- a/recipes/bioconductor-epimutacionsdata/post-link.sh +++ b/recipes/bioconductor-epimutacionsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "epimutacionsdata-1.4.0" +installBiocDataPackage.sh "epimutacionsdata-1.6.0" diff --git a/recipes/bioconductor-epinem/meta.yaml b/recipes/bioconductor-epinem/meta.yaml index dfbe44e395c46..704d6f0117daf 100644 --- a/recipes/bioconductor-epinem/meta.yaml +++ b/recipes/bioconductor-epinem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "epiNEM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d3c178dac61b79d58666db49073ead75 + md5: 03702ef94f047496994ebaf19f750787 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epinem", max_pin="x.x") }}' noarch: generic # Suggests: knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db, BiocStyle requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-mnem >=1.16.0,<1.17.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-mnem >=1.18.0,<1.19.0' - r-base - r-boolnet - r-e1071 @@ -35,9 +36,9 @@ requirements: - r-pcalg - r-rcolorbrewer run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-mnem >=1.16.0,<1.17.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-mnem >=1.18.0,<1.19.0' - r-base - r-boolnet - r-e1071 diff --git a/recipes/bioconductor-epistack/meta.yaml b/recipes/bioconductor-epistack/meta.yaml index 2765821eb8517..3dab4be583771 100644 --- a/recipes/bioconductor-epistack/meta.yaml +++ b/recipes/bioconductor-epistack/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "epistack" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c555b4279771d26c7cfe9334d694fcbb + md5: 7d06dbae71f93e2c3cb91ba3d16fa916 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epistack", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-plotrix run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-plotrix test: diff --git a/recipes/bioconductor-epistasisga/meta.yaml b/recipes/bioconductor-epistasisga/meta.yaml index fa6e9e8a58c30..f7bb792a8c68a 100644 --- a/recipes/bioconductor-epistasisga/meta.yaml +++ b/recipes/bioconductor-epistasisga/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "epistasisGA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 62ed9886878fc33fd72be12e391cccee + md5: 79635d9683f002813e51fa3c17e49b39 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epistasisga", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-batchtools - r-bh @@ -36,7 +37,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-batchtools - r-bh diff --git a/recipes/bioconductor-epitxdb.hs.hg38/meta.yaml b/recipes/bioconductor-epitxdb.hs.hg38/meta.yaml index a8255a97fe06e..9edb215bfcecc 100644 --- a/recipes/bioconductor-epitxdb.hs.hg38/meta.yaml +++ b/recipes/bioconductor-epitxdb.hs.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.7" %} {% set name = "EpiTxDb.Hs.hg38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e30af95f285788a9777a8207a8ef73a9 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epitxdb.hs.hg38", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, Modstrings, rtracklayer requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-epitxdb >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-epitxdb >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-epitxdb >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-epitxdb >=1.14.0,<1.15.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-epitxdb.mm.mm10/meta.yaml b/recipes/bioconductor-epitxdb.mm.mm10/meta.yaml index fe37e709b6bc8..526e3d97d4b4e 100644 --- a/recipes/bioconductor-epitxdb.mm.mm10/meta.yaml +++ b/recipes/bioconductor-epitxdb.mm.mm10/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.6" %} {% set name = "EpiTxDb.Mm.mm10" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 518e4967f7f038e3cbf2865b74dc4f1b build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epitxdb.mm.mm10", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-epitxdb >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-epitxdb >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-epitxdb >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-epitxdb >=1.14.0,<1.15.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-epitxdb.sc.saccer3/meta.yaml b/recipes/bioconductor-epitxdb.sc.saccer3/meta.yaml index f0df4cc359c84..69da19dba72fc 100644 --- a/recipes/bioconductor-epitxdb.sc.saccer3/meta.yaml +++ b/recipes/bioconductor-epitxdb.sc.saccer3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.5" %} {% set name = "EpiTxDb.Sc.sacCer3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6d9e5f37e5dcb60e890d99d80fddda00 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epitxdb.sc.saccer3", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, Modstrings, rtracklayer requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-epitxdb >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-epitxdb >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-epitxdb >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-epitxdb >=1.14.0,<1.15.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-epitxdb/meta.yaml b/recipes/bioconductor-epitxdb/meta.yaml index faa034bbfa391..9120d238c9984 100644 --- a/recipes/bioconductor-epitxdb/meta.yaml +++ b/recipes/bioconductor-epitxdb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "EpiTxDb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 55ab42b455431e070e058b65a43784da + md5: a693697bcccd27be6e57c304438d94a6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epitxdb", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, httptest, AnnotationHub, ensembldb, ggplot2, EpiTxDb.Hs.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Scerevisiae.UCSC.sacCer3, TxDb.Hsapiens.UCSC.hg38.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-modstrings >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-trnadbimport >=1.18.0,<1.19.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-modstrings >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-trnadbimport >=1.20.0,<1.21.0' - r-base - r-curl - r-dbi @@ -39,17 +40,17 @@ requirements: - r-rsqlite - r-xml2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-modstrings >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-trnadbimport >=1.18.0,<1.19.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-modstrings >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-trnadbimport >=1.20.0,<1.21.0' - r-base - r-curl - r-dbi diff --git a/recipes/bioconductor-epivizr/meta.yaml b/recipes/bioconductor-epivizr/meta.yaml index 556f6962606bd..51bbf203d8997 100644 --- a/recipes/bioconductor-epivizr/meta.yaml +++ b/recipes/bioconductor-epivizr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "epivizr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 710f534004dc7cbf1364255f3b42ad0d + md5: aaf997f0c4eccf72d795d79a3ebd7bfe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epivizr", max_pin="x.x") }}' noarch: generic # Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, minfi, rmarkdown requirements: host: - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-epivizrdata >=1.28.0,<1.29.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-epivizrdata >=1.30.0,<1.31.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-epivizrdata >=1.28.0,<1.29.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-epivizrdata >=1.30.0,<1.31.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-epivizrchart/meta.yaml b/recipes/bioconductor-epivizrchart/meta.yaml index 6cc148b0b6716..f66a753816ffa 100644 --- a/recipes/bioconductor-epivizrchart/meta.yaml +++ b/recipes/bioconductor-epivizrchart/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "epivizrChart" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: baf134b11bf7e3f3957f76f35091b317 + md5: 076ebf7f9141cb71df0867f480ff960c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epivizrchart", max_pin="x.x") }}' noarch: generic # Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-epivizrdata >=1.28.0,<1.29.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-epivizrdata >=1.30.0,<1.31.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' - r-base - r-htmltools - r-rjson run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-epivizrdata >=1.28.0,<1.29.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-epivizrdata >=1.30.0,<1.31.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' - r-base - r-htmltools - r-rjson diff --git a/recipes/bioconductor-epivizrdata/meta.yaml b/recipes/bioconductor-epivizrdata/meta.yaml index 67c2c1574e7d4..412409f2896f3 100644 --- a/recipes/bioconductor-epivizrdata/meta.yaml +++ b/recipes/bioconductor-epivizrdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "epivizrData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d8c2385e4c9f9a37c1f8314bf817a2f + md5: aa9cf42fdbb0ad293964de33fc62e27a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epivizrdata", max_pin="x.x") }}' noarch: generic # Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI, matrixStats requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-epivizrserver/meta.yaml b/recipes/bioconductor-epivizrserver/meta.yaml index 52893be238b8b..7b384efc68bd6 100644 --- a/recipes/bioconductor-epivizrserver/meta.yaml +++ b/recipes/bioconductor-epivizrserver/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "epivizrServer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d78bdc9e29069b92d87d127c49608c8 + md5: 4bc67106aa169616232174c422fb6e2b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epivizrserver", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: diff --git a/recipes/bioconductor-epivizrstandalone/meta.yaml b/recipes/bioconductor-epivizrstandalone/meta.yaml index 71477decd623c..fba6c056e868e 100644 --- a/recipes/bioconductor-epivizrstandalone/meta.yaml +++ b/recipes/bioconductor-epivizrstandalone/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "epivizrStandalone" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1948048074aed3f5221e8cdaa4ea1fbb + md5: aa34f18a7a4f4340f2e4a0ecc46af0a2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epivizrstandalone", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9), Mus.musculus, Biobase, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-epivizr >=2.30.0,<2.31.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-epivizr >=2.32.0,<2.33.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-git2r run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-epivizr >=2.30.0,<2.31.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-epivizr >=2.32.0,<2.33.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-git2r test: diff --git a/recipes/bioconductor-erccdashboard/meta.yaml b/recipes/bioconductor-erccdashboard/meta.yaml index fb60c3517521d..f0d714a1af896 100644 --- a/recipes/bioconductor-erccdashboard/meta.yaml +++ b/recipes/bioconductor-erccdashboard/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "erccdashboard" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b74db4e015a32aea7a4a5b691d79b6d3 + md5: fa211269012a775dcdc114f3eb0282bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-erccdashboard", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - 'r-ggplot2 >=2.1.0' - r-gplots @@ -36,9 +37,9 @@ requirements: - r-scales - r-stringr run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - 'r-ggplot2 >=2.1.0' - r-gplots diff --git a/recipes/bioconductor-erma/meta.yaml b/recipes/bioconductor-erma/meta.yaml index a57e31ec5e0c0..18cea096ef670 100644 --- a/recipes/bioconductor-erma/meta.yaml +++ b/recipes/bioconductor-erma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "erma" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,44 +11,45 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5ec82c451352c22d4b909caab6002683 + md5: 38679c439fbeb31db81c90c90ba4f79d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-erma", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, BiocStyle, knitr, GO.db, png, DT, doParallel requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-shiny run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-shiny diff --git a/recipes/bioconductor-erssa/meta.yaml b/recipes/bioconductor-erssa/meta.yaml index 047e3402fbd51..aa706e6ec05ae 100644 --- a/recipes/bioconductor-erssa/meta.yaml +++ b/recipes/bioconductor-erssa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "ERSSA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1388c9ab46a0d5d765a0a8871bcd5387 + md5: 160e82bdb1b7af9f6452d4767a7e8a1a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-erssa", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - 'r-ggplot2 >=3.0.0' - 'r-plyr >=1.8.4' - 'r-rcolorbrewer >=1.1-2' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - 'r-ggplot2 >=3.0.0' - 'r-plyr >=1.8.4' diff --git a/recipes/bioconductor-esatac/meta.yaml b/recipes/bioconductor-esatac/meta.yaml index 8ae1df64adff7..6959b5764686a 100644 --- a/recipes/bioconductor-esatac/meta.yaml +++ b/recipes/bioconductor-esatac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "esATAC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4672f9eba4a66406890a4cfdf9f552dd + md5: 6ea63da6e75365243df878d55d6b39f9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-esatac", max_pin="x.x") }}' # Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat, webshot, prettydoc # SystemRequirements: C++11 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-chipseeker >=1.36.0,<1.37.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-chipseeker >=1.38.0,<1.39.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-pipeframe >=1.16.0,<1.17.0' - - 'bioconductor-rbowtie2 >=2.6.0,<2.7.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-pipeframe >=1.18.0,<1.19.0' + - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-biocmanager - r-corrplot @@ -57,26 +58,26 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-chipseeker >=1.36.0,<1.37.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-chipseeker >=1.38.0,<1.39.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-pipeframe >=1.16.0,<1.17.0' - - 'bioconductor-rbowtie2 >=2.6.0,<2.7.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-pipeframe >=1.18.0,<1.19.0' + - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-biocmanager - r-corrplot diff --git a/recipes/bioconductor-escape/meta.yaml b/recipes/bioconductor-escape/meta.yaml index 48b004148c4b3..86ec8bba522ff 100644 --- a/recipes/bioconductor-escape/meta.yaml +++ b/recipes/bioconductor-escape/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "escape" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 52dc55acb0a04f9030f1aae725e57af8 + md5: e3dc22e072190e21938689fc0f3ab112 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-escape", max_pin="x.x") }}' noarch: generic # Suggests: Seurat, SeuratObject, knitr, rmarkdown, markdown, BiocStyle, testthat, dittoSeq (>= 1.1.2) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-ucell >=2.4.0,<2.5.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-ucell >=2.6.0,<2.7.0' - r-base - r-broom - r-data.table @@ -41,13 +42,13 @@ requirements: - r-rlang - r-stringr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-ucell >=2.4.0,<2.5.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-ucell >=2.6.0,<2.7.0' - r-base - r-broom - r-data.table diff --git a/recipes/bioconductor-escher/meta.yaml b/recipes/bioconductor-escher/meta.yaml index 758e49c0a1c5d..e8649e5391cf2 100644 --- a/recipes/bioconductor-escher/meta.yaml +++ b/recipes/bioconductor-escher/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "escheR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df1ed86f7963992371c853e9b05284b7 + md5: ed2586d2e42f89db85790889863421b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-escher", max_pin="x.x") }}' noarch: generic -# Suggests: STexampleData, knitr, rmarkdown, BiocStyle +# Suggests: STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle, ggpubr, scran, scater, scuttle, Seurat requirements: host: - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-spatiallibd >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-rlang run: - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-spatiallibd >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-rlang diff --git a/recipes/bioconductor-esetvis/meta.yaml b/recipes/bioconductor-esetvis/meta.yaml index 119e0e8661341..7ce7e35074dd0 100644 --- a/recipes/bioconductor-esetvis/meta.yaml +++ b/recipes/bioconductor-esetvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.1" %} +{% set version = "1.28.0" %} {% set name = "esetVis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e6f18d6b3474a5018f138bafe1324542 + md5: 2edbf6b1764a5ebfdcefaf7a8b6c247d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-esetvis", max_pin="x.x") }}' noarch: generic # Suggests: ggplot2, ggvis, rbokeh, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment, GO.db requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-mlp >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-mlp >=1.50.0,<1.51.0' - r-base - r-hexbin - r-mass - r-mpm - r-rtsne run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-mlp >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-mlp >=1.50.0,<1.51.0' - r-base - r-hexbin - r-mass diff --git a/recipes/bioconductor-estrogen/meta.yaml b/recipes/bioconductor-estrogen/meta.yaml index c188aec2e2eb2..cd11513496376 100644 --- a/recipes/bioconductor-estrogen/meta.yaml +++ b/recipes/bioconductor-estrogen/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "estrogen" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c7f687b7e46c1e224e9008143926f12e + md5: 41a3321678d1a9cb057e979d675f0cee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-estrogen", max_pin="x.x") }}' noarch: generic -# Suggests: affy, hgu95av2.db, hgu95av2cdf, vsn, knitr +# Suggests: affy, hgu95av2.db, hgu95av2cdf, vsn, knitr, genefilter requirements: host: - r-base run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-estrogen/post-link.sh b/recipes/bioconductor-estrogen/post-link.sh index 422fccdd666d7..92a917b9ef078 100644 --- a/recipes/bioconductor-estrogen/post-link.sh +++ b/recipes/bioconductor-estrogen/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "estrogen-1.46.0" +installBiocDataPackage.sh "estrogen-1.48.0" diff --git a/recipes/bioconductor-etec16s/meta.yaml b/recipes/bioconductor-etec16s/meta.yaml index bfe9834af0a45..e4180b711643d 100644 --- a/recipes/bioconductor-etec16s/meta.yaml +++ b/recipes/bioconductor-etec16s/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "etec16s" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b2540d5e5287458a7fbec76b5656d3c6 + md5: 86353b5f2f77274b883120dc043f8ce5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-etec16s", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-etec16s/post-link.sh b/recipes/bioconductor-etec16s/post-link.sh index d48158fae1247..7ab2be62ab9c5 100644 --- a/recipes/bioconductor-etec16s/post-link.sh +++ b/recipes/bioconductor-etec16s/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "etec16s-1.28.0" +installBiocDataPackage.sh "etec16s-1.30.0" diff --git a/recipes/bioconductor-eudysbiome/meta.yaml b/recipes/bioconductor-eudysbiome/meta.yaml index bfc0c4700fa42..c4d7c109e3260 100644 --- a/recipes/bioconductor-eudysbiome/meta.yaml +++ b/recipes/bioconductor-eudysbiome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "eudysbiome" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 491deafab7090ce11e0eaac79537dc15 + md5: 76023a8328d58f7d5b783679a08c7ea8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-eudysbiome", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-plyr - r-r.utils run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-plyr - r-r.utils diff --git a/recipes/bioconductor-eupathdb/meta.yaml b/recipes/bioconductor-eupathdb/meta.yaml index 0a9428b37d14f..c302fc335cb08 100644 --- a/recipes/bioconductor-eupathdb/meta.yaml +++ b/recipes/bioconductor-eupathdb/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "EuPathDB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,33 +13,34 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1451c3ab6c224d9a4cfbdf27dc5c2680 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-eupathdb", max_pin="x.x") }}' noarch: generic # Suggests: dplyr, knitr, BiocStyle, rmarkdown, jsonlite requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-annotationhubdata >=1.30.0,<1.31.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-biocmanager run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-annotationhubdata >=1.30.0,<1.31.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-biocmanager - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-evaluomer/meta.yaml b/recipes/bioconductor-evaluomer/meta.yaml index 66d0c27267921..d60206052a04d 100644 --- a/recipes/bioconductor-evaluomer/meta.yaml +++ b/recipes/bioconductor-evaluomer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "evaluomeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e64f5dc7c769522b12dff9613a3c0e65 + md5: 2cee372b9bb28916d6ab543be8eca9b2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-evaluomer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, magrittr requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-class - 'r-cluster >=2.0.9' @@ -41,8 +42,8 @@ requirements: - r-rdpack - r-reshape2 run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-class - 'r-cluster >=2.0.9' diff --git a/recipes/bioconductor-eventpointer/meta.yaml b/recipes/bioconductor-eventpointer/meta.yaml index 2077e89eacca9..5bf12d43a71a1 100644 --- a/recipes/bioconductor-eventpointer/meta.yaml +++ b/recipes/bioconductor-eventpointer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.8.0" %} +{% set version = "3.10.0" %} {% set name = "EventPointer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f97dd94868c28a966269c717e4cfccff + md5: d25561e0288a54ed43c823b371941972 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-eventpointer", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra requirements: host: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sgseq >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sgseq >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-abind - r-base - r-cobs @@ -57,23 +58,23 @@ requirements: - libblas - liblapack run: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sgseq >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sgseq >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-abind - r-base - r-cobs diff --git a/recipes/bioconductor-ewce/meta.yaml b/recipes/bioconductor-ewce/meta.yaml index e63814309ad73..f085f9b01d230 100644 --- a/recipes/bioconductor-ewce/meta.yaml +++ b/recipes/bioconductor-ewce/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.2" %} +{% set version = "1.10.2" %} {% set name = "EWCE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0c8b7db118292d3cbd6c01c1fd6e15d7 + md5: b00b3feb36956603c46e6de1f03e9c09 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ewce", max_pin="x.x") }}' noarch: generic # Suggests: rworkflows, remotes, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2, MAST, DelayedMatrixStats, ggdendro, scales, patchwork requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-ewcedata >=1.8.0,<1.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-orthogene >=1.6.0,<1.7.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-ewcedata >=1.10.0,<1.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-orthogene >=1.8.0,<1.9.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr @@ -38,13 +39,13 @@ requirements: - 'r-rnomni >=1.0' - r-stringr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-ewcedata >=1.8.0,<1.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-orthogene >=1.6.0,<1.7.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-ewcedata >=1.10.0,<1.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-orthogene >=1.8.0,<1.9.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-ewcedata/meta.yaml b/recipes/bioconductor-ewcedata/meta.yaml index fe81c8bb10775..e46f489867173 100644 --- a/recipes/bioconductor-ewcedata/meta.yaml +++ b/recipes/bioconductor-ewcedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ewceData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3107bac6cd0fb07a4cba3ad59cabb665 + md5: d2ee91be35e2c5433ce16e94717c50e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ewcedata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, ggplot2, cowplot, rmarkdown, markdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ewcedata/post-link.sh b/recipes/bioconductor-ewcedata/post-link.sh index c5cd6c05609bd..16e7f83675a3c 100644 --- a/recipes/bioconductor-ewcedata/post-link.sh +++ b/recipes/bioconductor-ewcedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ewcedata-1.8.0" +installBiocDataPackage.sh "ewcedata-1.10.0" diff --git a/recipes/bioconductor-excluderanges/meta.yaml b/recipes/bioconductor-excluderanges/meta.yaml index 29c4ecd94fd1e..01959646c16da 100644 --- a/recipes/bioconductor-excluderanges/meta.yaml +++ b/recipes/bioconductor-excluderanges/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.8" %} {% set name = "excluderanges" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2ec19df8a51df1900a339f7f505cd5fa build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-excluderanges", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, RefManageR, rmarkdown, ggridges, httr, readr, pheatmap, rtracklayer, AnnotationHub requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-excluster/meta.yaml b/recipes/bioconductor-excluster/meta.yaml index e77fe8a171463..d71771d5759d4 100644 --- a/recipes/bioconductor-excluster/meta.yaml +++ b/recipes/bioconductor-excluster/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "ExCluster" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8cf0ecfe19ff1a9a9a461ff9d9738cfb + md5: 2f60d612945a7f431831ce690d01d042 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-excluster", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-matrixstats run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-matrixstats test: diff --git a/recipes/bioconductor-eximir/meta.yaml b/recipes/bioconductor-eximir/meta.yaml index a78f2e6588bfa..5aea5abeb29f4 100644 --- a/recipes/bioconductor-eximir/meta.yaml +++ b/recipes/bioconductor-eximir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.42.0" %} +{% set version = "2.44.0" %} {% set name = "ExiMiR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5339767954f9bdc5eb05a5e62529d80f + md5: a68c067ab91567287317a760f9e4c738 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-eximir", max_pin="x.x") }}' noarch: generic # Suggests: mirna10cdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base test: commands: diff --git a/recipes/bioconductor-exomecopy/meta.yaml b/recipes/bioconductor-exomecopy/meta.yaml index f6a9d1547655d..f7971f0ae0e21 100644 --- a/recipes/bioconductor-exomecopy/meta.yaml +++ b/recipes/bioconductor-exomecopy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "exomeCopy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 589525e05086f9d2387c287beb8c35e7 + md5: 068f1f0cb675297a1b7940330fae0cbe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-exomecopy", max_pin="x.x") }}' # Suggests: Biostrings requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - libblas - liblapack run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-exomepeak2/meta.yaml b/recipes/bioconductor-exomepeak2/meta.yaml index 7c62eee295e28..c86fb924cebde 100644 --- a/recipes/bioconductor-exomepeak2/meta.yaml +++ b/recipes/bioconductor-exomepeak2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.3" %} {% set name = "exomePeak2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,50 +11,51 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0281b3cf39ab0e2dd661c6b95b899a9a + md5: 078608012fb7c2dc3a60d02a4e2fcbbc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-exomepeak2", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown +# Suggests: knitr, rmarkdown, BiocManager, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-magrittr - r-mclust - r-speedglm run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-magrittr @@ -67,5 +68,5 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Peak Calling and differential analysis for MeRIP-Seq' - description: 'exomePeak2 provides peak detection and differential methylation for Methylated RNA Immunoprecipitation Sequencing (MeRIP-Seq) data. MeRIP-Seq is a commonly applied sequencing assay that measures the location and abundance of RNA modification sites under specific cellular conditions. In practice, the technique is sensitive to PCR amplification biases commonly found in NGS data. In addition, the efficiency of immunoprecipitation often varies between different IP samples. exomePeak2 can perform peak calling and differential analysis independent of GC content bias and IP efficiency changes.' + description: 'exomePeak2 provides peak detection and differential methylation for Methylated RNA Immunoprecipitation Sequencing (MeRIP-Seq) data. MeRIP-Seq is a commonly applied sequencing assay that measures the location and abundance of RNA modification sites under specific cellular conditions. The technique is sensitive to PCR amplification biases commonly found in NGS data. In addition, the efficiency of immunoprecipitation often varies between different IP samples. exomePeak2 can perform peak calling and differential analysis independent of GC content bias and IP efficiency changes.' diff --git a/recipes/bioconductor-experimenthub/meta.yaml b/recipes/bioconductor-experimenthub/meta.yaml index 09bc1a50ca50b..931b307d36148 100644 --- a/recipes/bioconductor-experimenthub/meta.yaml +++ b/recipes/bioconductor-experimenthub/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "ExperimentHub" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c7f87d5d1ab426cae3083029b6d345f5 + md5: bea896eadb8eb999e48d1cf5974dfe9e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-experimenthub", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, BiocStyle, rmarkdown, HubPub +# Suggests: knitr, BiocStyle, rmarkdown, HubPub, GenomicAlignments requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-rappdirs run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-rappdirs diff --git a/recipes/bioconductor-experimenthubdata/meta.yaml b/recipes/bioconductor-experimenthubdata/meta.yaml index 48f5e4a1939f5..67fe9eb4addd6 100644 --- a/recipes/bioconductor-experimenthubdata/meta.yaml +++ b/recipes/bioconductor-experimenthubdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "ExperimentHubData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 55726da02a14f0b5b2805153bbb0fbe7 + md5: 9e36d1a7958213cce85feccfd46fd7d5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-experimenthubdata", max_pin="x.x") }}' noarch: generic # Suggests: GenomeInfoDb, RUnit, knitr, BiocStyle, rmarkdown, HubPub requirements: host: - - 'bioconductor-annotationhubdata >=1.30.0,<1.31.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-curl - r-dbi - r-httr run: - - 'bioconductor-annotationhubdata >=1.30.0,<1.31.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-curl diff --git a/recipes/bioconductor-experimentsubset/meta.yaml b/recipes/bioconductor-experimentsubset/meta.yaml index 747fd0314fe40..b3c0f29e6a81f 100644 --- a/recipes/bioconductor-experimentsubset/meta.yaml +++ b/recipes/bioconductor-experimentsubset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ExperimentSubset" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ae8e83b163d8d2394af49d2c3c2a333c + md5: fc52b3d67f7f9641a3851f987af7cdee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-experimentsubset", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, covr, stats, scran, scater, scds, TENxPBMCData, airway requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-matrix run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-exploremodelmatrix/meta.yaml b/recipes/bioconductor-exploremodelmatrix/meta.yaml index 73eb8daa5103a..810de26338c61 100644 --- a/recipes/bioconductor-exploremodelmatrix/meta.yaml +++ b/recipes/bioconductor-exploremodelmatrix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ExploreModelMatrix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e5317164fd3206c56c7e566b8a7ef102 + md5: 86f96045b0ae6877428f28466b113097 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-exploremodelmatrix", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), knitr, rmarkdown, htmltools, BiocStyle requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-dplyr @@ -38,8 +39,8 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-dplyr diff --git a/recipes/bioconductor-expressionatlas/meta.yaml b/recipes/bioconductor-expressionatlas/meta.yaml index c61896e634c13..07e7c2df9194b 100644 --- a/recipes/bioconductor-expressionatlas/meta.yaml +++ b/recipes/bioconductor-expressionatlas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "ExpressionAtlas" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7abccba2bf2c9ebfd1ed02b907fb05b5 + md5: eb11568a0a2a81e1bf636eaa24e45906 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-expressionatlas", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-httr - r-jsonlite @@ -33,11 +34,11 @@ requirements: - r-xml - r-xml2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-httr - r-jsonlite diff --git a/recipes/bioconductor-extrachips/build_failure.osx-64.yaml b/recipes/bioconductor-extrachips/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..4061ce0faf29f --- /dev/null +++ b/recipes/bioconductor-extrachips/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: cd6c654642b58a1ae021676e3516975dbc01a6ba6e27b668bc181e21ad457739 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + dependency issue +log: |2- + /opt/mambaforge/envs/bioconda/conda-bld/work + Test: + /opt/mambaforge/envs/bioconda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/mambaforge/envs/bioconda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + Build: + source activate /opt/mambaforge/envs/bioconda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - r-ggside >=0.2.2 + - r-glue + - libblas 3.9.* *netlib + - r-ggplot2 >=3.4.0 + - bioconductor-interactionset >=1.30.0,<1.31.0 + - r-dplyr >=1.1.1 + - liblapack 3.9.* *netlib + - bioconductor-enrichedheatmap >=1.32.0,<1.33.0 + - bioconductor-limma >=3.58.0,<3.59.0 + - bioconductor-rtracklayer >=1.62.0,<1.63.0 + - r-tidyr + - r-ggforce + - bioconductor-genomicranges >=1.54.0,<1.55.0 + - bioconductor-genomicinteractions >=1.36.0,<1.37.0 + - r-stringr + - r-scales + - r-tidyselect + - r-ggrepel + - r-base 4.3.* + - r-rlang + - bioconductor-iranges >=2.36.0,<2.37.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - bioconductor-edger >=4.0.0,<4.1.0 + - r-vctrs + - r-broom + - r-complexupset + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-genomeinfodb >=1.38.0,<1.39.0 + - r-matrixstats + - r-patchwork + - bioconductor-csaw >=1.36.0,<1.37.0 + - r-forcats + - r-venndiagram + - bioconductor-biocio >=1.12.0,<1.13.0 + - bioconductor-gviz >=1.46.0,<1.47.0 + - r-rcolorbrewer + - r-tibble + - bioconductor-rsamtools >=2.18.0,<2.19.0 + - bioconductor-biocparallel >=1.36.0,<1.37.0 + + with channels: + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-enrichedheatmap >=1.32.0,<1.33.0 + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-enrichedheatmap[version='>=1.32.0,<1.33.0']")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-extrachips/meta.yaml b/recipes/bioconductor-extrachips/meta.yaml index 6a323e02d4b8a..678c82cbb0c55 100644 --- a/recipes/bioconductor-extrachips/meta.yaml +++ b/recipes/bioconductor-extrachips/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.5" %} +{% set version = "1.6.0" %} {% set name = "extraChIPs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c26b5ce1303129efe33efebc2fa60dd5 + md5: 462672c12f16f912b7e3d4b30a07162f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-extrachips", max_pin="x.x") }}' # Suggests: BiocStyle, covr, cqn, harmonicmeanp, here, knitr, magrittr, plyranges, quantro, rmarkdown, testthat (>= 3.0.0), tidyverse requirements: host: - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-enrichedheatmap >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicinteractions >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-enrichedheatmap >=1.32.0,<1.33.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom - r-complexupset - - 'r-dplyr >=1.1.0' + - 'r-dplyr >=1.1.1' - r-forcats - r-ggforce - 'r-ggplot2 >=3.4.0' - r-ggrepel - - r-ggside + - 'r-ggside >=0.2.2' - r-glue - r-matrixstats - r-patchwork @@ -60,31 +61,31 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-enrichedheatmap >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicinteractions >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-enrichedheatmap >=1.32.0,<1.33.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom - r-complexupset - - 'r-dplyr >=1.1.0' + - 'r-dplyr >=1.1.1' - r-forcats - r-ggforce - 'r-ggplot2 >=3.4.0' - r-ggrepel - - r-ggside + - 'r-ggside >=0.2.2' - r-glue - r-matrixstats - r-patchwork diff --git a/recipes/bioconductor-faahko/meta.yaml b/recipes/bioconductor-faahko/meta.yaml index 5b4d091c85cb5..16959e9059ddd 100644 --- a/recipes/bioconductor-faahko/meta.yaml +++ b/recipes/bioconductor-faahko/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "faahKO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 29697c16b4e90b21fd8515dfdfea7fde + md5: 3525f525973323d33955a68ca38b5cd7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-faahko", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base run: - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-faahko/post-link.sh b/recipes/bioconductor-faahko/post-link.sh index 091dc51972ffa..8d50d83771269 100644 --- a/recipes/bioconductor-faahko/post-link.sh +++ b/recipes/bioconductor-faahko/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "faahko-1.40.0" +installBiocDataPackage.sh "faahko-1.42.0" diff --git a/recipes/bioconductor-fabia/meta.yaml b/recipes/bioconductor-fabia/meta.yaml index 2371256f1c4b2..aadcaa307b6c8 100644 --- a/recipes/bioconductor-fabia/meta.yaml +++ b/recipes/bioconductor-fabia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "fabia" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9920fe1cb40cc35e9c53a0b15e4f56e5 + md5: 9d336b3c9a97aca0a6b062ec137f5566 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fabia", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-fabiadata/meta.yaml b/recipes/bioconductor-fabiadata/meta.yaml index 343950c36eaed..8de5e015973e7 100644 --- a/recipes/bioconductor-fabiadata/meta.yaml +++ b/recipes/bioconductor-fabiadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "fabiaData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 970fc1894222fe7eac67b8c94d9a2eab + md5: 7fd64db4d15610a66c609e60624bbff9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fabiadata", max_pin="x.x") }}' noarch: generic # Suggests: fabia requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fabiadata/post-link.sh b/recipes/bioconductor-fabiadata/post-link.sh index 77a1795a9f905..561c4ec71758f 100644 --- a/recipes/bioconductor-fabiadata/post-link.sh +++ b/recipes/bioconductor-fabiadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fabiadata-1.38.0" +installBiocDataPackage.sh "fabiadata-1.40.0" diff --git a/recipes/bioconductor-factdesign/meta.yaml b/recipes/bioconductor-factdesign/meta.yaml index df24a022421cc..695bb48686cab 100644 --- a/recipes/bioconductor-factdesign/meta.yaml +++ b/recipes/bioconductor-factdesign/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "factDesign" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cb6bfbecf160000664037c0bf51f9953 + md5: 774d444f3227bbac6bc13e48d3974b20 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-factdesign", max_pin="x.x") }}' noarch: generic # Suggests: affy, genefilter, multtest requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-factr/meta.yaml b/recipes/bioconductor-factr/meta.yaml index 98f77eee10aa2..a9c19a5db30aa 100644 --- a/recipes/bioconductor-factr/meta.yaml +++ b/recipes/bioconductor-factr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "factR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,64 +11,65 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4494ae41081395fd86e88600af5d4ada + md5: 55b088d84e382a7068b40062151e4bec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-factr", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationHub (>= 2.22), BSgenome (>= 1.58), BSgenome.Mmusculus.UCSC.mm10, testthat, knitr, rmarkdown, markdown, zeallot, rmdformats, bio3d (>= 2.4), signalHsmm (>= 1.5), tidyverse (>= 1.3), covr, patchwork requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-drawproteins >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-wiggleplotr >=1.24.0,<1.25.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-drawproteins >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-wiggleplotr >=1.26.0,<1.27.0' - r-base - - r-crayon + - 'r-crayon >=1.5' - 'r-data.table >=1.14' - - 'r-dplyr >=1.0' - - 'r-ggplot2 >=3.3' - - 'r-pbapply >=1.5' - - 'r-purrr >=0.3' + - 'r-dplyr >=1.1' + - 'r-ggplot2 >=3.4' + - 'r-pbapply >=1.7' + - 'r-purrr >=1.0' - 'r-rcurl >=1.98' - - 'r-rlang >=1.0' - - 'r-stringr >=1.4' - - 'r-tibble >=3.1' - - 'r-tidyr >=1.1' + - 'r-rlang >=1.1' + - 'r-stringr >=1.5' + - 'r-tibble >=3.2' + - 'r-tidyr >=1.3' - 'r-xml >=3.99' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-drawproteins >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-wiggleplotr >=1.24.0,<1.25.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-drawproteins >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-wiggleplotr >=1.26.0,<1.27.0' - r-base - - r-crayon + - 'r-crayon >=1.5' - 'r-data.table >=1.14' - - 'r-dplyr >=1.0' - - 'r-ggplot2 >=3.3' - - 'r-pbapply >=1.5' - - 'r-purrr >=0.3' + - 'r-dplyr >=1.1' + - 'r-ggplot2 >=3.4' + - 'r-pbapply >=1.7' + - 'r-purrr >=1.0' - 'r-rcurl >=1.98' - - 'r-rlang >=1.0' - - 'r-stringr >=1.4' - - 'r-tibble >=3.1' - - 'r-tidyr >=1.1' + - 'r-rlang >=1.1' + - 'r-stringr >=1.5' + - 'r-tibble >=3.2' + - 'r-tidyr >=1.3' - 'r-xml >=3.99' test: commands: diff --git a/recipes/bioconductor-famagg/meta.yaml b/recipes/bioconductor-famagg/meta.yaml index d524237b721d7..b68b0c8f34645 100644 --- a/recipes/bioconductor-famagg/meta.yaml +++ b/recipes/bioconductor-famagg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "FamAgg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 62218f2a42b754c17175ce542c0850fc + md5: 0169ebe9c05d0b540946e2d111fe6437 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-famagg", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, RUnit, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - 'r-gap >=1.1-17' - r-igraph @@ -29,7 +30,7 @@ requirements: - r-matrix - r-survey run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - 'r-gap >=1.1-17' - r-igraph diff --git a/recipes/bioconductor-famat/meta.yaml b/recipes/bioconductor-famat/meta.yaml index ccdc6dda84ad4..425dee5ad0e88 100644 --- a/recipes/bioconductor-famat/meta.yaml +++ b/recipes/bioconductor-famat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "famat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e59deb7c41a3ecec355312a5db76f4cf + md5: 12883ce4989ed35758a8902493e2bb07 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-famat", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, BiocManager requirements: host: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-rwikipathways >=1.20.0,<1.21.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-rwikipathways >=1.22.0,<1.23.0' - r-base - r-biasedurn - r-dplyr @@ -42,12 +43,12 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-rwikipathways >=1.20.0,<1.21.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-rwikipathways >=1.22.0,<1.23.0' - r-base - r-biasedurn - r-dplyr diff --git a/recipes/bioconductor-fantom3and4cage/meta.yaml b/recipes/bioconductor-fantom3and4cage/meta.yaml index ffd1135dc5f77..bffc9cb885992 100644 --- a/recipes/bioconductor-fantom3and4cage/meta.yaml +++ b/recipes/bioconductor-fantom3and4cage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "FANTOM3and4CAGE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 049d0b3978f16771bd7e48aa80e8fb93 + md5: 5d964e7a085d6a7b00e2b2215b765861 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fantom3and4cage", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fantom3and4cage/post-link.sh b/recipes/bioconductor-fantom3and4cage/post-link.sh index 7ad71e3469da9..53f3c97e37d5f 100644 --- a/recipes/bioconductor-fantom3and4cage/post-link.sh +++ b/recipes/bioconductor-fantom3and4cage/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fantom3and4cage-1.36.0" +installBiocDataPackage.sh "fantom3and4cage-1.38.0" diff --git a/recipes/bioconductor-fastliquidassociation/meta.yaml b/recipes/bioconductor-fastliquidassociation/meta.yaml index cd2ac541108b7..c8a5f515cdf33 100644 --- a/recipes/bioconductor-fastliquidassociation/meta.yaml +++ b/recipes/bioconductor-fastliquidassociation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "fastLiquidAssociation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 19cd90ee83e1fe666279d7656fb9cb78 + md5: b57e0af4700d6a6872d88ca0d2eda5d1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fastliquidassociation", max_pin="x.x") }}' noarch: generic # Suggests: GOstats, yeastCC, org.Sc.sgd.db requirements: host: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-liquidassociation >=1.54.0,<1.55.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-liquidassociation >=1.56.0,<1.57.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-doparallel - r-hmisc - r-wgcna run: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-liquidassociation >=1.54.0,<1.55.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-liquidassociation >=1.56.0,<1.57.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-doparallel - r-hmisc diff --git a/recipes/bioconductor-fastqcleaner/meta.yaml b/recipes/bioconductor-fastqcleaner/meta.yaml index ed4e50ec8a0b8..d19fbfc3143e2 100644 --- a/recipes/bioconductor-fastqcleaner/meta.yaml +++ b/recipes/bioconductor-fastqcleaner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "FastqCleaner" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f5a185e44c2e087d9cd502343839a20 + md5: bace77f4e33bd7fe58cbbadaefd896d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fastqcleaner", max_pin="x.x") }}' # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-dt - r-htmltools @@ -33,10 +34,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-dt - r-htmltools diff --git a/recipes/bioconductor-fastreer/meta.yaml b/recipes/bioconductor-fastreer/meta.yaml index 43941e0d8973d..cf391745726da 100644 --- a/recipes/bioconductor-fastreer/meta.yaml +++ b/recipes/bioconductor-fastreer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "fastreeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8992e9982a96e461d83174b1e401637c + md5: e2b7164aeaa305f819536d9b85e4de12 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fastreer", max_pin="x.x") }}' noarch: generic # Suggests: BiocFileCache, BiocStyle, graphics, knitr, memuse, rmarkdown, spelling, testthat (>= 3.0.0) # SystemRequirements: Java (>= 8) diff --git a/recipes/bioconductor-fastseg/meta.yaml b/recipes/bioconductor-fastseg/meta.yaml index 868ab493238d2..2a67786842c05 100644 --- a/recipes/bioconductor-fastseg/meta.yaml +++ b/recipes/bioconductor-fastseg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "fastseg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 742f51d390453aca568b16001d3d674f + md5: ca8ead071a9b881b19dea7b71e0e73b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: DNAcopy, oligo + run_exports: '{{ pin_subpackage("bioconductor-fastseg", max_pin="x.x") }}' +# Suggests: DNAcopy, oligo, BiocStyle, knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-fccac/meta.yaml b/recipes/bioconductor-fccac/meta.yaml index 4f60ddf7d6845..e2b8cff1c58c2 100644 --- a/recipes/bioconductor-fccac/meta.yaml +++ b/recipes/bioconductor-fccac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "fCCAC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 78d5504a05fdc9fe1b993a0244a06ace + md5: f4152105666120b6529f55983c4e2aa3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fccac", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomation >=1.32.0,<1.33.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomation >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fda - r-ggplot2 - r-rcolorbrewer run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomation >=1.32.0,<1.33.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomation >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fda - r-ggplot2 diff --git a/recipes/bioconductor-fci/meta.yaml b/recipes/bioconductor-fci/meta.yaml index 22d517c7944cd..de6bb8839434c 100644 --- a/recipes/bioconductor-fci/meta.yaml +++ b/recipes/bioconductor-fci/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "fCI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c5f500670ac386e7cb2318b3f93891b + md5: 5a6ec7dcf6303ef44018924283b87586 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fci", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: diff --git a/recipes/bioconductor-fcscan/meta.yaml b/recipes/bioconductor-fcscan/meta.yaml index 57a171acf4588..bcf4f078fb8c9 100644 --- a/recipes/bioconductor-fcscan/meta.yaml +++ b/recipes/bioconductor-fcscan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "fcScan" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 497ff22cdc8e837d2a49fa931c6aa162 + md5: a23eab38b0106852ecca920f1f1db0bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fcscan", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-doparallel - r-foreach - r-plyr run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml b/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml index 9c850222c2153..3a5d0aac46574 100644 --- a/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "FDb.FANTOM4.promoters.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,25 +13,26 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 99a610eb895470e3d945acc5cfb3ebe6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fdb.fantom4.promoters.hg19", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19, rtracklayer, matrixStats requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml b/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml index fe8afec3ab01b..66990d70a99d3 100644 --- a/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml +++ b/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.2.0" %} {% set name = "FDb.InfiniumMethylation.hg18" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,28 +13,29 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 95ceab50d0a7c3d417cee12fbe3defb3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fdb.infiniummethylation.hg18", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml b/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml index 9a89db96412bf..3f4a764d09a61 100644 --- a/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.2.0" %} {% set name = "FDb.InfiniumMethylation.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,29 +13,30 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b8b1abc599b9556b9fe9c6e824cb2697 build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fdb.infiniummethylation.hg19", max_pin="x.x") }}' noarch: generic # Suggests: FDb.UCSC.snp135common.hg19 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml b/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml index f54c865e42788..76eab4357415e 100644 --- a/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "FDb.UCSC.snp135common.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0cdca5fa595bb69464016ceb97635f78 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fdb.ucsc.snp135common.hg19", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP.20111119 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml b/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml index a1ff83de10f2b..0fd1755b911dc 100644 --- a/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "FDb.UCSC.snp137common.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: dac83f2d2f9ea9f033e50beac5c44838 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fdb.ucsc.snp137common.hg19", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml b/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml index f007f80703caa..c95a592d717ad 100644 --- a/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml +++ b/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "FDb.UCSC.tRNAs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 77bfdadd4d9f995a72b001e4e41792fa build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fdb.ucsc.trnas", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fdrame/meta.yaml b/recipes/bioconductor-fdrame/meta.yaml index 03ae4ceea9649..37166d2fd75f6 100644 --- a/recipes/bioconductor-fdrame/meta.yaml +++ b/recipes/bioconductor-fdrame/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "fdrame" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4ed3cd1054bb77ea566bc89e8fe00285 + md5: d7fafba89f784f421a43b4b4d9a10000 build: number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fdrame", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-feast/meta.yaml b/recipes/bioconductor-feast/meta.yaml index 68598a4aa23b0..1ba80d9f1fc73 100644 --- a/recipes/bioconductor-feast/meta.yaml +++ b/recipes/bioconductor-feast/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "FEAST" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1337d86557f7c377f5a80484bff003f4 + md5: 5b32fdf869bc97368c62f50ccd8fe9f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-feast", max_pin="x.x") }}' # Suggests: rmarkdown, Seurat, ggpubr, knitr, testthat (>= 3.0.0), BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-sc3 >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tscan >=1.38.0,<1.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-sc3 >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tscan >=1.40.0,<1.41.0' - r-base - r-irlba - r-matrixstats @@ -32,11 +33,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-sc3 >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tscan >=1.38.0,<1.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-sc3 >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tscan >=1.40.0,<1.41.0' - r-base - r-irlba - r-matrixstats diff --git a/recipes/bioconductor-featseekr/meta.yaml b/recipes/bioconductor-featseekr/meta.yaml index cd2969666b135..b13b10cada5f1 100644 --- a/recipes/bioconductor-featseekr/meta.yaml +++ b/recipes/bioconductor-featseekr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "FeatSeekR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14bd43f9ea1a98d7c049f34d20c1a66d + md5: 9792a703c1ec0b4a58c759274c2cb571 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-featseekr", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, BiocStyle, DmelSGI, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-mass - r-pheatmap - r-pracma run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-mass - r-pheatmap diff --git a/recipes/bioconductor-fedup/meta.yaml b/recipes/bioconductor-fedup/meta.yaml index 9fadc2a2d359a..ab157eb4d27ac 100644 --- a/recipes/bioconductor-fedup/meta.yaml +++ b/recipes/bioconductor-fedup/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "fedup" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1264d858aa93e0c49dd71e11c6215848 + md5: a5ac34da42c1a460ab50e307c73f8116 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fedup", max_pin="x.x") }}' noarch: generic # Suggests: biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr requirements: host: - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-data.table - r-dplyr @@ -32,7 +33,7 @@ requirements: - r-rcolorbrewer - r-tibble run: - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-fella/meta.yaml b/recipes/bioconductor-fella/meta.yaml index c282fc3e1af17..0b00c88027e81 100644 --- a/recipes/bioconductor-fella/meta.yaml +++ b/recipes/bioconductor-fella/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "FELLA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9b1bee53b4cef474ce91c2920b8ca4dd + md5: 106f8558197df891cfb6e28e406363e1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fella", max_pin="x.x") }}' noarch: generic # Suggests: shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown, testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, GOSemSim requirements: host: - - 'bioconductor-keggrest >=1.40.0,<1.41.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' - r-base - r-igraph - r-matrix - r-plyr run: - - 'bioconductor-keggrest >=1.40.0,<1.41.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' - r-base - r-igraph - r-matrix diff --git a/recipes/bioconductor-fenr/build.sh b/recipes/bioconductor-fenr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-fenr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fenr/meta.yaml b/recipes/bioconductor-fenr/meta.yaml new file mode 100644 index 0000000000000..1c2c8d0c43996 --- /dev/null +++ b/recipes/bioconductor-fenr/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.0.0" %} +{% set name = "fenr" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f908fa38bd91672d7d0567d6232d2214 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fenr", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, testthat, knitr, rmarkdown, topGO, org.Hs.eg.db +requirements: + host: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - r-assertthat + - r-base + - r-dplyr + - r-ggplot2 + - r-httr + - r-jsonlite + - r-progress + - r-purrr + - r-readr + - r-rlang + - r-shiny + - r-stringr + - r-tibble + - r-tidyr + - r-tidyselect + - r-xml + run: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - r-assertthat + - r-base + - r-dplyr + - r-ggplot2 + - r-httr + - r-jsonlite + - r-progress + - r-purrr + - r-readr + - r-rlang + - r-shiny + - r-stringr + - r-tibble + - r-tidyr + - r-tidyselect + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Fast functional enrichment for interactive applications' + description: 'Perform fast functional enrichment on feature lists (like genes or proteins) using the hypergeometric distribution. Tailored for speed, this package is ideal for interactive platforms such as Shiny. It supports the retrieval of functional data from sources like GO, KEGG, Reactome, and WikiPathways. By downloading and preparing data first, it allows for rapid successive tests on various feature selections without the need for repetitive, time-consuming preparatory steps typical of other packages.' + license_file: LICENSE + diff --git a/recipes/bioconductor-ffpe/meta.yaml b/recipes/bioconductor-ffpe/meta.yaml index f9e56c7cab696..0a41ce9b5dabf 100644 --- a/recipes/bioconductor-ffpe/meta.yaml +++ b/recipes/bioconductor-ffpe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "ffpe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2cb6393fc9ed1d1286a10016f95d8b56 + md5: c2a3dbd53e85caf82d7c8f91a8277454 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ffpe", max_pin="x.x") }}' noarch: generic # Suggests: genefilter, ffpeExampleData requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' - r-base - r-sfsmisc - r-ttr run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' - r-base - r-sfsmisc - r-ttr diff --git a/recipes/bioconductor-ffpeexampledata/meta.yaml b/recipes/bioconductor-ffpeexampledata/meta.yaml index 5affb00b25589..e47fc10975fe9 100644 --- a/recipes/bioconductor-ffpeexampledata/meta.yaml +++ b/recipes/bioconductor-ffpeexampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "ffpeExampleData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5b4c1bcd2467b0b82973b2e70243ef0 + md5: 6ea474bdf448ff6026ec4f1f376b7d69 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ffpeexampledata", max_pin="x.x") }}' noarch: generic # Suggests: genefilter, affy requirements: host: - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ffpeexampledata/post-link.sh b/recipes/bioconductor-ffpeexampledata/post-link.sh index bb74729fed1f2..8070c5cbda31e 100644 --- a/recipes/bioconductor-ffpeexampledata/post-link.sh +++ b/recipes/bioconductor-ffpeexampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ffpeexampledata-1.38.0" +installBiocDataPackage.sh "ffpeexampledata-1.40.0" diff --git a/recipes/bioconductor-fgga/meta.yaml b/recipes/bioconductor-fgga/meta.yaml index 0a9b21b325fc1..5988b466d1305 100644 --- a/recipes/bioconductor-fgga/meta.yaml +++ b/recipes/bioconductor-fgga/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.9.0" %} {% set name = "fgga" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 47ae70169f23e0631cd50fc840dd2973 + md5: eaa84557f2fd00490bb5f9f12e8ca1d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fgga", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, GOstats, GO.db, BiocGenerics, pROC, RUnit, BiocStyle requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-curl - r-e1071 - r-grbase - r-jsonlite run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-curl - r-e1071 diff --git a/recipes/bioconductor-fgnet/meta.yaml b/recipes/bioconductor-fgnet/meta.yaml index ffe2941c90507..c90b268edfc43 100644 --- a/recipes/bioconductor-fgnet/meta.yaml +++ b/recipes/bioconductor-fgnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.34.0" %} +{% set version = "3.36.0" %} {% set name = "FGNet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46da20768d223011b2691e3f8575addb + md5: 00da241d84bdc16ec9a8b1e27a3db509 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fgnet", max_pin="x.x") }}' noarch: generic # Suggests: RCurl, gage, topGO, GO.db, reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, BiocManager requirements: diff --git a/recipes/bioconductor-fgsea/meta.yaml b/recipes/bioconductor-fgsea/meta.yaml index b9ff9dc799c78..1d179f86b50b2 100644 --- a/recipes/bioconductor-fgsea/meta.yaml +++ b/recipes/bioconductor-fgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "fgsea" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3b02276027800535421f38bbe5e83921 + md5: 53b8ab8a13390a0920bc13eeba3aa1b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fgsea", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery, msigdbr, aggregation, Seurat # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-bh - r-cowplot @@ -34,7 +35,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-bh - r-cowplot diff --git a/recipes/bioconductor-fibroeset/meta.yaml b/recipes/bioconductor-fibroeset/meta.yaml index 1a3674c445420..8f520b8b38f59 100644 --- a/recipes/bioconductor-fibroeset/meta.yaml +++ b/recipes/bioconductor-fibroeset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "fibroEset" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 42efffdc75032b3305ebdceb55f3754f + md5: cbc13cc5c4ac4f6445dc69383ad183ff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fibroeset", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fibroeset/post-link.sh b/recipes/bioconductor-fibroeset/post-link.sh index 646fd7df45ff7..bee7497a33fcb 100644 --- a/recipes/bioconductor-fibroeset/post-link.sh +++ b/recipes/bioconductor-fibroeset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fibroeset-1.42.0" +installBiocDataPackage.sh "fibroeset-1.44.0" diff --git a/recipes/bioconductor-fieldeffectcrc/meta.yaml b/recipes/bioconductor-fieldeffectcrc/meta.yaml index 6221d1d18f340..a75f40d2d0445 100644 --- a/recipes/bioconductor-fieldeffectcrc/meta.yaml +++ b/recipes/bioconductor-fieldeffectcrc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "FieldEffectCrc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b20c0c45eec814e077d124b45d6589a6 + md5: 73fa4e8649f3c4a523764d35afd421f2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fieldeffectcrc", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocGenerics, sva, BiocManager requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-runit run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-runit - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fieldeffectcrc/post-link.sh b/recipes/bioconductor-fieldeffectcrc/post-link.sh index b9e9fdb703e71..dca22c34d2083 100644 --- a/recipes/bioconductor-fieldeffectcrc/post-link.sh +++ b/recipes/bioconductor-fieldeffectcrc/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fieldeffectcrc-1.10.0" +installBiocDataPackage.sh "fieldeffectcrc-1.12.0" diff --git a/recipes/bioconductor-filterffpe/meta.yaml b/recipes/bioconductor-filterffpe/meta.yaml index 2348708871e68..94d1f62824669 100644 --- a/recipes/bioconductor-filterffpe/meta.yaml +++ b/recipes/bioconductor-filterffpe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "FilterFFPE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 596fa16e66e1e46fdf0776b50b4b0ae2 + md5: e2aabe533af9d2779d1ffc2f76017ecd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-filterffpe", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-foreach run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-findit2/meta.yaml b/recipes/bioconductor-findit2/meta.yaml index 06bf8a8711aeb..62b26bed34e95 100644 --- a/recipes/bioconductor-findit2/meta.yaml +++ b/recipes/bioconductor-findit2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "FindIT2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d09d40b53c0d856a804d4735d816fae8 + md5: d48fffebc5ff34ec3276d3f4675d6c71 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-findit2", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), TxDb.Athaliana.BioMart.plantsmart28 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -46,17 +47,17 @@ requirements: - r-tidyr - r-withr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-fis/meta.yaml b/recipes/bioconductor-fis/meta.yaml index 7cc084d4f9fbb..bc6ce25a237ce 100644 --- a/recipes/bioconductor-fis/meta.yaml +++ b/recipes/bioconductor-fis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "FIs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a79abe38c53faa7176cd1dc4189351b + md5: ef807b75136742a1dcb5ea70993d5c38 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fis", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fis/post-link.sh b/recipes/bioconductor-fis/post-link.sh index b6c6f347761a8..081f3868dae51 100644 --- a/recipes/bioconductor-fis/post-link.sh +++ b/recipes/bioconductor-fis/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fis-1.28.0" +installBiocDataPackage.sh "fis-1.30.0" diff --git a/recipes/bioconductor-fishalyser/meta.yaml b/recipes/bioconductor-fishalyser/meta.yaml index a65b079aeaf85..54a8f41dc04b4 100644 --- a/recipes/bioconductor-fishalyser/meta.yaml +++ b/recipes/bioconductor-fishalyser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "FISHalyseR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8263bd2ee43d6c8e6c05aedd5901b81f + md5: fea17ba4629a7d53c62eef47a3cdfab2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fishalyser", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-abind - r-base run: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-abind - r-base test: diff --git a/recipes/bioconductor-fishpond/meta.yaml b/recipes/bioconductor-fishpond/meta.yaml index a2589b18d6606..92bd84c80a051 100644 --- a/recipes/bioconductor-fishpond/meta.yaml +++ b/recipes/bioconductor-fishpond/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.2" %} +{% set version = "2.8.0" %} {% set name = "fishpond" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fb2d9b6d5b1ec1938baca42fd8936fbc + md5: 407bd027d801c207371750eba2c9d735 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fishpond", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, samr, DESeq2, apeglm, tximportData, limma, ensembldb, EnsDb.Hsapiens.v86, GenomicFeatures, AnnotationDbi, pheatmap, Gviz, GenomeInfoDb, data.table requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-gtools @@ -35,12 +36,12 @@ requirements: - r-matrixstats - r-svmisc run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-gtools diff --git a/recipes/bioconductor-fission/meta.yaml b/recipes/bioconductor-fission/meta.yaml index 3dc988c615684..113cdd94fae1d 100644 --- a/recipes/bioconductor-fission/meta.yaml +++ b/recipes/bioconductor-fission/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "fission" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bf744d1be1f95417b4379e55aadfcef3 + md5: 7d404509808bfc439270093b647ccd80 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fission", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fission/post-link.sh b/recipes/bioconductor-fission/post-link.sh index e8b0b2176a5b1..e0380f99e57cd 100644 --- a/recipes/bioconductor-fission/post-link.sh +++ b/recipes/bioconductor-fission/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fission-1.20.0" +installBiocDataPackage.sh "fission-1.22.0" diff --git a/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml b/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml index 9e954926a6341..8d3045a648c6b 100644 --- a/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml +++ b/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.1" %} {% set name = "fitCons.UCSC.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 53d954890ec9b91084664a10161ce391 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fitcons.ucsc.hg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fithic/meta.yaml b/recipes/bioconductor-fithic/meta.yaml index bc8693d7cc3d1..adf18559a5108 100644 --- a/recipes/bioconductor-fithic/meta.yaml +++ b/recipes/bioconductor-fithic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "FitHiC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e2333d06cb1378d9cd9301db5988bb7c + md5: ee894d402d0c5567935ade4f8dc75c29 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fithic", max_pin="x.x") }}' # Suggests: knitr, rmarkdown requirements: host: diff --git a/recipes/bioconductor-flagme/meta.yaml b/recipes/bioconductor-flagme/meta.yaml index 8f1e4e65d55c1..90086340aa522 100644 --- a/recipes/bioconductor-flagme/meta.yaml +++ b/recipes/bioconductor-flagme/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "flagme" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 59bf39feefe5d755928a32e05016cf6b + md5: ada68435478c0172b282919125008b1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flagme", max_pin="x.x") }}' requirements: host: - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-gcspikelite >=1.38.0,<1.39.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-gcspikelite >=1.40.0,<1.41.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-gplots - r-mass @@ -29,9 +30,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-gcspikelite >=1.38.0,<1.39.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-gcspikelite >=1.40.0,<1.41.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-gplots - r-mass diff --git a/recipes/bioconductor-flames/meta.yaml b/recipes/bioconductor-flames/meta.yaml index 133956e55a0ca..05cea2c22df0e 100644 --- a/recipes/bioconductor-flames/meta.yaml +++ b/recipes/bioconductor-flames/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "FLAMES" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,42 +11,45 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94fd7ed1565fc08d6f858123b0aa23b3 + md5: ecfe856c54464ffd2c27f8e10063d494 build: - skip: true # [osx] + skip: True # [osx] number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flames", max_pin="x.x") }}' # Suggests: BiocStyle, GEOquery, knitr, rmarkdown, markdown, BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0) -# SystemRequirements: GNU make, C++11 +# SystemRequirements: GNU make, C++17 requirements: host: - - 'bioconductor-bambu >=3.2.0,<3.3.0' - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-bambu >=3.4.0,<3.5.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-circlize - r-cowplot - r-dplyr + - r-future - r-ggplot2 - r-gridextra - r-igraph @@ -62,31 +65,33 @@ requirements: - libblas - liblapack run: - - 'bioconductor-bambu >=3.2.0,<3.3.0' - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-bambu >=3.4.0,<3.5.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-circlize - r-cowplot - r-dplyr + - r-future - r-ggplot2 - r-gridextra - r-igraph diff --git a/recipes/bioconductor-fletcher2013a/meta.yaml b/recipes/bioconductor-fletcher2013a/meta.yaml index ba4901cef0bb8..e4bd34e45937a 100644 --- a/recipes/bioconductor-fletcher2013a/meta.yaml +++ b/recipes/bioconductor-fletcher2013a/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "Fletcher2013a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 69ea86d2f1e6aa8e8716c4db65f81cf0 + md5: e4c4f9a4e8b24a7a72f9c63337a0eef9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fletcher2013a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-gplots - r-venndiagram run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-gplots - r-venndiagram - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fletcher2013a/post-link.sh b/recipes/bioconductor-fletcher2013a/post-link.sh index 76947f653f606..36042cfbda031 100644 --- a/recipes/bioconductor-fletcher2013a/post-link.sh +++ b/recipes/bioconductor-fletcher2013a/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fletcher2013a-1.36.0" +installBiocDataPackage.sh "fletcher2013a-1.38.0" diff --git a/recipes/bioconductor-fletcher2013b/meta.yaml b/recipes/bioconductor-fletcher2013b/meta.yaml index 278b7c8f0bb5a..5c2e191438443 100644 --- a/recipes/bioconductor-fletcher2013b/meta.yaml +++ b/recipes/bioconductor-fletcher2013b/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "Fletcher2013b" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fd7177b33cc525534e80c197f4a14b0b + md5: cf656c92425c8a63ef584be08e8b742e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fletcher2013b", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-fletcher2013a >=1.36.0,<1.37.0' - - 'bioconductor-reder >=2.4.0,<2.5.0' - - 'bioconductor-rtn >=2.24.0,<2.25.0' + - 'bioconductor-fletcher2013a >=1.38.0,<1.39.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' + - 'bioconductor-rtn >=2.26.0,<2.27.0' - r-base - r-igraph - r-rcolorbrewer run: - - 'bioconductor-fletcher2013a >=1.36.0,<1.37.0' - - 'bioconductor-reder >=2.4.0,<2.5.0' - - 'bioconductor-rtn >=2.24.0,<2.25.0' + - 'bioconductor-fletcher2013a >=1.38.0,<1.39.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' + - 'bioconductor-rtn >=2.26.0,<2.27.0' - r-base - r-igraph - r-rcolorbrewer - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fletcher2013b/post-link.sh b/recipes/bioconductor-fletcher2013b/post-link.sh index d9bf248107be3..94b06ce4f03df 100644 --- a/recipes/bioconductor-fletcher2013b/post-link.sh +++ b/recipes/bioconductor-fletcher2013b/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fletcher2013b-1.36.0" +installBiocDataPackage.sh "fletcher2013b-1.38.0" diff --git a/recipes/bioconductor-flowai/meta.yaml b/recipes/bioconductor-flowai/meta.yaml index 7a54cd4064d1c..2a294b9332201 100644 --- a/recipes/bioconductor-flowai/meta.yaml +++ b/recipes/bioconductor-flowai/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "flowAI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d59cf6bed0f7b6837d83b2e9fd90573b + md5: 714cb015ac01ee026e02fc24536770e5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowai", max_pin="x.x") }}' noarch: generic # Suggests: testthat, shiny, BiocStyle requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-changepoint - r-ggplot2 @@ -32,7 +33,7 @@ requirements: - r-rmarkdown - r-scales run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-changepoint - r-ggplot2 diff --git a/recipes/bioconductor-flowbeads/meta.yaml b/recipes/bioconductor-flowbeads/meta.yaml index 19e782c06a121..275b1e5c29f2b 100644 --- a/recipes/bioconductor-flowbeads/meta.yaml +++ b/recipes/bioconductor-flowbeads/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "flowBeads" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1e744c88fbbc189754bb9e3006333355 + md5: 3c9aa4f78c8b1b2397d6004773311174 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowbeads", max_pin="x.x") }}' noarch: generic # Suggests: flowViz requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-knitr - r-rrcov - r-xtable run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-knitr - r-rrcov diff --git a/recipes/bioconductor-flowbin/meta.yaml b/recipes/bioconductor-flowbin/meta.yaml index b202a7db84c28..50962c3a7aee2 100644 --- a/recipes/bioconductor-flowbin/meta.yaml +++ b/recipes/bioconductor-flowbin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "flowBin" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 60f858355d66f8ee8f09f2968d82a440 + md5: 3d761d597ff6b4f6929e9f68ea83b366 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowbin", max_pin="x.x") }}' noarch: generic # Suggests: parallel requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowfp >=1.58.0,<1.59.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowfp >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-class - r-snow run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowfp >=1.58.0,<1.59.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowfp >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-class - r-snow diff --git a/recipes/bioconductor-flowcatchr/meta.yaml b/recipes/bioconductor-flowcatchr/meta.yaml index 538ea1b9f3d0c..5f47ecd63335c 100644 --- a/recipes/bioconductor-flowcatchr/meta.yaml +++ b/recipes/bioconductor-flowcatchr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "flowcatchR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91c941bf107a4f973859adcd584d0ac2 + md5: a823367e5e1e432980ca41c1516c97f2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowcatchr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown # SystemRequirements: ImageMagick requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-abind - r-base - r-colorramps @@ -31,8 +32,8 @@ requirements: - r-shiny - imagemagick run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-abind - r-base - r-colorramps diff --git a/recipes/bioconductor-flowchic/meta.yaml b/recipes/bioconductor-flowchic/meta.yaml index a6bad36cb85d0..2aaf6235bb116 100644 --- a/recipes/bioconductor-flowchic/meta.yaml +++ b/recipes/bioconductor-flowchic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "flowCHIC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 72229b8e073b7f7beaab5d3718dfdc2e + md5: 72e50628c116c31eebd78d620514dca1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowchic", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-ggplot2 - r-hexbin - r-vegan run: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-ggplot2 - r-hexbin diff --git a/recipes/bioconductor-flowclean/meta.yaml b/recipes/bioconductor-flowclean/meta.yaml index 6fe89720fe2ee..02be800eea903 100644 --- a/recipes/bioconductor-flowclean/meta.yaml +++ b/recipes/bioconductor-flowclean/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "flowClean" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd29baeeed9e6883aeb1dd592ec63e82 + md5: 77f86a84c8ed6dbd2df24d9458765205 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowclean", max_pin="x.x") }}' noarch: generic # Suggests: flowViz, grid, gridExtra requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-bit - r-changepoint - r-sfsmisc run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-bit - r-changepoint diff --git a/recipes/bioconductor-flowclust/meta.yaml b/recipes/bioconductor-flowclust/meta.yaml index 1c81b8b9cc239..946cfdb1cd414 100644 --- a/recipes/bioconductor-flowclust/meta.yaml +++ b/recipes/bioconductor-flowclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.38.0" %} +{% set version = "3.40.0" %} {% set name = "flowClust" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 843149c02cec1b6eedac82c6faf3ecd0 + md5: 50e5d774ae44b8aaca69069733c175e3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowclust", max_pin="x.x") }}' # Suggests: testthat, flowWorkspace, flowWorkspaceData, knitr, rmarkdown, openCyto, flowStats(>= 4.7.1) # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-flowcore/meta.yaml b/recipes/bioconductor-flowcore/meta.yaml index 5c0b25e087f4f..bb31c70c0c63a 100644 --- a/recipes/bioconductor-flowcore/meta.yaml +++ b/recipes/bioconductor-flowcore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "flowCore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46283d4ef07328f5a7824471bbd6e2ef + md5: 3b0696fd3fc45a87531ab3503be00277 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowcore", max_pin="x.x") }}' # Suggests: Rgraphviz, flowViz, flowStats (>= 3.43.4), testthat, flowWorkspace, flowWorkspaceData, openCyto, knitr, ggcyto, gridExtra # SystemRequirements: GNU make, C++11 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-cytolib >=2.12.0,<2.13.0' - - 'bioconductor-rprotobuflib >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-cytolib >=2.14.0,<2.15.0' + - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - - 'r-bh >=1.65.0.1' + - 'r-bh >=1.81.0.0' - r-cpp11 - r-matrixstats - r-rcpp - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-cytolib >=2.12.0,<2.13.0' - - 'bioconductor-rprotobuflib >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-cytolib >=2.14.0,<2.15.0' + - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - - 'r-bh >=1.65.0.1' + - 'r-bh >=1.81.0.0' - r-cpp11 - r-matrixstats - r-rcpp diff --git a/recipes/bioconductor-flowcut/meta.yaml b/recipes/bioconductor-flowcut/meta.yaml index a9b4ed4154841..f60fa58a8ac7a 100644 --- a/recipes/bioconductor-flowcut/meta.yaml +++ b/recipes/bioconductor-flowcut/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "flowCut" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a879badc8fb1ccd7f4bd8b7fdf560255 + md5: b79bc38dd887cef19040c2d7178311d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowcut", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, markdown, rmarkdown requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowdensity >=1.34.0,<1.35.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowdensity >=1.36.0,<1.37.0' - r-base - r-cairo - r-e1071 run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowdensity >=1.34.0,<1.35.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowdensity >=1.36.0,<1.37.0' - r-base - r-cairo - r-e1071 diff --git a/recipes/bioconductor-flowcybar/meta.yaml b/recipes/bioconductor-flowcybar/meta.yaml index f0290c51cd3ae..cf71a394b6ac8 100644 --- a/recipes/bioconductor-flowcybar/meta.yaml +++ b/recipes/bioconductor-flowcybar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "flowCyBar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5666ea536602365882d54be550274877 + md5: 9236c02598960d4536906fb7449a7dd4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowcybar", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-flowdensity/meta.yaml b/recipes/bioconductor-flowdensity/meta.yaml index f4be69a59e827..7a7978ac58c3d 100644 --- a/recipes/bioconductor-flowdensity/meta.yaml +++ b/recipes/bioconductor-flowdensity/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.1" %} {% set name = "flowDensity" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9582e24db40a4754b375f0ee675bf635 + md5: 30c661d010484bff6c2eb427a7056aa1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowdensity", max_pin="x.x") }}' noarch: generic # Suggests: knitr,rmarkdown # SystemRequirements: xml2, GNU make, C++11 requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' - r-base - r-car - r-gplots - - r-rfoc - - r-rgeos - - r-sp + - r-polyclip - libxml2 run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' - r-base - r-car - r-gplots - - r-rfoc - - r-rgeos - - r-sp + - r-polyclip - libxml2 test: commands: diff --git a/recipes/bioconductor-flowfp/meta.yaml b/recipes/bioconductor-flowfp/meta.yaml index 447cd63812bb6..680a77375956c 100644 --- a/recipes/bioconductor-flowfp/meta.yaml +++ b/recipes/bioconductor-flowfp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "flowFP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0a826a5cf4c655b5f0fc9d5f80655f30 + md5: 5f0424d8a662d2d65bacbcff080d9c7a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowfp", max_pin="x.x") }}' # Suggests: RUnit requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-flowgate/meta.yaml b/recipes/bioconductor-flowgate/meta.yaml index b9a3005511cce..c565637710606 100644 --- a/recipes/bioconductor-flowgate/meta.yaml +++ b/recipes/bioconductor-flowgate/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "flowGate" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 06253e3ee0f40cfd6446ec6aba2a4562 + md5: d5b19dee6139d26306d14563f445a64f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowgate", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, stringr, tidyverse, testthat requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-ggcyto >=1.28.0,<1.29.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-ggcyto >=1.30.0,<1.31.0' - r-base - 'r-biocmanager >=1.30.10' - 'r-dplyr >=1.0.0' @@ -33,9 +34,9 @@ requirements: - 'r-shiny >=1.5.0' - r-tibble run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-ggcyto >=1.28.0,<1.29.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-ggcyto >=1.30.0,<1.31.0' - r-base - 'r-biocmanager >=1.30.10' - 'r-dplyr >=1.0.0' diff --git a/recipes/bioconductor-flowgraph/meta.yaml b/recipes/bioconductor-flowgraph/meta.yaml index 0cb0ad7fa10fe..a0e5db9f2c1f9 100644 --- a/recipes/bioconductor-flowgraph/meta.yaml +++ b/recipes/bioconductor-flowgraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "flowGraph" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ae032bd4f1c462d1643902facf008dd6 + md5: 68abd457f6a200f435ebbf41183c0e94 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowgraph", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, dplyr, knitr, rmarkdown, testthat (>= 2.1.0) requirements: diff --git a/recipes/bioconductor-flowmatch/meta.yaml b/recipes/bioconductor-flowmatch/meta.yaml index cfb3a59262ef2..fbbc71e016972 100644 --- a/recipes/bioconductor-flowmatch/meta.yaml +++ b/recipes/bioconductor-flowmatch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "flowMatch" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2642ae3123f2b7fa6715d5f23a1d76bc + md5: 78b2b9dc87eec35dbc65c59dadb1ffd9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowmatch", max_pin="x.x") }}' # Suggests: healthyFlowData requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - 'r-rcpp >=0.11.0' - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - 'r-rcpp >=0.11.0' build: diff --git a/recipes/bioconductor-flowmeans/meta.yaml b/recipes/bioconductor-flowmeans/meta.yaml index c33e164d34bfd..4830d38e0f6a9 100644 --- a/recipes/bioconductor-flowmeans/meta.yaml +++ b/recipes/bioconductor-flowmeans/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "flowMeans" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 907da9157eecd2bcf4ff53536254bbc9 + md5: 5cbb796502f09bf65cae60e4f0f53c1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowmeans", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-feature - r-rrcov run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-feature - r-rrcov diff --git a/recipes/bioconductor-flowmerge/meta.yaml b/recipes/bioconductor-flowmerge/meta.yaml index 63020aae225c2..cb220a14afbac 100644 --- a/recipes/bioconductor-flowmerge/meta.yaml +++ b/recipes/bioconductor-flowmerge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.48.0" %} +{% set version = "2.50.0" %} {% set name = "flowMerge" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f0c37b4e9c43ab26edaae92dd9b1fb2e + md5: c0d4d124e3d94a0eab8fc138f9044d2c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowmerge", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-feature - r-foreach - r-rrcov - r-snow run: - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-feature - r-foreach diff --git a/recipes/bioconductor-flowpeaks/meta.yaml b/recipes/bioconductor-flowpeaks/meta.yaml index 4965ed48624d1..ac3d20f1f9a9d 100644 --- a/recipes/bioconductor-flowpeaks/meta.yaml +++ b/recipes/bioconductor-flowpeaks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "flowPeaks" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d8481859adf962408c139342e9eac893 + md5: f68db373a0d053a7eabd112df80a25f1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowpeaks", max_pin="x.x") }}' # SystemRequirements: gsl requirements: host: diff --git a/recipes/bioconductor-flowploidy/meta.yaml b/recipes/bioconductor-flowploidy/meta.yaml index b71d6983cf655..c1569c3b88b46 100644 --- a/recipes/bioconductor-flowploidy/meta.yaml +++ b/recipes/bioconductor-flowploidy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "flowPloidy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14afd95deaa59263b9e2ccc3140cb5a0 + md5: 1020981a0f645d2dcbf1a38a3e42b7e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowploidy", max_pin="x.x") }}' noarch: generic # Suggests: flowPloidyData, testthat requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-car - r-catools @@ -30,7 +31,7 @@ requirements: - r-rmarkdown - r-shiny run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-car - r-catools diff --git a/recipes/bioconductor-flowploidydata/meta.yaml b/recipes/bioconductor-flowploidydata/meta.yaml index 29f71f910219a..1df2c16869432 100644 --- a/recipes/bioconductor-flowploidydata/meta.yaml +++ b/recipes/bioconductor-flowploidydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "flowPloidyData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 10d8e5d5d636d7a78c7dd5aa79ba41a4 + md5: 993a663f6d1cdc791c3f4e88d5b3b047 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowploidydata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, flowCore requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowploidydata/post-link.sh b/recipes/bioconductor-flowploidydata/post-link.sh index d1acd28276c1f..dbb4d93fd487f 100644 --- a/recipes/bioconductor-flowploidydata/post-link.sh +++ b/recipes/bioconductor-flowploidydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowploidydata-1.26.0" +installBiocDataPackage.sh "flowploidydata-1.28.0" diff --git a/recipes/bioconductor-flowplots/meta.yaml b/recipes/bioconductor-flowplots/meta.yaml index da76dc7f6737a..e7893a2db7cac 100644 --- a/recipes/bioconductor-flowplots/meta.yaml +++ b/recipes/bioconductor-flowplots/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "flowPlots" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6960c2567067f71bab67d0de646533ad + md5: 523b0d79646813f56d711d3e0f38a5e9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowplots", max_pin="x.x") }}' noarch: generic # Suggests: vcd requirements: diff --git a/recipes/bioconductor-flowsom/meta.yaml b/recipes/bioconductor-flowsom/meta.yaml index 69e70f2f2330d..e8708a748755e 100644 --- a/recipes/bioconductor-flowsom/meta.yaml +++ b/recipes/bioconductor-flowsom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "FlowSOM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c801e147f4137a9b7c5157f8536e44c3 + md5: 9bc309cc9948473d101d91ba6f1a37f2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowsom", max_pin="x.x") }}' # Suggests: BiocStyle, testthat, CytoML, flowWorkspace, ggrepel, scattermore, pheatmap, ggpointdensity requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-colorramps - r-dplyr @@ -39,9 +40,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-colorramps - r-dplyr diff --git a/recipes/bioconductor-flowsorted.blood.450k/meta.yaml b/recipes/bioconductor-flowsorted.blood.450k/meta.yaml index 828f4aae39fba..9c9dcba953274 100644 --- a/recipes/bioconductor-flowsorted.blood.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.blood.450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "FlowSorted.Blood.450k" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 68977c1bf508dda29bc067929aecc006 + md5: f88422c2d8a2f7ce4ca968292adfc8ab build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowsorted.blood.450k", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowsorted.blood.450k/post-link.sh b/recipes/bioconductor-flowsorted.blood.450k/post-link.sh index c04ffe255ad90..291888eff33cc 100644 --- a/recipes/bioconductor-flowsorted.blood.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.blood.450k/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowsorted.blood.450k-1.38.0" +installBiocDataPackage.sh "flowsorted.blood.450k-1.40.0" diff --git a/recipes/bioconductor-flowsorted.blood.epic/meta.yaml b/recipes/bioconductor-flowsorted.blood.epic/meta.yaml index a4e32da09fc49..90ba4f67f6423 100644 --- a/recipes/bioconductor-flowsorted.blood.epic/meta.yaml +++ b/recipes/bioconductor-flowsorted.blood.epic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.2" %} +{% set version = "2.6.0" %} {% set name = "FlowSorted.Blood.EPIC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d9d98db39792aac4fe1ec1db0b0366b + md5: e94cbb0480a032595cdb5d9714065bed build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowsorted.blood.epic", max_pin="x.x") }}' noarch: generic # Suggests: knitr,rmarkdown, FlowSorted.CordBlood.450k, FlowSorted.Blood.450k(>= 1.0.1), EpiDISH,FlowSorted.CordBloodNorway.450k, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b4.hg19 requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-nlme - r-quadprog run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-nlme - r-quadprog - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowsorted.blood.epic/post-link.sh b/recipes/bioconductor-flowsorted.blood.epic/post-link.sh index 7d84a33bceaaf..82feccd703411 100644 --- a/recipes/bioconductor-flowsorted.blood.epic/post-link.sh +++ b/recipes/bioconductor-flowsorted.blood.epic/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowsorted.blood.epic-2.4.2" +installBiocDataPackage.sh "flowsorted.blood.epic-2.6.0" diff --git a/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml b/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml index 26dde86b085e7..20523ec1de672 100644 --- a/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "FlowSorted.CordBlood.450k" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dbef432e31c78c82fe4498a341d3a5a8 + md5: fca81b7412af68100d7aed4d57d5fc59 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowsorted.cordblood.450k", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh b/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh index 3d72e98279d82..0b82dabf176d0 100644 --- a/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowsorted.cordblood.450k-1.28.0" +installBiocDataPackage.sh "flowsorted.cordblood.450k-1.30.0" diff --git a/recipes/bioconductor-flowsorted.cordbloodcombined.450k/meta.yaml b/recipes/bioconductor-flowsorted.cordbloodcombined.450k/meta.yaml index 57947ff21176b..6aef7e141a811 100644 --- a/recipes/bioconductor-flowsorted.cordbloodcombined.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.cordbloodcombined.450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "FlowSorted.CordBloodCombined.450k" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0579c0d8bcb50c77d579b082a7bf4158 + md5: 769113b80606820ab2918dcacf1076b2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowsorted.cordbloodcombined.450k", max_pin="x.x") }}' noarch: generic # Suggests: FlowSorted.Blood.EPIC, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylationEPICanno.ilm10b2.hg19 requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowsorted.cordbloodcombined.450k/post-link.sh b/recipes/bioconductor-flowsorted.cordbloodcombined.450k/post-link.sh index b4b08defd7136..c540b53ecf269 100644 --- a/recipes/bioconductor-flowsorted.cordbloodcombined.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.cordbloodcombined.450k/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowsorted.cordbloodcombined.450k-1.16.0" +installBiocDataPackage.sh "flowsorted.cordbloodcombined.450k-1.18.0" diff --git a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml index 90c84b67f76c8..13471afc01d9a 100644 --- a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "FlowSorted.CordBloodNorway.450k" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a399952bf229258fe47964a8d3db910 + md5: 40016224becf643102bc3054f4e2508d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowsorted.cordbloodnorway.450k", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh index 504978723041e..142aa56ecf3a3 100644 --- a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowsorted.cordbloodnorway.450k-1.26.0" +installBiocDataPackage.sh "flowsorted.cordbloodnorway.450k-1.28.0" diff --git a/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml b/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml index f0f6ed40e091e..b9bfdbe04b88e 100644 --- a/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "FlowSorted.DLPFC.450k" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb70a712a95eaa879d62d7751567aed5 + md5: ad95a51f7e8bcf7c0bec6dda80eb0a92 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowsorted.dlpfc.450k", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh b/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh index dc693b027192e..bdd7e31f4b074 100644 --- a/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowsorted.dlpfc.450k-1.36.0" +installBiocDataPackage.sh "flowsorted.dlpfc.450k-1.38.0" diff --git a/recipes/bioconductor-flowspecs/meta.yaml b/recipes/bioconductor-flowspecs/meta.yaml index a695590b17669..f3dea0389b41d 100644 --- a/recipes/bioconductor-flowspecs/meta.yaml +++ b/recipes/bioconductor-flowspecs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "flowSpecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84af2116cc90cb4c1df4b384ab9a232c + md5: 502f1e04027fab8076745a5386401f2e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowspecs", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle, DepecheR requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - 'r-ggplot2 >=3.1.0' - 'r-reshape2 >=1.4.3' - 'r-zoo >=1.8.6' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - 'r-ggplot2 >=3.1.0' - 'r-reshape2 >=1.4.3' diff --git a/recipes/bioconductor-flowstats/meta.yaml b/recipes/bioconductor-flowstats/meta.yaml index f9909cc9d27de..6ea2f22d7384f 100644 --- a/recipes/bioconductor-flowstats/meta.yaml +++ b/recipes/bioconductor-flowstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.12.0" %} +{% set version = "4.14.0" %} {% set name = "flowStats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 730df788ab11668488ede56d8c65362c + md5: 2817bb2cbd74b07bb948d0988be2a57e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowstats", max_pin="x.x") }}' noarch: generic # Suggests: xtable, testthat, openCyto, ggcyto, ggridges requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-ncdfflow >=2.46.0,<2.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' - r-base + - r-clue - r-cluster - r-corpcor - 'r-fda >=2.2.6' @@ -39,13 +41,14 @@ requirements: - r-rcolorbrewer - r-rrcov run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-ncdfflow >=2.46.0,<2.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' - r-base + - r-clue - r-cluster - r-corpcor - 'r-fda >=2.2.6' diff --git a/recipes/bioconductor-flowtime/meta.yaml b/recipes/bioconductor-flowtime/meta.yaml index b684b98a569de..eb87ab80635af 100644 --- a/recipes/bioconductor-flowtime/meta.yaml +++ b/recipes/bioconductor-flowtime/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "flowTime" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 00a06c20b516ba2a70acecd10b8c73cc + md5: 04ca452b54e7309493c814844fc1b772 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowtime", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, stats, flowClust, openCyto, flowStats, ggcyto requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - 'r-dplyr >=1.0.0' - r-magrittr @@ -29,7 +30,7 @@ requirements: - r-rlang - r-tibble run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - 'r-dplyr >=1.0.0' - r-magrittr diff --git a/recipes/bioconductor-flowtrans/meta.yaml b/recipes/bioconductor-flowtrans/meta.yaml index e5cc7f9552b92..ebddba32b3bfd 100644 --- a/recipes/bioconductor-flowtrans/meta.yaml +++ b/recipes/bioconductor-flowtrans/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "flowTrans" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 362e389a46df4c08fbdacebb047a0b88 + md5: d98daa4177e5f6b8cda8d8475e34c09a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowtrans", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' - r-base run: - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' - r-base test: commands: diff --git a/recipes/bioconductor-flowviz/meta.yaml b/recipes/bioconductor-flowviz/meta.yaml index dd1d975d2d390..46eab38ac8366 100644 --- a/recipes/bioconductor-flowviz/meta.yaml +++ b/recipes/bioconductor-flowviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "flowViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5c581bc7787fdf9bb136087fb6f966f5 + md5: 320d8392618efe06e6c2a8923b3c6652 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowviz", max_pin="x.x") }}' noarch: generic # Suggests: colorspace, flowStats, knitr, rmarkdown, markdown, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-hexbin - r-idpmisc @@ -32,8 +33,8 @@ requirements: - r-mass - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-hexbin - r-idpmisc diff --git a/recipes/bioconductor-flowvs/meta.yaml b/recipes/bioconductor-flowvs/meta.yaml index 10f2837f82420..9469254038a37 100644 --- a/recipes/bioconductor-flowvs/meta.yaml +++ b/recipes/bioconductor-flowvs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "flowVS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a44cf1a01b17b9a3a28422aca0ac438 + md5: 43fc57f2be5ccbfcff9ac9b9bc0bb857 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowvs", max_pin="x.x") }}' noarch: generic # Suggests: knitr, vsn, requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowstats >=4.12.0,<4.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowstats >=4.14.0,<4.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' - r-base run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowstats >=4.12.0,<4.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowstats >=4.14.0,<4.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' - r-base test: commands: diff --git a/recipes/bioconductor-flowworkspace/meta.yaml b/recipes/bioconductor-flowworkspace/meta.yaml index 85970ddc4fd59..5df796f644a70 100644 --- a/recipes/bioconductor-flowworkspace/meta.yaml +++ b/recipes/bioconductor-flowworkspace/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.12.0" %} +{% set version = "4.14.0" %} {% set name = "flowWorkspace" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8f80cf16553cc9099512c1c86c6f60d + md5: e97cd561c6a61ae778261cb55f29af90 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowworkspace", max_pin="x.x") }}' # Suggests: testthat, flowWorkspaceData (>= 2.23.2), knitr, rmarkdown, ggcyto, parallel, CytoML, openCyto # SystemRequirements: GNU make, C++11 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-cytolib >=2.12.0,<2.13.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-ncdfflow >=2.46.0,<2.47.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-rprotobuflib >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-cytolib >=2.14.0,<2.15.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-bh >=1.62.0-1' - r-cpp11 @@ -45,18 +46,18 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-cytolib >=2.12.0,<2.13.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-ncdfflow >=2.46.0,<2.47.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-rprotobuflib >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-cytolib >=2.14.0,<2.15.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-bh >=1.62.0-1' - r-cpp11 diff --git a/recipes/bioconductor-flowworkspacedata/meta.yaml b/recipes/bioconductor-flowworkspacedata/meta.yaml index c9a33f5504dfb..ec95026f5f295 100644 --- a/recipes/bioconductor-flowworkspacedata/meta.yaml +++ b/recipes/bioconductor-flowworkspacedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.12.0" %} +{% set version = "3.14.0" %} {% set name = "flowWorkspaceData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d91993dd5a5c5b561a8063ec91046d3 + md5: 96655cef2a21f1b9d303ec775597a2dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowworkspacedata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowworkspacedata/post-link.sh b/recipes/bioconductor-flowworkspacedata/post-link.sh index 4f4de031dce66..f0331f23198c7 100644 --- a/recipes/bioconductor-flowworkspacedata/post-link.sh +++ b/recipes/bioconductor-flowworkspacedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowworkspacedata-3.12.0" +installBiocDataPackage.sh "flowworkspacedata-3.14.0" diff --git a/recipes/bioconductor-fly.db0/meta.yaml b/recipes/bioconductor-fly.db0/meta.yaml index 58fee2b2ea22c..0ed06aa0d7e48 100644 --- a/recipes/bioconductor-fly.db0/meta.yaml +++ b/recipes/bioconductor-fly.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "fly.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 04b3d22c5825c9a31f5253746df5c4e0 + md5: 49722b8a538d02f71631a418b92c44d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fly.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fly.db0/post-link.sh b/recipes/bioconductor-fly.db0/post-link.sh index 213a32552081d..3fab31db8f277 100644 --- a/recipes/bioconductor-fly.db0/post-link.sh +++ b/recipes/bioconductor-fly.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fly.db0-3.17.0" +installBiocDataPackage.sh "fly.db0-3.18.0" diff --git a/recipes/bioconductor-fmcsr/meta.yaml b/recipes/bioconductor-fmcsr/meta.yaml index f86bf2cd4b73e..d62cc7de82aea 100644 --- a/recipes/bioconductor-fmcsr/meta.yaml +++ b/recipes/bioconductor-fmcsr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "fmcsR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2687c7aa47141346582b5b6dac68e906 + md5: 21a6242a61cba8dd537bf846af3260c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fmcsr", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap,rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - r-runit - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - r-runit build: diff --git a/recipes/bioconductor-fmrs/meta.yaml b/recipes/bioconductor-fmrs/meta.yaml index f858ab078409a..667e0c6c78dac 100644 --- a/recipes/bioconductor-fmrs/meta.yaml +++ b/recipes/bioconductor-fmrs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "fmrs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1f73155e7e3d066f5e59fedeb0dcd725 + md5: ccf41504ab27d93464e555b363ef406a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fmrs", max_pin="x.x") }}' # Suggests: BiocGenerics, testthat, knitr, utils requirements: host: diff --git a/recipes/bioconductor-fobitools/meta.yaml b/recipes/bioconductor-fobitools/meta.yaml index 0d734261bb591..d9b0d175e64b0 100644 --- a/recipes/bioconductor-fobitools/meta.yaml +++ b/recipes/bioconductor-fobitools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "fobitools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fe95da3fe13e9bb17165048bbe6f4799 + md5: 24ebda3aed06055ab55d7cdf88a7c2a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fobitools", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, ggrepel, kableExtra, knitr, metabolomicsWorkbenchR, POMA, rmarkdown, rvest, SummarizedExperiment, testthat (>= 2.3.2), tidyverse requirements: host: - - 'bioconductor-fgsea >=1.26.0,<1.27.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' - r-base - r-clisymbols - r-crayon @@ -39,7 +40,7 @@ requirements: - r-tidyr - r-vroom run: - - 'bioconductor-fgsea >=1.26.0,<1.27.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' - r-base - r-clisymbols - r-crayon diff --git a/recipes/bioconductor-fourdndata/meta.yaml b/recipes/bioconductor-fourdndata/meta.yaml index fe82086bd827c..4b1339af9b5b5 100644 --- a/recipes/bioconductor-fourdndata/meta.yaml +++ b/recipes/bioconductor-fourdndata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "fourDNData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2bea3be8c2abed679fc99cf6bdaee98f + md5: bca623e919f7c17a40ffb4eae27cfe59 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fourdndata", max_pin="x.x") }}' noarch: generic # Suggests: rtracklayer, dplyr, testthat, methods, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hicexperiment >=1.0.0,<1.1.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hicexperiment >=1.0.0,<1.1.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fourdndata/post-link.sh b/recipes/bioconductor-fourdndata/post-link.sh index b46b9ff5f46a2..f062b27931ef6 100644 --- a/recipes/bioconductor-fourdndata/post-link.sh +++ b/recipes/bioconductor-fourdndata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fourdndata-1.0.0" +installBiocDataPackage.sh "fourdndata-1.2.0" diff --git a/recipes/bioconductor-fraser/meta.yaml b/recipes/bioconductor-fraser/meta.yaml index f5696e6fec261..e2d50e16fbc6a 100644 --- a/recipes/bioconductor-fraser/meta.yaml +++ b/recipes/bioconductor-fraser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "FRASER" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f569aff29dbec9bc4d7797b30d05e593 + md5: 07e7f6a03b43d2111015d4fc051f3a00 build: skip: True # [osx] number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fraser", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat, covr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-outrider >=1.18.0,<1.19.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-outrider >=1.20.0,<1.21.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bbmisc - r-cowplot @@ -63,27 +64,27 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-outrider >=1.18.0,<1.19.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-outrider >=1.20.0,<1.21.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bbmisc - r-cowplot diff --git a/recipes/bioconductor-frenchfish/meta.yaml b/recipes/bioconductor-frenchfish/meta.yaml index 9a694f3d1d414..3b703c9f03fda 100644 --- a/recipes/bioconductor-frenchfish/meta.yaml +++ b/recipes/bioconductor-frenchfish/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "frenchFISH" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a5cd6ee3dcf999336cd1dfc10c583ec + md5: 170f9e757e12e766a8a455d6d3ca9f81 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-frenchfish", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-frgepistasis/meta.yaml b/recipes/bioconductor-frgepistasis/meta.yaml index 6bd5277ce9f25..18dcf4c202ea4 100644 --- a/recipes/bioconductor-frgepistasis/meta.yaml +++ b/recipes/bioconductor-frgepistasis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "FRGEpistasis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0726b7195c31f91dbf12b46ea0514d0d + md5: a5804d62a4e375df7706ebc0573929f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-frgepistasis", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-frma/meta.yaml b/recipes/bioconductor-frma/meta.yaml index f28bc4bae5195..6e27095a3ca5a 100644 --- a/recipes/bioconductor-frma/meta.yaml +++ b/recipes/bioconductor-frma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "frma" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f74abf15385619ab89738bc0aeee913c + md5: 4892707c54a5698c48151bd630feb0e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-frma", max_pin="x.x") }}' noarch: generic # Suggests: hgu133afrmavecs, frmaExampleData requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dbi - r-mass run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dbi - r-mass diff --git a/recipes/bioconductor-frmaexampledata/meta.yaml b/recipes/bioconductor-frmaexampledata/meta.yaml index c28effa9ce690..9f29cd6e5963e 100644 --- a/recipes/bioconductor-frmaexampledata/meta.yaml +++ b/recipes/bioconductor-frmaexampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "frmaExampleData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 057a53ead8fde2bab4ee0cb71a4faaf6 + md5: 9713801ffd08145323ca4d31a3631995 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-frmaexampledata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-frmaexampledata/post-link.sh b/recipes/bioconductor-frmaexampledata/post-link.sh index ab1764237f9ab..11252f324dcf4 100644 --- a/recipes/bioconductor-frmaexampledata/post-link.sh +++ b/recipes/bioconductor-frmaexampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "frmaexampledata-1.36.0" +installBiocDataPackage.sh "frmaexampledata-1.38.0" diff --git a/recipes/bioconductor-frmatools/meta.yaml b/recipes/bioconductor-frmatools/meta.yaml index 6cdde49420424..113507f7441f4 100644 --- a/recipes/bioconductor-frmatools/meta.yaml +++ b/recipes/bioconductor-frmatools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "frmaTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4fc17910da8e1a1f2b006edd1c122156 + md5: 270e71dc903bb77add1154782cf17342 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-frmatools", max_pin="x.x") }}' noarch: generic # Suggests: oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM, hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf, hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dbi run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dbi test: diff --git a/recipes/bioconductor-funchip/meta.yaml b/recipes/bioconductor-funchip/meta.yaml index 80163f7e1dedd..d78b00121ddb0 100644 --- a/recipes/bioconductor-funchip/meta.yaml +++ b/recipes/bioconductor-funchip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "FunChIP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d4be7e4b7194e6c6baf5aa80d938b4a + md5: 93a91487d2e6b0841094c9eb7c997be2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-funchip", max_pin="x.x") }}' requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-doparallel - r-fda @@ -33,10 +34,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-doparallel - r-fda diff --git a/recipes/bioconductor-funtoonorm/meta.yaml b/recipes/bioconductor-funtoonorm/meta.yaml index db61dccd9c11f..ecdc54d66593c 100644 --- a/recipes/bioconductor-funtoonorm/meta.yaml +++ b/recipes/bioconductor-funtoonorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "funtooNorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 50104886edef68e9248446c34efcb714 + md5: 32208fd7734fe0fcfb1278b80a98c28e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-funtoonorm", max_pin="x.x") }}' noarch: generic # Suggests: prettydoc, minfiData, knitr, rmarkdown requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - r-matrixstats - r-pls run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - r-matrixstats - r-pls diff --git a/recipes/bioconductor-furrowseg/meta.yaml b/recipes/bioconductor-furrowseg/meta.yaml index f5835bbc9cb5e..19e3d0d33ddfd 100644 --- a/recipes/bioconductor-furrowseg/meta.yaml +++ b/recipes/bioconductor-furrowseg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "furrowSeg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ee1d6bc3d7fe7c1855a6b96b429190b + md5: f41e88a4d47949b3b8b126b0fc7852eb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-furrowseg", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, ggplot2, knitr requirements: host: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-abind - r-base - r-dplyr - r-locfit - r-tiff run: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-abind - r-base - r-dplyr - r-locfit - r-tiff - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-furrowseg/post-link.sh b/recipes/bioconductor-furrowseg/post-link.sh index f6edea536462d..1cf285a2cc4fd 100644 --- a/recipes/bioconductor-furrowseg/post-link.sh +++ b/recipes/bioconductor-furrowseg/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "furrowseg-1.28.0" +installBiocDataPackage.sh "furrowseg-1.30.0" diff --git a/recipes/bioconductor-fusesom/meta.yaml b/recipes/bioconductor-fusesom/meta.yaml index 9000fbe7a3415..972591b6661df 100644 --- a/recipes/bioconductor-fusesom/meta.yaml +++ b/recipes/bioconductor-fusesom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "FuseSOM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c90411cb119ef9c54cf54f49b909d5a + md5: 8f53b251d77ea648cb8e56bb5eb72b18 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fusesom", max_pin="x.x") }}' # Suggests: knitr, BiocStyle, rmarkdown, SingleCellExperiment requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-analogue - r-base - r-cluster @@ -41,8 +42,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-analogue - r-base - r-cluster diff --git a/recipes/bioconductor-ga4ghclient/meta.yaml b/recipes/bioconductor-ga4ghclient/meta.yaml index 8591a0b9dc674..aef75f3842b74 100644 --- a/recipes/bioconductor-ga4ghclient/meta.yaml +++ b/recipes/bioconductor-ga4ghclient/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "GA4GHclient" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: da57780acaf8f06eb3efdd6aeff4446c + md5: d0e8b9a21eda6320d15642c12fcb8392 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ga4ghclient", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-dplyr - r-httr - r-jsonlite run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-dplyr - r-httr diff --git a/recipes/bioconductor-ga4ghshiny/meta.yaml b/recipes/bioconductor-ga4ghshiny/meta.yaml index cc143cb834480..ae26ca82d7726 100644 --- a/recipes/bioconductor-ga4ghshiny/meta.yaml +++ b/recipes/bioconductor-ga4ghshiny/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "GA4GHshiny" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2e537faaa9cbb451eaf972f495c6de06 + md5: 629ca5d338b8435b238169892016d447 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ga4ghshiny", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ga4ghclient >=1.24.0,<1.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ga4ghclient >=1.26.0,<1.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-dt @@ -37,12 +38,12 @@ requirements: - r-shinythemes - r-tidyr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ga4ghclient >=1.24.0,<1.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ga4ghclient >=1.26.0,<1.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-dt diff --git a/recipes/bioconductor-gaga/meta.yaml b/recipes/bioconductor-gaga/meta.yaml index 2c252a1df70a7..e96e988b0e664 100644 --- a/recipes/bioconductor-gaga/meta.yaml +++ b/recipes/bioconductor-gaga/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "gaga" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9a616f28ab9876f7725629d62946aadd + md5: d1b404912b9a23365c9085dc91e20a10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gaga", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ebarrays >=2.64.0,<2.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ebarrays >=2.66.0,<2.67.0' - r-base - r-coda - r-mgcv - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ebarrays >=2.64.0,<2.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ebarrays >=2.66.0,<2.67.0' - r-base - r-coda - r-mgcv diff --git a/recipes/bioconductor-gage/meta.yaml b/recipes/bioconductor-gage/meta.yaml index 792d38f878e67..4724a254b4280 100644 --- a/recipes/bioconductor-gage/meta.yaml +++ b/recipes/bioconductor-gage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.50.0" %} +{% set version = "2.52.0" %} {% set name = "gage" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7981df2c7c9c8bb91d12f0b207f3b380 + md5: ffb5ec419d5e08f9b31154202e0e04c8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gage", max_pin="x.x") }}' noarch: generic # Suggests: pathview, gageData, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq2, edgeR, limma requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' - r-base test: commands: diff --git a/recipes/bioconductor-gagedata/meta.yaml b/recipes/bioconductor-gagedata/meta.yaml index b5c3d7c318906..eeef14a1c426c 100644 --- a/recipes/bioconductor-gagedata/meta.yaml +++ b/recipes/bioconductor-gagedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.38.0" %} +{% set version = "2.40.0" %} {% set name = "gageData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04f7869c72f70f6726372af0a4688d5d + md5: 889e4b6ceda6c2a80f61ad4e867c3b59 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gagedata", max_pin="x.x") }}' noarch: generic # Suggests: gage, pathview, genefilter requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gagedata/post-link.sh b/recipes/bioconductor-gagedata/post-link.sh index ae7f71a1154ae..1e6ddee3415bd 100644 --- a/recipes/bioconductor-gagedata/post-link.sh +++ b/recipes/bioconductor-gagedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gagedata-2.38.0" +installBiocDataPackage.sh "gagedata-2.40.0" diff --git a/recipes/bioconductor-gaggle/meta.yaml b/recipes/bioconductor-gaggle/meta.yaml index b5cfe52719523..10757fa0844f0 100644 --- a/recipes/bioconductor-gaggle/meta.yaml +++ b/recipes/bioconductor-gaggle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.0" %} {% set name = "gaggle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c86f7ecb5db49b11939c8d9f6077c976 + md5: 3dc385e959f454cd56dec418800c33a6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gaggle", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - 'r-rjava >=0.4' - 'r-runit >=0.4.17' run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - 'r-rjava >=0.4' - 'r-runit >=0.4.17' diff --git a/recipes/bioconductor-gaprediction/meta.yaml b/recipes/bioconductor-gaprediction/meta.yaml index 71297ee496db1..04d4db4123a5b 100644 --- a/recipes/bioconductor-gaprediction/meta.yaml +++ b/recipes/bioconductor-gaprediction/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "GAprediction" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 28fd8f9a1b37806405ac3a5aed4d64fe + md5: 5aceb1005e134eeeb2fc6a77941d8348 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gaprediction", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-garfield/meta.yaml b/recipes/bioconductor-garfield/meta.yaml index bf5fef693a02b..0f71b3e382829 100644 --- a/recipes/bioconductor-garfield/meta.yaml +++ b/recipes/bioconductor-garfield/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "garfield" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 269dabdfcc22cb722db4cdf8fb78ad6c + md5: bf1974925a6c10b95ada01ff6d46bf15 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-garfield", max_pin="x.x") }}' # Suggests: knitr requirements: host: diff --git a/recipes/bioconductor-gars/meta.yaml b/recipes/bioconductor-gars/meta.yaml index 6fab0879d810b..aadcd040d41db 100644 --- a/recipes/bioconductor-gars/meta.yaml +++ b/recipes/bioconductor-gars/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GARS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67cee7307c638973430218e416e4ae01 + md5: 205eceff8f152fa6ac308b7830ef2876 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gars", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-damirseq >=2.12.0,<2.13.0' - - 'bioconductor-mlseq >=2.18.0,<2.19.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-damirseq >=2.14.0,<2.15.0' + - 'bioconductor-mlseq >=2.20.0,<2.21.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-ggplot2 run: - - 'bioconductor-damirseq >=2.12.0,<2.13.0' - - 'bioconductor-mlseq >=2.18.0,<2.19.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-damirseq >=2.14.0,<2.15.0' + - 'bioconductor-mlseq >=2.20.0,<2.21.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-ggplot2 @@ -43,7 +44,7 @@ about: summary: 'GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasets' description: 'Feature selection aims to identify and remove redundant, irrelevant and noisy variables from high-dimensional datasets. Selecting informative features affects the subsequent classification and regression analyses by improving their overall performances. Several methods have been proposed to perform feature selection: most of them relies on univariate statistics, correlation, entropy measurements or the usage of backward/forward regressions. Herein, we propose an efficient, robust and fast method that adopts stochastic optimization approaches for high-dimensional. GARS is an innovative implementation of a genetic algorithm that selects robust features in high-dimensional and challenging datasets.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - extra: container: - extended-base: True + extended-base: true + diff --git a/recipes/bioconductor-gaschyhs/meta.yaml b/recipes/bioconductor-gaschyhs/meta.yaml index 924b406a8798c..0bbd7d13201a1 100644 --- a/recipes/bioconductor-gaschyhs/meta.yaml +++ b/recipes/bioconductor-gaschyhs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "gaschYHS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: adb36d86b4890c4f4c714d99aa3b3f93 + md5: 29983eadb2a2a20f7c5475206367d641 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gaschyhs", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gaschyhs/post-link.sh b/recipes/bioconductor-gaschyhs/post-link.sh index a0d77e2feb121..51ff00a4819a6 100644 --- a/recipes/bioconductor-gaschyhs/post-link.sh +++ b/recipes/bioconductor-gaschyhs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gaschyhs-1.38.0" +installBiocDataPackage.sh "gaschyhs-1.40.0" diff --git a/recipes/bioconductor-gatefinder/meta.yaml b/recipes/bioconductor-gatefinder/meta.yaml index fead106644f34..ac9a8afe6eacc 100644 --- a/recipes/bioconductor-gatefinder/meta.yaml +++ b/recipes/bioconductor-gatefinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GateFinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b893327eec1564d4da0596cc6822b44b + md5: 4fcb13ba6ee293d3ffb30122b652df12 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gatefinder", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowfp >=1.58.0,<1.59.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowfp >=1.60.0,<1.61.0' - r-base - r-diptest - r-mvoutlier - r-splancs run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowfp >=1.58.0,<1.59.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowfp >=1.60.0,<1.61.0' - r-base - r-diptest - r-mvoutlier diff --git a/recipes/bioconductor-gatom/build.sh b/recipes/bioconductor-gatom/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gatom/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cancer/build_failure.linux-64.yaml b/recipes/bioconductor-gatom/build_failure.linux-64.yaml similarity index 81% rename from recipes/bioconductor-cancer/build_failure.linux-64.yaml rename to recipes/bioconductor-gatom/build_failure.linux-64.yaml index e0fc6e1bb323f..253ed0b0d61b5 100644 --- a/recipes/bioconductor-cancer/build_failure.linux-64.yaml +++ b/recipes/bioconductor-gatom/build_failure.linux-64.yaml @@ -1,26 +1,25 @@ -recipe_sha: c8371d76491173a2c71d6f48bd4a6acaa34dccfc9e093843f1f28fd72dac3536 # The commit at which this recipe failed to build. +recipe_sha: 7ebb01aa7b6769d098059934bddb98ded4a89c60a59b8400436d8a3a28fb92c1 # The commit at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + dependency issue log: |2- - - bioconductor-gseabase >=1.62.0,<1.63.0 - - r-circlize - - r-httr - - r-r.oo - - r-survival - - bioconductor-phenotest >=1.48.0,<1.49.0 + - r-mwcsr + - r-pryr + - r-data.table + - r-plyr + - r-shinycyjs >=1.0.0 - r-base 4.3.* - - r-r.methodss3 - - r-rpart - - r-runit - - bioconductor-genetclassifier >=1.40.0,<1.41.0 with channels: + - file:///opt/host-conda-bld - conda-forge - bioconda - defaults The reported errors are: - Encountered problems while solving: - - - nothing provides icu 54.* needed by r-base-3.3.2-0 + - - nothing provides requested r-mwcsr + - - nothing provides requested r-shinycyjs >=1.0.0 - Leaving build/test directories: @@ -43,30 +42,33 @@ log: |2- File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve raise RuntimeError("Solver could not find solution." error_string) RuntimeError: Solver could not find solution.Mamba failed to solve: + - r-ggally + - r-xml + - r-sna + - r-htmltools + - r-htmlwidgets + - r-intergraph + - r-ggplot2 + - bioconductor-bionet >=1.62.0,<1.63.0 + - r-network + - r-igraph + - r-mwcsr + - r-pryr + - r-data.table - r-plyr - - r-formula - - r-tkrplot - - bioconductor-biobase >=2.60.0,<2.61.0 - - bioconductor-gseabase >=1.62.0,<1.63.0 - - r-circlize - - r-httr - - r-r.oo - - r-survival - - bioconductor-phenotest >=1.48.0,<1.49.0 + - r-shinycyjs >=1.0.0 - r-base 4.3.* - - r-r.methodss3 - - r-rpart - - r-runit - - bioconductor-genetclassifier >=1.40.0,<1.41.0 with channels: + - file:///opt/host-conda-bld - conda-forge - bioconda - defaults The reported errors are: - Encountered problems while solving: - - - nothing provides icu 54.* needed by r-base-3.3.2-0 + - - nothing provides requested r-mwcsr + - - nothing provides requested r-shinycyjs >=1.0.0 - During handling of the above exception, another exception occurred: @@ -100,5 +102,5 @@ log: |2- actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("icu=54"), MatchSpec("r-base==3.3.2=0")} + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-mwcsr"), MatchSpec("r-shinycyjs[version='>=1.0.0']")} # Last 100 lines of the build log. diff --git a/recipes/bioconductor-gatom/meta.yaml b/recipes/bioconductor-gatom/meta.yaml new file mode 100644 index 0000000000000..e51c528dd385d --- /dev/null +++ b/recipes/bioconductor-gatom/meta.yaml @@ -0,0 +1,66 @@ +{% set version = "1.0.0" %} +{% set name = "gatom" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0e86773c5bafed3a4c13b7db82015463 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gatom", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat, knitr, rmarkdown, KEGGREST, AnnotationDbi, org.Mm.eg.db, reactome.db, fgsea, readr, BiocStyle, R.utils +requirements: + host: + - 'bioconductor-bionet >=1.62.0,<1.63.0' + - r-base + - r-data.table + - r-ggally + - r-ggplot2 + - r-htmltools + - r-htmlwidgets + - r-igraph + - r-intergraph + - r-mwcsr + - r-network + - r-plyr + - r-pryr + - 'r-shinycyjs >=1.0.0' + - r-sna + - r-xml + run: + - 'bioconductor-bionet >=1.62.0,<1.63.0' + - r-base + - r-data.table + - r-ggally + - r-ggplot2 + - r-htmltools + - r-htmlwidgets + - r-igraph + - r-intergraph + - r-mwcsr + - r-network + - r-plyr + - r-pryr + - 'r-shinycyjs >=1.0.0' + - r-sna + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENCE' + summary: 'Finding an Active Metabolic Module in Atom Transition Network' + description: 'This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module) most regulated between the two conditions of interest. The package further provides functions for module post-processing, annotation and visualization.' + diff --git a/recipes/bioconductor-gbscleanr/meta.yaml b/recipes/bioconductor-gbscleanr/meta.yaml index 9f9a3b75a8f5e..7b565ff74bd52 100644 --- a/recipes/bioconductor-gbscleanr/meta.yaml +++ b/recipes/bioconductor-gbscleanr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.4" %} +{% set version = "1.6.0" %} {% set name = "GBScleanR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b1a99a09d42d9cf271d30f570835d9d8 + md5: f54a8356b8931c5c6dd6150a021c56cf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gbscleanr", max_pin="x.x") }}' # Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown # SystemRequirements: GNU make, C++11 requirements: host: - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' - r-base - r-expm - r-ggplot2 @@ -32,8 +33,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' - r-base - r-expm - r-ggplot2 diff --git a/recipes/bioconductor-gcapc/meta.yaml b/recipes/bioconductor-gcapc/meta.yaml index 3c3a16a0c8b79..9270c58bf5303 100644 --- a/recipes/bioconductor-gcapc/meta.yaml +++ b/recipes/bioconductor-gcapc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "gcapc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9974c87d810bf0e80de4672cdee15c6e + md5: 16c0a9ac78843641871680c0e0d48dfc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gcapc", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-mass - r-matrixstats run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-mass - r-matrixstats diff --git a/recipes/bioconductor-gcatest/meta.yaml b/recipes/bioconductor-gcatest/meta.yaml index 9cfd490a3165d..82f540b32e039 100644 --- a/recipes/bioconductor-gcatest/meta.yaml +++ b/recipes/bioconductor-gcatest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.7" %} +{% set version = "2.2.0" %} {% set name = "gcatest" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e0cfb7c0ad56c72aaf703b153456d091 + md5: ddfda402a2332e9c16ecfaa035b689a9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gcatest", max_pin="x.x") }}' noarch: generic # Suggests: knitr, ggplot2, testthat, BEDMatrix, genio requirements: host: - - 'bioconductor-lfa >=2.0.0,<2.1.0' + - 'bioconductor-lfa >=2.2.0,<2.3.0' - r-base run: - - 'bioconductor-lfa >=2.0.0,<2.1.0' + - 'bioconductor-lfa >=2.2.0,<2.3.0' - r-base test: commands: diff --git a/recipes/bioconductor-gcrisprtools/meta.yaml b/recipes/bioconductor-gcrisprtools/meta.yaml index d07f2c85d5031..421388b058ba2 100644 --- a/recipes/bioconductor-gcrisprtools/meta.yaml +++ b/recipes/bioconductor-gcrisprtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "gCrisprTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a1ff3be1f85750ef41124d7768602df + md5: 113ef693d51de0459865934e9a16d90a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gcrisprtools", max_pin="x.x") }}' noarch: generic # Suggests: edgeR, knitr, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-rmarkdown - r-robustrankaggreg run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-rmarkdown diff --git a/recipes/bioconductor-gcrma/meta.yaml b/recipes/bioconductor-gcrma/meta.yaml index ba148e347ab47..c742e33709f8f 100644 --- a/recipes/bioconductor-gcrma/meta.yaml +++ b/recipes/bioconductor-gcrma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.72.0" %} +{% set version = "2.74.0" %} {% set name = "gcrma" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 78807a1c603b84cf1f0a1eed3ea140a4 + md5: d28b6c225b2677e476da8d0348af4695 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gcrma", max_pin="x.x") }}' # Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-biocmanager - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-biocmanager build: diff --git a/recipes/bioconductor-gcspikelite/meta.yaml b/recipes/bioconductor-gcspikelite/meta.yaml index bcda48ebb7fc7..c6c53cd0af3c6 100644 --- a/recipes/bioconductor-gcspikelite/meta.yaml +++ b/recipes/bioconductor-gcspikelite/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "gcspikelite" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 721566ac21590bc7f1e56dd1c716d30c + md5: 91b995753732f0d5508fdc2d7dcb998f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gcspikelite", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gcspikelite/post-link.sh b/recipes/bioconductor-gcspikelite/post-link.sh index e77ece496b3d2..56da58607707c 100644 --- a/recipes/bioconductor-gcspikelite/post-link.sh +++ b/recipes/bioconductor-gcspikelite/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gcspikelite-1.38.0" +installBiocDataPackage.sh "gcspikelite-1.40.0" diff --git a/recipes/bioconductor-gdcrnatools/meta.yaml b/recipes/bioconductor-gdcrnatools/meta.yaml index 75681a20e8676..4ce47ee1d8f08 100644 --- a/recipes/bioconductor-gdcrnatools/meta.yaml +++ b/recipes/bioconductor-gdcrnatools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GDCRNATools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a375e07fa500196928c1c10daf6585ac + md5: bf97cefce864ca1443cb0b0d53601799 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdcrnatools", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, testthat, rmarkdown +# Suggests: knitr, testthat, prettydoc, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicdatacommons >=1.24.0,<1.25.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicdatacommons >=1.26.0,<1.27.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' - r-base - r-dt - r-ggplot2 @@ -42,16 +43,16 @@ requirements: - r-survminer - r-xml run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicdatacommons >=1.24.0,<1.25.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicdatacommons >=1.26.0,<1.27.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' - r-base - r-dt - r-ggplot2 diff --git a/recipes/bioconductor-gdnainrnaseqdata/meta.yaml b/recipes/bioconductor-gdnainrnaseqdata/meta.yaml index 9f347cd9c4adc..bb3142cbcf0d4 100644 --- a/recipes/bioconductor-gdnainrnaseqdata/meta.yaml +++ b/recipes/bioconductor-gdnainrnaseqdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "gDNAinRNAseqData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de757712c6890eb225ad26790e2a23f6 + md5: 52e275ca255493684657a091667f987f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdnainrnaseqdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-rcurl - r-xml run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-rcurl - r-xml - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gdnainrnaseqdata/post-link.sh b/recipes/bioconductor-gdnainrnaseqdata/post-link.sh index 828d3fe116d3a..4daf109d60fca 100644 --- a/recipes/bioconductor-gdnainrnaseqdata/post-link.sh +++ b/recipes/bioconductor-gdnainrnaseqdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gdnainrnaseqdata-1.0.0" +installBiocDataPackage.sh "gdnainrnaseqdata-1.2.0" diff --git a/recipes/bioconductor-gdnax/build.sh b/recipes/bioconductor-gdnax/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gdnax/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gdnax/meta.yaml b/recipes/bioconductor-gdnax/meta.yaml new file mode 100644 index 0000000000000..d582e28ee690b --- /dev/null +++ b/recipes/bioconductor-gdnax/meta.yaml @@ -0,0 +1,70 @@ +{% set version = "1.0.0" %} +{% set name = "gDNAx" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ca3a7370388bf64ba5ccae7161c64ebd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdnax", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, RUnit, TxDb.Hsapiens.UCSC.hg38.knownGene, gDNAinRNAseqData +requirements: + host: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-bitops + - r-plotrix + - r-rcolorbrewer + run: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-bitops + - r-plotrix + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Diagnostics for assessing genomic DNA contamination in RNA-seq data' + description: 'Provides diagnostics for assessing genomic DNA contamination in RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and, in case of strand-specific libraries, the strandedness of the data. Furthermore, it provides functionality to filter out reads of potential gDNA origin.' + diff --git a/recipes/bioconductor-gdr/build.sh b/recipes/bioconductor-gdr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gdr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gdr/meta.yaml b/recipes/bioconductor-gdr/meta.yaml new file mode 100644 index 0000000000000..8b311b353ff7d --- /dev/null +++ b/recipes/bioconductor-gdr/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.0.0" %} +{% set name = "gDR" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: abefb906e5c9ec014a443b0367844ac9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdr", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, BumpyMatrix, futile.logger, gDRstyle (>= 0.99.11), gDRtestData (>= 0.99.11), kableExtra, knitr, markdown, purrr, rmarkdown, SummarizedExperiment, testthat, yaml +requirements: + host: + - 'bioconductor-gdrcore >=1.0.0,<1.1.0' + - 'bioconductor-gdrimport >=1.0.0,<1.1.0' + - 'bioconductor-gdrutils >=1.0.0,<1.1.0' + - r-base + run: + - 'bioconductor-gdrcore >=1.0.0,<1.1.0' + - 'bioconductor-gdrimport >=1.0.0,<1.1.0' + - 'bioconductor-gdrutils >=1.0.0,<1.1.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Umbrella package for R packages in the gDR suite' + description: 'Package is a part of the gDR suite. It reexports functions from other packages in the gDR suite that contain critical processing functions and utilities. The vignette walks through the full processing pipeline for drug response analyses that the gDR suite offers.' + diff --git a/recipes/bioconductor-gdrcore/build.sh b/recipes/bioconductor-gdrcore/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gdrcore/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gdrcore/meta.yaml b/recipes/bioconductor-gdrcore/meta.yaml new file mode 100644 index 0000000000000..91fd6a2760db8 --- /dev/null +++ b/recipes/bioconductor-gdrcore/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.0.0" %} +{% set name = "gDRcore" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 76f729e9fce669107120d0ec73c32bfc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdrcore", max_pin="x.x") }}' +# Suggests: BiocStyle, gDRstyle (>= 0.99.15), gDRimport (>= 0.99.10), gDRtestData (>= 0.99.20), IRanges, knitr, pkgbuild, qs, testthat, yaml +requirements: + host: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-gdrutils >=1.0.0,<1.1.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-checkmate + - r-data.table + - r-futile.logger + - r-purrr + - r-stringr + - libblas + - liblapack + run: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-gdrutils >=1.0.0,<1.1.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-checkmate + - r-data.table + - r-futile.logger + - r-purrr + - r-stringr + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Processing functions and interface to process and analyze drug dose-response data' + description: 'This package contains core functions to process and analyze drug response data. The package provides tools for normalizing, averaging, and calculation of gDR metrics data. All core functions are wrapped into the pipeline function allowing analyzing the data in a straightforward way.' + diff --git a/recipes/bioconductor-gdrimport/build.sh b/recipes/bioconductor-gdrimport/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gdrimport/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gdrimport/meta.yaml b/recipes/bioconductor-gdrimport/meta.yaml new file mode 100644 index 0000000000000..2b32dd59962bc --- /dev/null +++ b/recipes/bioconductor-gdrimport/meta.yaml @@ -0,0 +1,74 @@ +{% set version = "1.0.0" %} +{% set name = "gDRimport" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0390ee6a16f21624044bc509ebdbabd1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdrimport", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, gDRtestData (>= 0.99.10), gDRstyle (>= 0.99.11), knitr, purrr, qs, testthat +requirements: + host: + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-gdrutils >=1.0.0,<1.1.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-pharmacogx >=3.6.0,<3.7.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-assertthat + - r-base + - r-checkmate + - r-data.table + - r-futile.logger + - r-magrittr + - r-openxlsx + - r-readxl + - r-rio + - r-stringi + - r-tibble + - r-xml + - r-yaml + run: + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-gdrutils >=1.0.0,<1.1.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-pharmacogx >=3.6.0,<3.7.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-assertthat + - r-base + - r-checkmate + - r-data.table + - r-futile.logger + - r-magrittr + - r-openxlsx + - r-readxl + - r-rio + - r-stringi + - r-tibble + - r-xml + - r-yaml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package for handling the import of dose-response data' + description: 'The package is a part of the gDR suite. It helps to prepare raw drug response data for downstream processing. It mainly contains helper functions for importing/loading/validating dose-response data provided in different file formats.' + diff --git a/recipes/bioconductor-gdrstyle/build.sh b/recipes/bioconductor-gdrstyle/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gdrstyle/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gdrstyle/meta.yaml b/recipes/bioconductor-gdrstyle/meta.yaml new file mode 100644 index 0000000000000..e8ec2ff8fdf2a --- /dev/null +++ b/recipes/bioconductor-gdrstyle/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.0.0" %} +{% set name = "gDRstyle" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 473f3c2e73e05f50ec3af2b72bb18a55 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdrstyle", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-bioccheck >=1.38.0,<1.39.0' + - r-base + - r-biocmanager + - r-desc + - r-git2r + - 'r-lintr >=3.0.0' + - r-pkgbuild + - r-rcmdcheck + - r-remotes + - r-rjson + - r-withr + - r-yaml + run: + - 'bioconductor-bioccheck >=1.38.0,<1.39.0' + - r-base + - r-biocmanager + - r-desc + - r-git2r + - 'r-lintr >=3.0.0' + - r-pkgbuild + - r-rcmdcheck + - r-remotes + - r-rjson + - r-withr + - r-yaml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A package with style requirements for the gDR suite' + description: 'Package fills a helper package role for whole gDR suite. It helps to support good development practices by keeping style requirements and style tests for other packages. It also contains build helpers to make all package requirements met.' + diff --git a/recipes/bioconductor-gdrtestdata/meta.yaml b/recipes/bioconductor-gdrtestdata/meta.yaml new file mode 100644 index 0000000000000..0118da30f9290 --- /dev/null +++ b/recipes/bioconductor-gdrtestdata/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.0.0" %} +{% set name = "gDRtestData" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8de3dea2673f0e7dc9412e36da2c4f9d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdrtestdata", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, data.table, gDRstyle (>= 0.99.16), knitr, qs, reshape2, rmarkdown, SummarizedExperiment, testthat +requirements: + host: + - r-base + - r-checkmate + run: + - r-base + - r-checkmate + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'gDRtestData - R data package with testing dose reponse data' + description: 'R package with internal dose-response test data. Package provides functions to generate input testing data that can be used as the input for gDR pipeline. It also contains RDS files with MAE data processed by gDR.' + diff --git a/recipes/bioconductor-gdrtestdata/post-link.sh b/recipes/bioconductor-gdrtestdata/post-link.sh new file mode 100644 index 0000000000000..1e1afaeb5de88 --- /dev/null +++ b/recipes/bioconductor-gdrtestdata/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "gdrtestdata-1.0.0" diff --git a/recipes/bioconductor-gdrtestdata/pre-unlink.sh b/recipes/bioconductor-gdrtestdata/pre-unlink.sh new file mode 100644 index 0000000000000..d04affb324053 --- /dev/null +++ b/recipes/bioconductor-gdrtestdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ gDRtestData diff --git a/recipes/bioconductor-gdrutils/build.sh b/recipes/bioconductor-gdrutils/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gdrutils/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gdrutils/meta.yaml b/recipes/bioconductor-gdrutils/meta.yaml new file mode 100644 index 0000000000000..ea940ee0ab23d --- /dev/null +++ b/recipes/bioconductor-gdrutils/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "1.0.0" %} +{% set name = "gDRutils" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fdf71802bbd5967b163447eda2fe37ef +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdrutils", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocManager, BiocStyle, futile.logger, gDRstyle (>= 0.99.15), gDRtestData (>= 0.99.12), IRanges, knitr, lintr, purrr, qs, rcmdcheck, rmarkdown, testthat, tools, yaml +requirements: + host: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-checkmate + - r-data.table + - r-drc + - r-jsonlite + - r-jsonvalidate + - r-magrittr + - r-stringr + run: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-checkmate + - r-data.table + - r-drc + - r-jsonlite + - r-jsonvalidate + - r-magrittr + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A package with helper functions for processing drug response data' + description: 'This package contains utility functions used throughout the gDR platform to fit data, manipulate data, and convert and validate data structures. This package also has the necessary default constants for gDR platform. Many of the functions are utilized by the gDRcore package.' + diff --git a/recipes/bioconductor-gdsarray/meta.yaml b/recipes/bioconductor-gdsarray/meta.yaml index 25d7d2c956c81..66ec184fb02c7 100644 --- a/recipes/bioconductor-gdsarray/meta.yaml +++ b/recipes/bioconductor-gdsarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GDSArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bbc6fe4ba9fe9379724590bb868e6332 + md5: 3ae99d95017d67dd67e17f47436f0301 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdsarray", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, BiocManager requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' - r-base test: commands: diff --git a/recipes/bioconductor-gdsfmt/meta.yaml b/recipes/bioconductor-gdsfmt/meta.yaml index eb66ba4b7c045..e69a5c33b929e 100644 --- a/recipes/bioconductor-gdsfmt/meta.yaml +++ b/recipes/bioconductor-gdsfmt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.1" %} +{% set version = "1.38.0" %} {% set name = "gdsfmt" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7e54216f1539f908f188665986552ab5 + md5: 8851c188356c12f7e99488ceb4daeca8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdsfmt", max_pin="x.x") }}' # Suggests: parallel, digest, Matrix, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics requirements: host: diff --git a/recipes/bioconductor-gem/meta.yaml b/recipes/bioconductor-gem/meta.yaml index 72cf2fdcff018..3cb07be59e5e2 100644 --- a/recipes/bioconductor-gem/meta.yaml +++ b/recipes/bioconductor-gem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "GEM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3380a1e025f9cae67a0d51dba6afa7a + md5: 2c2c8e79fda151dee0060411c9610ff4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gem", max_pin="x.x") }}' noarch: generic # Suggests: knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown requirements: diff --git a/recipes/bioconductor-gemini/meta.yaml b/recipes/bioconductor-gemini/meta.yaml index 67a4b1e9adcb7..974ee79f5a978 100644 --- a/recipes/bioconductor-gemini/meta.yaml +++ b/recipes/bioconductor-gemini/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "gemini" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a753f3c9edcc5daa937e60bdf51defa6 + md5: e8c26d0e8208f56017c8c83a17582f37 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gemini", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-gemma.r/meta.yaml b/recipes/bioconductor-gemma.r/meta.yaml index ad53496689310..d15d66baff3ab 100644 --- a/recipes/bioconductor-gemma.r/meta.yaml +++ b/recipes/bioconductor-gemma.r/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "2.0.0" %} {% set name = "gemma.R" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9a3bb3ba1d43da242f629d1fbe0025fd + md5: 404ce4fa50032ebf727cfdccece32ba2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gemma.r", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis, poolr, digest requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-bit64 - r-data.table + - r-digest - r-glue - r-httr - r-jsonlite @@ -39,15 +41,15 @@ requirements: - r-stringr - r-tibble - r-tidyr - - r-digest run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-bit64 - r-data.table + - r-digest - r-glue - r-httr - r-jsonlite @@ -59,7 +61,6 @@ requirements: - r-stringr - r-tibble - r-tidyr - - r-digest test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genarise/meta.yaml b/recipes/bioconductor-genarise/meta.yaml index 4ab4cff3db280..ade2b312fe4f8 100644 --- a/recipes/bioconductor-genarise/meta.yaml +++ b/recipes/bioconductor-genarise/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "genArise" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ae9d863347d759aeac2262402b9ba2f + md5: d81489147ccfe688c07c228b7fcfcf7d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genarise", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-geneattribution/meta.yaml b/recipes/bioconductor-geneattribution/meta.yaml index c548dc31b64f9..e0e87d633ea5f 100644 --- a/recipes/bioconductor-geneattribution/meta.yaml +++ b/recipes/bioconductor-geneattribution/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "geneAttribution" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3dfe81a4044fe2d88cdef174a85cb7b8 + md5: 62d05af7aabb146fb41a5d91fa460dff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneattribution", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-genebreak/meta.yaml b/recipes/bioconductor-genebreak/meta.yaml index b137ef0843179..fded2e8fdf46a 100644 --- a/recipes/bioconductor-genebreak/meta.yaml +++ b/recipes/bioconductor-genebreak/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "GeneBreak" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ba0252965f6f22957eb6ecbd57e8fb32 + md5: 32b69bf4150c25c908235217dc805ed3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genebreak", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-cghbase >=1.60.0,<1.61.0' - - 'bioconductor-cghcall >=2.62.0,<2.63.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' + - 'bioconductor-cghcall >=2.64.0,<2.65.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-cghbase >=1.60.0,<1.61.0' - - 'bioconductor-cghcall >=2.62.0,<2.63.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' + - 'bioconductor-cghcall >=2.64.0,<2.65.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - r-base test: commands: diff --git a/recipes/bioconductor-geneclassifiers/meta.yaml b/recipes/bioconductor-geneclassifiers/meta.yaml index 9e957638335a5..1bbd879fd921b 100644 --- a/recipes/bioconductor-geneclassifiers/meta.yaml +++ b/recipes/bioconductor-geneclassifiers/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "geneClassifiers" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1718d2e4ca0d91d6d292acb46a3c712a + md5: 79b7de2354913e5a91e6026f3f815a46 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneclassifiers", max_pin="x.x") }}' noarch: generic # Suggests: testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-geneexpressionsignature/meta.yaml b/recipes/bioconductor-geneexpressionsignature/meta.yaml index 8a88f5ad130c6..784b7d4b4cc8a 100644 --- a/recipes/bioconductor-geneexpressionsignature/meta.yaml +++ b/recipes/bioconductor-geneexpressionsignature/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "GeneExpressionSignature" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 13984cbd32793c3241e81ab4ca1fa33e + md5: ee82254ee781e3cd6657c89d94e052b3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneexpressionsignature", max_pin="x.x") }}' noarch: generic # Suggests: apcluster, GEOquery, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-genefilter/meta.yaml b/recipes/bioconductor-genefilter/meta.yaml index c39b2d22d053c..1e6cb5b05ad13 100644 --- a/recipes/bioconductor-genefilter/meta.yaml +++ b/recipes/bioconductor-genefilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.82.1" %} +{% set version = "1.84.0" %} {% set name = "genefilter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 06f347aaeeb8cb036bb7df7dfe1c67fb + md5: 15011d1662a58967aeb3e89f1f660e40 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genefilter", max_pin="x.x") }}' # Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - r-base - r-survival - libblas - liblapack run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - r-base - r-survival build: diff --git a/recipes/bioconductor-genefu/meta.yaml b/recipes/bioconductor-genefu/meta.yaml index 6480c3e1fad27..c9f8b815ed663 100644 --- a/recipes/bioconductor-genefu/meta.yaml +++ b/recipes/bioconductor-genefu/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "genefu" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c0fe8ccf39d5090209936c71224c2301 + md5: cfaef57b66d09a355ae7df0db21c107d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genefu", max_pin="x.x") }}' noarch: generic # Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival, BiocStyle, magick, rmarkdown requirements: host: - - 'bioconductor-aims >=1.32.0,<1.33.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-survcomp >=1.50.0,<1.51.0' + - 'bioconductor-aims >=1.34.0,<1.35.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-survcomp >=1.52.0,<1.53.0' - r-amap - r-base - r-ic10 - r-mclust run: - - 'bioconductor-aims >=1.32.0,<1.33.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-survcomp >=1.50.0,<1.51.0' + - 'bioconductor-aims >=1.34.0,<1.35.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-survcomp >=1.52.0,<1.53.0' - r-amap - r-base - r-ic10 diff --git a/recipes/bioconductor-genega/build.sh b/recipes/bioconductor-genega/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-genega/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genega/meta.yaml b/recipes/bioconductor-genega/meta.yaml new file mode 100644 index 0000000000000..296123222ca7a --- /dev/null +++ b/recipes/bioconductor-genega/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.52.0" %} +{% set name = "GeneGA" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3047f864af1845ce91869fc2560733c4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genega", max_pin="x.x") }}' + noarch: generic +requirements: + host: + - r-base + - r-hash + - r-seqinr + run: + - r-base + - r-hash + - r-seqinr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL version 2' + summary: 'Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm' + description: 'R based Genetic algorithm for gene expression optimization by considering both mRNA secondary structure and codon usage bias, GeneGA includes the information of highly expressed genes of almost 200 genomes. Meanwhile, Vienna RNA Package is needed to ensure GeneGA to function properly.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + diff --git a/recipes/bioconductor-genegeneinter/meta.yaml b/recipes/bioconductor-genegeneinter/meta.yaml index 03f30e758faf8..666e48ad08da2 100644 --- a/recipes/bioconductor-genegeneinter/meta.yaml +++ b/recipes/bioconductor-genegeneinter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "GeneGeneInteR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4764cc9239b96f79d0dd56ad6774ec44 + md5: 119efde24626155c173e9b24b5f2c9e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genegeneinter", max_pin="x.x") }}' requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' - r-base - r-data.table - r-factominer @@ -32,10 +33,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' - r-base - r-data.table - r-factominer diff --git a/recipes/bioconductor-genelendatabase/meta.yaml b/recipes/bioconductor-genelendatabase/meta.yaml index af599c18cb481..7619efdaf2175 100644 --- a/recipes/bioconductor-genelendatabase/meta.yaml +++ b/recipes/bioconductor-genelendatabase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "geneLenDataBase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3063a75a94ecd65185c3490a1baba601 + md5: c29099d3142aad07590e22ce37c6acf3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genelendatabase", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genelendatabase/post-link.sh b/recipes/bioconductor-genelendatabase/post-link.sh index 70d73fa6e2f73..5423b1add506e 100644 --- a/recipes/bioconductor-genelendatabase/post-link.sh +++ b/recipes/bioconductor-genelendatabase/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "genelendatabase-1.36.0" +installBiocDataPackage.sh "genelendatabase-1.38.0" diff --git a/recipes/bioconductor-genemeta/meta.yaml b/recipes/bioconductor-genemeta/meta.yaml index 79f0a57e7e661..46829e4dab0d2 100644 --- a/recipes/bioconductor-genemeta/meta.yaml +++ b/recipes/bioconductor-genemeta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "GeneMeta" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa838d8d2428d4d9337732db43dc84f8 + md5: 9d9d2d3dff0ee8a497ac86b5ef8ddac7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genemeta", max_pin="x.x") }}' noarch: generic # Suggests: RColorBrewer requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - r-base test: commands: diff --git a/recipes/bioconductor-genenetworkbuilder/meta.yaml b/recipes/bioconductor-genenetworkbuilder/meta.yaml index 2ef96e766b715..40e22076b24fd 100644 --- a/recipes/bioconductor-genenetworkbuilder/meta.yaml +++ b/recipes/bioconductor-genenetworkbuilder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "GeneNetworkBuilder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 17f9146e215456d82474c6afd253cbcd + md5: aedb0b143d59865acfad5ce4d635ff77 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genenetworkbuilder", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-htmlwidgets - r-plyr @@ -31,8 +32,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-htmlwidgets - r-plyr diff --git a/recipes/bioconductor-geneoverlap/meta.yaml b/recipes/bioconductor-geneoverlap/meta.yaml index f2da503615aa5..3912599cb2a10 100644 --- a/recipes/bioconductor-geneoverlap/meta.yaml +++ b/recipes/bioconductor-geneoverlap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "GeneOverlap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ddbc52b3f7cb42b24e0563c3d1039181 + md5: 0b5179a1183a82869935ca6c2c55aab3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneoverlap", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, BiocStyle requirements: diff --git a/recipes/bioconductor-geneplast.data.string.v91/meta.yaml b/recipes/bioconductor-geneplast.data.string.v91/meta.yaml index 8e04e55589622..db3e08458d885 100644 --- a/recipes/bioconductor-geneplast.data.string.v91/meta.yaml +++ b/recipes/bioconductor-geneplast.data.string.v91/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.6" %} {% set name = "geneplast.data.string.v91" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 86433f8489d9228c5ed73e2b75a55398 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneplast.data.string.v91", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-geneplast.data/meta.yaml b/recipes/bioconductor-geneplast.data/meta.yaml index a7873a0336455..20f45bdf6867b 100644 --- a/recipes/bioconductor-geneplast.data/meta.yaml +++ b/recipes/bioconductor-geneplast.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.99.6" %} +{% set version = "0.99.7" %} {% set name = "geneplast.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 08ddcdb9b1cf56dab5fe358c85fe1526 + md5: ef658e131138d87033fcd985c38cf45f build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneplast.data", max_pin="x.x") }}' noarch: generic # Suggests: geneplast, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-geneplast >=1.28.0,<1.29.0' + - 'bioconductor-treeio >=1.26.0,<1.27.0' + - r-ape - r-base + - r-dplyr + - r-igraph + - r-purrr + - r-readr + - r-tibble run: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-geneplast >=1.28.0,<1.29.0' + - 'bioconductor-treeio >=1.26.0,<1.27.0' + - r-ape - r-base + - r-dplyr + - r-igraph + - r-purrr + - r-readr + - r-tibble - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-geneplast.data/post-link.sh b/recipes/bioconductor-geneplast.data/post-link.sh index 970dff7551c64..879df13431c7f 100644 --- a/recipes/bioconductor-geneplast.data/post-link.sh +++ b/recipes/bioconductor-geneplast.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "geneplast.data-0.99.6" +installBiocDataPackage.sh "geneplast.data-0.99.7" diff --git a/recipes/bioconductor-geneplast/meta.yaml b/recipes/bioconductor-geneplast/meta.yaml index 5f40829a0c17c..c78eca2385118 100644 --- a/recipes/bioconductor-geneplast/meta.yaml +++ b/recipes/bioconductor-geneplast/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "geneplast" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 38d4e706cda6dee7ef9ca9e3bf4e7c23 + md5: 2cb6b3ec6dbd0978146ea5139cc06e60 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneplast", max_pin="x.x") }}' noarch: generic # Suggests: RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data, geneplast.data.string.v91, ggplot2, ggpubr, plyr requirements: diff --git a/recipes/bioconductor-geneplotter/meta.yaml b/recipes/bioconductor-geneplotter/meta.yaml index e1dd4c0c5091a..67627719ca339 100644 --- a/recipes/bioconductor-geneplotter/meta.yaml +++ b/recipes/bioconductor-geneplotter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "geneplotter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 58bd98605be308d6dd876b6d9fcb10b5 + md5: 29d4ec34db2e953fc9b7306f4d3b7733 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneplotter", max_pin="x.x") }}' noarch: generic -# Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db +# Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db, BiocStyle, knitr requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-lattice - r-rcolorbrewer run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-lattice - r-rcolorbrewer diff --git a/recipes/bioconductor-generecommender/meta.yaml b/recipes/bioconductor-generecommender/meta.yaml index fa96fc46b2655..55b5c7e1ae759 100644 --- a/recipes/bioconductor-generecommender/meta.yaml +++ b/recipes/bioconductor-generecommender/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "geneRecommender" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cafc0026010c2cd8bbe5b81fe0957e46 + md5: cd697c11912a8f48b5ceaf0abfbb206e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-generecommender", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-generegionscan/meta.yaml b/recipes/bioconductor-generegionscan/meta.yaml index a6525458e7681..c81ed957e93b0 100644 --- a/recipes/bioconductor-generegionscan/meta.yaml +++ b/recipes/bioconductor-generegionscan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "GeneRegionScan" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5c4b75b0cc7beb7f8b3ad6a3e52a93a5 + md5: 9b3e0cfd305d2db2aae5cfd4003e56a7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-generegionscan", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome, affy, AnnotationDbi requirements: host: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rcolorbrewer test: diff --git a/recipes/bioconductor-generxcluster/meta.yaml b/recipes/bioconductor-generxcluster/meta.yaml index fac45bf16a238..47294fc1e4560 100644 --- a/recipes/bioconductor-generxcluster/meta.yaml +++ b/recipes/bioconductor-generxcluster/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "geneRxCluster" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8ec6aade79eab7d5be66b90c84b9588e + md5: 61f7d4c5cd314cf84f8648b3097f65b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-generxcluster", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-geneselectmmd/meta.yaml b/recipes/bioconductor-geneselectmmd/meta.yaml index 576bc392a9563..ca85264568320 100644 --- a/recipes/bioconductor-geneselectmmd/meta.yaml +++ b/recipes/bioconductor-geneselectmmd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.44.1" %} +{% set version = "2.46.0" %} {% set name = "GeneSelectMMD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6552e99f88c6a84d5a34da69b07fb137 + md5: dd6cd07bbe095fca03ce4b134c1507b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneselectmmd", max_pin="x.x") }}' # Suggests: ALL requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-mass - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-mass build: diff --git a/recipes/bioconductor-genesis/meta.yaml b/recipes/bioconductor-genesis/meta.yaml index 7a545c218c54d..49123fdd70790 100644 --- a/recipes/bioconductor-genesis/meta.yaml +++ b/recipes/bioconductor-genesis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "GENESIS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 505a2cf97bef5db3db33657c43937f25 + md5: 909c6b6ea17b2de1716f3a5102caa0df build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genesis", max_pin="x.x") }}' # Suggests: CompQuadForm, COMPoissonReg, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gwastools >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' - - 'bioconductor-seqvartools >=1.38.0,<1.39.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gwastools >=1.48.0,<1.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - 'bioconductor-seqvartools >=1.40.0,<1.41.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' - r-base - r-data.table - r-igraph @@ -39,17 +40,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gwastools >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' - - 'bioconductor-seqvartools >=1.38.0,<1.39.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gwastools >=1.48.0,<1.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - 'bioconductor-seqvartools >=1.40.0,<1.41.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' - r-base - r-data.table - r-igraph diff --git a/recipes/bioconductor-genestructuretools/meta.yaml b/recipes/bioconductor-genestructuretools/meta.yaml index bf24c68b375c4..b68d6a11f06d2 100644 --- a/recipes/bioconductor-genestructuretools/meta.yaml +++ b/recipes/bioconductor-genestructuretools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GeneStructureTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 328a3a8ae004e92c4bf515807fe4878c + md5: 513385498b639ea6acc724bb3795de38 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genestructuretools", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-plyr - r-stringdist - r-stringr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-plyr diff --git a/recipes/bioconductor-genesummary/meta.yaml b/recipes/bioconductor-genesummary/meta.yaml index 1f56999b19e6c..3f59623599845 100644 --- a/recipes/bioconductor-genesummary/meta.yaml +++ b/recipes/bioconductor-genesummary/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.99.4" %} +{% set version = "0.99.6" %} {% set name = "GeneSummary" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 39ee728e42c42ccf200568c9c736b15c + md5: 9df029a96bf0fa5bb76ee8b8923c458c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genesummary", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, markdown, testthat requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genesummary/post-link.sh b/recipes/bioconductor-genesummary/post-link.sh index 536bca09030a3..542c1ac8a9539 100644 --- a/recipes/bioconductor-genesummary/post-link.sh +++ b/recipes/bioconductor-genesummary/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "genesummary-0.99.4" +installBiocDataPackage.sh "genesummary-0.99.6" diff --git a/recipes/bioconductor-genetclassifier/meta.yaml b/recipes/bioconductor-genetclassifier/meta.yaml index 4b1142313a1ff..d449d168bddc2 100644 --- a/recipes/bioconductor-genetclassifier/meta.yaml +++ b/recipes/bioconductor-genetclassifier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "geNetClassifier" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 225d0b3e450c41009734391c48982794 + md5: 7fed3e42e9ec93956b71960e271aa090 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genetclassifier", max_pin="x.x") }}' noarch: generic # Suggests: leukemiasEset, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ebarrays >=2.64.0,<2.65.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ebarrays >=2.66.0,<2.67.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' - r-base - r-e1071 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ebarrays >=2.64.0,<2.65.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ebarrays >=2.66.0,<2.67.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' - r-base - r-e1071 test: diff --git a/recipes/bioconductor-geneticsped/meta.yaml b/recipes/bioconductor-geneticsped/meta.yaml index 96bda76dee472..50a50397e73b2 100644 --- a/recipes/bioconductor-geneticsped/meta.yaml +++ b/recipes/bioconductor-geneticsped/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.1" %} +{% set version = "1.64.0" %} {% set name = "GeneticsPed" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 49e37937196a5ec28dafaa5f2c6c0dda + md5: 7d2a79c363e79459dd3edf3b4571f313 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneticsped", max_pin="x.x") }}' # Suggests: RUnit, gtools requirements: host: diff --git a/recipes/bioconductor-genetonic/meta.yaml b/recipes/bioconductor-genetonic/meta.yaml index 7d83f66968092..4c8e329fd8f3d 100644 --- a/recipes/bioconductor-genetonic/meta.yaml +++ b/recipes/bioconductor-genetonic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "GeneTonic" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 012923a30c9d452dd7c826205ecc487d + md5: efbbb39095cb7ff8af87ed47d058d8d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genetonic", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-backbone - r-base - 'r-bs4dash >=2.0.0' @@ -60,12 +61,12 @@ requirements: - r-viridis - r-visnetwork run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-backbone - r-base - 'r-bs4dash >=2.0.0' diff --git a/recipes/bioconductor-genextender/meta.yaml b/recipes/bioconductor-genextender/meta.yaml index 896b13b8fdf81..7676ab9d54672 100644 --- a/recipes/bioconductor-genextender/meta.yaml +++ b/recipes/bioconductor-genextender/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "geneXtendeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 39265282123addaf808976a865e308a1 + md5: 63ab36f83aa3d05bf932dc3c0e0c173a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genextender", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Pt.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-dplyr @@ -36,11 +37,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-genie3/meta.yaml b/recipes/bioconductor-genie3/meta.yaml index 9bbb0aef73375..bfc164119e27e 100644 --- a/recipes/bioconductor-genie3/meta.yaml +++ b/recipes/bioconductor-genie3/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "GENIE3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,13 +11,14 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37c69218e0e7a1e204d4762de1125c4f + md5: fb7d197e0e34175eba7dd31608aa67d6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ -# Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods + run_exports: '{{ pin_subpackage("bioconductor-genie3", max_pin="x.x") }}' +# Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods, BiocStyle requirements: host: - r-base diff --git a/recipes/bioconductor-genocn/meta.yaml b/recipes/bioconductor-genocn/meta.yaml index e52d58a4e1fff..5e9274f6a5ac2 100644 --- a/recipes/bioconductor-genocn/meta.yaml +++ b/recipes/bioconductor-genocn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "genoCN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b42af5b706f84966e90e5bc11fd129f + md5: ebc7fc5cb3b5c2bcd98718a7bcd95d6a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genocn", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-genomation/meta.yaml b/recipes/bioconductor-genomation/meta.yaml index c1238d45396e5..447d7838acc42 100644 --- a/recipes/bioconductor-genomation/meta.yaml +++ b/recipes/bioconductor-genomation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "genomation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9c6f6732f5e75f74f3f27c60de3640e5 + md5: 5453f50009f3f7227025431d4d10f4bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomation", max_pin="x.x") }}' # Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown, RUnit requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqpattern >=1.32.0,<1.33.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqpattern >=1.34.0,<1.35.0' - r-base - r-data.table - r-ggplot2 @@ -44,17 +45,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqpattern >=1.32.0,<1.33.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqpattern >=1.34.0,<1.35.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-genomationdata/meta.yaml b/recipes/bioconductor-genomationdata/meta.yaml index 0a5f89afe117f..8cb6a2198f75f 100644 --- a/recipes/bioconductor-genomationdata/meta.yaml +++ b/recipes/bioconductor-genomationdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "genomationData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4954915523744efa6d6b3be3feb376eb + md5: dc03eef7730719f7c66f72ca5e9915db build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomationdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genomationdata/post-link.sh b/recipes/bioconductor-genomationdata/post-link.sh index 8656156c48e81..e092bd607d41b 100644 --- a/recipes/bioconductor-genomationdata/post-link.sh +++ b/recipes/bioconductor-genomationdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "genomationdata-1.32.0" +installBiocDataPackage.sh "genomationdata-1.34.0" diff --git a/recipes/bioconductor-genomautomorphism/meta.yaml b/recipes/bioconductor-genomautomorphism/meta.yaml index 89852d60869f8..e16df4a231b76 100644 --- a/recipes/bioconductor-genomautomorphism/meta.yaml +++ b/recipes/bioconductor-genomautomorphism/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "GenomAutomorphism" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 53d0988019e357223e35df19cb2da04b + md5: 36ebcd90b454dc7450e875730537811b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomautomorphism", max_pin="x.x") }}' noarch: generic # Suggests: spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-doparallel @@ -35,13 +36,13 @@ requirements: - r-foreach - r-numbers run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-genomeinfodb/meta.yaml b/recipes/bioconductor-genomeinfodb/meta.yaml index 7cbd5ae154ce2..e033652eb641c 100644 --- a/recipes/bioconductor-genomeinfodb/meta.yaml +++ b/recipes/bioconductor-genomeinfodb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.1" %} +{% set version = "1.38.1" %} {% set name = "GenomeInfoDb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 635ff12af224e0f7902c35e3dc9166a8 + md5: 4bb1aef4ea2a6422141e3024e11b85e1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomeinfodb", max_pin="x.x") }}' noarch: generic # Suggests: GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rcurl run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rcurl test: diff --git a/recipes/bioconductor-genomeinfodbdata/meta.yaml b/recipes/bioconductor-genomeinfodbdata/meta.yaml index 4b55d8a8062a3..f4d61f874b1f7 100644 --- a/recipes/bioconductor-genomeinfodbdata/meta.yaml +++ b/recipes/bioconductor-genomeinfodbdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.10" %} +{% set version = "1.2.11" %} {% set name = "GenomeInfoDbData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ebd78c10d672c0eb6c893d6135bdeca9 + md5: 2a4cbfc2031992fed3c9445f450890a2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomeinfodbdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genomeinfodbdata/post-link.sh b/recipes/bioconductor-genomeinfodbdata/post-link.sh index af44f56f53dbb..42b37c9d4d1ca 100644 --- a/recipes/bioconductor-genomeinfodbdata/post-link.sh +++ b/recipes/bioconductor-genomeinfodbdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "genomeinfodbdata-1.2.10" +installBiocDataPackage.sh "genomeinfodbdata-1.2.11" diff --git a/recipes/bioconductor-genomeintervals/meta.yaml b/recipes/bioconductor-genomeintervals/meta.yaml index c885e2e647ba8..a0b7c1292199a 100644 --- a/recipes/bioconductor-genomeintervals/meta.yaml +++ b/recipes/bioconductor-genomeintervals/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "genomeIntervals" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61b757f3185a04ee582d4dc6e438049d + md5: c47b9bb1293b799a7ac75fef82f45589 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomeintervals", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-intervals >=0.14.0' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-intervals >=0.14.0' test: diff --git a/recipes/bioconductor-genomes/meta.yaml b/recipes/bioconductor-genomes/meta.yaml index dfc0cd2e55aa1..580bd6df948d1 100644 --- a/recipes/bioconductor-genomes/meta.yaml +++ b/recipes/bioconductor-genomes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.30.0" %} +{% set version = "3.32.0" %} {% set name = "genomes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 09a34e355a35b551f3729d436f8c0c68 + md5: 4c11ca2b7b1d4dfd1ffc178b1d9e87e2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomes", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml b/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml index 3bb6161ae7521..5c85ea0ef7f2e 100644 --- a/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml +++ b/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.6" %} {% set name = "genomewidesnp5Crlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: cc24140cd17758b8e09f4fe6c931526a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomewidesnp5crlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml b/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml index 86c00002d3b5a..097994bdee0b6 100644 --- a/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml +++ b/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.7" %} {% set name = "genomewidesnp6Crlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 13dd5aef3d814524896f2f3013beb78b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomewidesnp6crlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genomicalignments/meta.yaml b/recipes/bioconductor-genomicalignments/meta.yaml index 3342427f46583..7c60c29965ab8 100644 --- a/recipes/bioconductor-genomicalignments/meta.yaml +++ b/recipes/bioconductor-genomicalignments/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "GenomicAlignments" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9a9f56bd93dc00324d09899c195275c0 + md5: a5b7669b8ef7444527c2e43c49840014 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicalignments", max_pin="x.x") }}' # Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-genomicdatacommons/meta.yaml b/recipes/bioconductor-genomicdatacommons/meta.yaml index e07ffd0086e9d..fd0e442c7e4ad 100644 --- a/recipes/bioconductor-genomicdatacommons/meta.yaml +++ b/recipes/bioconductor-genomicdatacommons/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.2" %} +{% set version = "1.26.0" %} {% set name = "GenomicDataCommons" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ddc3c5db11c0776b0323b935b59b220 + md5: 6c945795f62ce3e0b470b07b892d3357 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicdatacommons", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools, BiocParallel, TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation, maftools, R.utils, data.table requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-dplyr - r-httr @@ -32,10 +33,11 @@ requirements: - r-readr - r-rlang - r-tibble + - r-tidyr - r-xml2 run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-dplyr - r-httr @@ -45,6 +47,7 @@ requirements: - r-readr - r-rlang - r-tibble + - r-tidyr - r-xml2 test: commands: diff --git a/recipes/bioconductor-genomicdistributions/meta.yaml b/recipes/bioconductor-genomicdistributions/meta.yaml index d1f2fedfc6aa1..fb182b1896bd6 100644 --- a/recipes/bioconductor-genomicdistributions/meta.yaml +++ b/recipes/bioconductor-genomicdistributions/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "GenomicDistributions" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 851fd18793882aecf6c63c84f9005ce9 + md5: 0b8c2d9df85f9884bb40e3fcd015c824 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicdistributions", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle, rmarkdown, GenomicDistributionsData requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-broom - r-data.table @@ -34,10 +35,10 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-broom - r-data.table diff --git a/recipes/bioconductor-genomicdistributionsdata/meta.yaml b/recipes/bioconductor-genomicdistributionsdata/meta.yaml index beca31a1d93ac..2cb349acc7580 100644 --- a/recipes/bioconductor-genomicdistributionsdata/meta.yaml +++ b/recipes/bioconductor-genomicdistributionsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "GenomicDistributionsData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 55e98f9b1fe5ee9ab222a5aa3866943a + md5: 84067e85ccbf3605bc1f5a1b7d8508ad build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicdistributionsdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-data.table run: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-data.table - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genomicdistributionsdata/post-link.sh b/recipes/bioconductor-genomicdistributionsdata/post-link.sh index cfc600cc2e0c5..08f6cdb719a09 100644 --- a/recipes/bioconductor-genomicdistributionsdata/post-link.sh +++ b/recipes/bioconductor-genomicdistributionsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "genomicdistributionsdata-1.8.0" +installBiocDataPackage.sh "genomicdistributionsdata-1.10.0" diff --git a/recipes/bioconductor-genomicfeatures/meta.yaml b/recipes/bioconductor-genomicfeatures/meta.yaml index e1a4b4a46bd5c..705fb92048fa5 100644 --- a/recipes/bioconductor-genomicfeatures/meta.yaml +++ b/recipes/bioconductor-genomicfeatures/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.1" %} +{% set version = "1.54.1" %} {% set name = "GenomicFeatures" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc478bb79f2628bc4c58de1ff8d33668 + md5: 863085394fd911039eca1603e6393c1d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicfeatures", max_pin="x.x") }}' noarch: generic # Suggests: RMariaDB, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, AnnotationFilter, RUnit, BiocStyle, knitr, markdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-dbi - r-rcurl - 'r-rsqlite >=2.0' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-dbi - r-rcurl diff --git a/recipes/bioconductor-genomicfiles/meta.yaml b/recipes/bioconductor-genomicfiles/meta.yaml index 36115b932696e..bb74043dc99a0 100644 --- a/recipes/bioconductor-genomicfiles/meta.yaml +++ b/recipes/bioconductor-genomicfiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "GenomicFiles" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,42 +11,43 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5de71058341eb16a65d666bbd2618e5a + md5: 7a58dc35c19ed34afe95d505d15db3f4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicfiles", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, RUnit, genefilter, deepSNV, snpStats, knitr, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-genomicinstability/meta.yaml b/recipes/bioconductor-genomicinstability/meta.yaml index a0061cbd2d814..01dd64732ea05 100644 --- a/recipes/bioconductor-genomicinstability/meta.yaml +++ b/recipes/bioconductor-genomicinstability/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "genomicInstability" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4f8709d46b6e2870ab2771f7099dc895 + md5: 0d7c244a904ea9286d4e965cddeaf2d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicinstability", max_pin="x.x") }}' noarch: generic # Suggests: SingleCellExperiment, ExperimentHub, pROC requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-mixtools run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-mixtools diff --git a/recipes/bioconductor-genomicinteractionnodes/meta.yaml b/recipes/bioconductor-genomicinteractionnodes/meta.yaml index a00e6f85b7526..322240c8d1118 100644 --- a/recipes/bioconductor-genomicinteractionnodes/meta.yaml +++ b/recipes/bioconductor-genomicinteractionnodes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "GenomicInteractionNodes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: da185a0ec49bd142ea1fb4c365599d45 + md5: bacb75bdd25ea06d5102c1ef2648c588 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicinteractionnodes", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-genomicinteractions/meta.yaml b/recipes/bioconductor-genomicinteractions/meta.yaml index 923de96395878..64e03a3fa483f 100644 --- a/recipes/bioconductor-genomicinteractions/meta.yaml +++ b/recipes/bioconductor-genomicinteractions/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "GenomicInteractions" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b50a2df0c508f4d8f54a739de6b9cfbe + md5: f4bccdd21d639ba8b9907ced202c0082 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicinteractions", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr @@ -39,16 +40,16 @@ requirements: - r-igraph - r-stringr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-genomicozone/meta.yaml b/recipes/bioconductor-genomicozone/meta.yaml index 307bc8ba7dd6a..6c9364066561c 100644 --- a/recipes/bioconductor-genomicozone/meta.yaml +++ b/recipes/bioconductor-genomicozone/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "GenomicOZone" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2ba77a29cf4e56d2fa6dcf8d38fc6982 + md5: c975a4b1c29d471efe90a5bba68247bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicozone", max_pin="x.x") }}' noarch: generic # Suggests: readxl, GEOquery, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-ckmeans.1d.dp >=4.3.0' - r-ggplot2 @@ -35,12 +36,12 @@ requirements: - r-plyr - r-rdpack run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-ckmeans.1d.dp >=4.3.0' - r-ggplot2 diff --git a/recipes/bioconductor-genomicplot/build.sh b/recipes/bioconductor-genomicplot/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-genomicplot/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genomicplot/meta.yaml b/recipes/bioconductor-genomicplot/meta.yaml new file mode 100644 index 0000000000000..de408ccbe32ff --- /dev/null +++ b/recipes/bioconductor-genomicplot/meta.yaml @@ -0,0 +1,87 @@ +{% set version = "1.0.0" %} +{% set name = "GenomicPlot" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ff0cee9d866f4cea69ee355bdac1f574 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicplot", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, AnnotationHub, AnnotationDbi, R.utils, Biobase, BSgenome.Hsapiens.UCSC.hg19, BiocFileCache, TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), BiocStyle, testthat +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomation >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rcas >=1.28.0,<1.29.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - r-base + - r-circlize + - 'r-cowplot >=1.1.1' + - r-dplyr + - 'r-ggplot2 >=3.3.5' + - r-ggplotify + - r-ggpubr + - 'r-ggsci >=2.9' + - 'r-ggsignif >=0.6.3' + - 'r-scales >=1.2.0' + - r-tidyr + - r-venndiagram + - r-viridis + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomation >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rcas >=1.28.0,<1.29.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - r-base + - r-circlize + - 'r-cowplot >=1.1.1' + - r-dplyr + - 'r-ggplot2 >=3.3.5' + - r-ggplotify + - r-ggpubr + - 'r-ggsci >=2.9' + - 'r-ggsignif >=0.6.3' + - 'r-scales >=1.2.0' + - r-tidyr + - r-venndiagram + - r-viridis +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Plot profiles of next generation sequencing data in genomic features' + description: 'Visualization of next generation sequencing (NGS) data is essential for interpreting high-throughput genomics experiment results. ''GenomicPlot'' facilitates plotting of NGS data in various formats (bam, bed, wig and bigwig); both coverage and enrichment over input can be computed and displayed with respect to genomic features (such as UTR, CDS, enhancer), and user defined genomic loci or regions. Statistical tests on signal intensity within user defined regions of interest can be performed and represented as boxplots or bar graphs. Parallel processing is used to speed up computation on multicore platforms. In addition to genomic plots which is suitable for displaying of coverage of genomic DNA (such as ChIPseq data), metagenomic (without introns) plots can also be made for RNAseq or CLIPseq data as well.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + diff --git a/recipes/bioconductor-genomicranges/meta.yaml b/recipes/bioconductor-genomicranges/meta.yaml index ab068d4503ce5..895ba1c23b7d2 100644 --- a/recipes/bioconductor-genomicranges/meta.yaml +++ b/recipes/bioconductor-genomicranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.1" %} {% set name = "GenomicRanges" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84ff182b349311589f7eece03f22a593 + md5: 19fe37133cae70c1c3a1a164e6c8eaed build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicranges", max_pin="x.x") }}' # Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-genomicscores/meta.yaml b/recipes/bioconductor-genomicscores/meta.yaml index e509330b4c55f..905f77be5004e 100644 --- a/recipes/bioconductor-genomicscores/meta.yaml +++ b/recipes/bioconductor-genomicscores/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.1" %} {% set name = "GenomicScores" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f26842350f8a2fc457e2f434dd415d0 + md5: 3f3be6b84303478d0d061081b2dcf261 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicscores", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, phastCons100way.UCSC.hg19, MafDb.1Kgenomes.phase1.hs37d5, SNPlocs.Hsapiens.dbSNP144.GRCh37, VariantAnnotation, TxDb.Hsapiens.UCSC.hg19.knownGene, gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader, data.table, DT, magrittr, shinydashboard requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-httr - r-xml run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-httr diff --git a/recipes/bioconductor-genomicstate/meta.yaml b/recipes/bioconductor-genomicstate/meta.yaml index 284f1eec4a561..641f4618a5d8d 100644 --- a/recipes/bioconductor-genomicstate/meta.yaml +++ b/recipes/bioconductor-genomicstate/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.15" %} {% set name = "GenomicState" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,37 +13,38 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 59c2d85a72f62cb12bad697fcbce5edc build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicstate", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, testthat (>= 2.1.0), glue, derfinderPlot, AnnotationHubData, RefManageR, GenomicRanges, covr requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genomicsupersignature/meta.yaml b/recipes/bioconductor-genomicsupersignature/meta.yaml index 8e732bb78eb01..231b42a102ceb 100644 --- a/recipes/bioconductor-genomicsupersignature/meta.yaml +++ b/recipes/bioconductor-genomicsupersignature/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "GenomicSuperSignature" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f66e1c6addf266e6aa5523260c415e1f + md5: ecb55ebec91620ff435715563d8ba304 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicsupersignature", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis, BiocStyle, testthat, forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-flextable @@ -34,11 +35,11 @@ requirements: - r-irlba - r-plotly run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-flextable diff --git a/recipes/bioconductor-genomictuples/meta.yaml b/recipes/bioconductor-genomictuples/meta.yaml index 6de63c4f52739..f664c665aa978 100644 --- a/recipes/bioconductor-genomictuples/meta.yaml +++ b/recipes/bioconductor-genomictuples/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "GenomicTuples" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 07e23d625f7467ef01b7eadaa4d6b19a + md5: 69e0c80982690604f35d9878f6640f37 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomictuples", max_pin="x.x") }}' # Suggests: testthat, knitr, BiocStyle, rmarkdown, covr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - 'r-rcpp >=0.11.2' - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - 'r-rcpp >=0.11.2' diff --git a/recipes/bioconductor-genproseq/meta.yaml b/recipes/bioconductor-genproseq/meta.yaml index b25797f9b5a78..0145607611a75 100644 --- a/recipes/bioconductor-genproseq/meta.yaml +++ b/recipes/bioconductor-genproseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.2" %} +{% set version = "1.6.0" %} {% set name = "GenProSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8dd618e58f4e340ab6af9604c2378b7 + md5: 15e772912f2019256df52d192edd5402 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genproseq", max_pin="x.x") }}' noarch: generic # Suggests: ggseqlogo, VAExprs, stringdist, knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-deeppincs >=1.8.0,<1.9.0' - - 'bioconductor-ttgsea >=1.8.0,<1.9.0' + - 'bioconductor-deeppincs >=1.10.0,<1.11.0' + - 'bioconductor-ttgsea >=1.10.0,<1.11.0' - r-base - r-catencoders - r-keras @@ -31,8 +32,8 @@ requirements: - r-tensorflow - r-word2vec run: - - 'bioconductor-deeppincs >=1.8.0,<1.9.0' - - 'bioconductor-ttgsea >=1.8.0,<1.9.0' + - 'bioconductor-deeppincs >=1.10.0,<1.11.0' + - 'bioconductor-ttgsea >=1.10.0,<1.11.0' - r-base - r-catencoders - r-keras diff --git a/recipes/bioconductor-genvisr/meta.yaml b/recipes/bioconductor-genvisr/meta.yaml index a380858ba5d5c..1358bedd1c531 100644 --- a/recipes/bioconductor-genvisr/meta.yaml +++ b/recipes/bioconductor-genvisr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.31.1" %} +{% set version = "1.34.0" %} {% set name = "GenVisR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b2548a895a14be3c9cabc9a5ddde0e33 + md5: f05fdc7c5736ba49ccf4eebcc1bc28ec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genvisr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-dbi @@ -44,17 +45,17 @@ requirements: - r-scales - r-viridis run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-dbi diff --git a/recipes/bioconductor-geodiff/meta.yaml b/recipes/bioconductor-geodiff/meta.yaml index 00b6d228b2275..71a1b028708ae 100644 --- a/recipes/bioconductor-geodiff/meta.yaml +++ b/recipes/bioconductor-geodiff/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "GeoDiff" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bfc04b2a9de212b7848725ccddd33b8a + md5: f719fddf3486b6aad1f36ca439b55114 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geodiff", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, dplyr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geomxtools >=3.4.0,<3.5.0' - - 'bioconductor-nanostringnctools >=1.8.0,<1.9.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geomxtools >=3.5.0,<3.6.0' + - 'bioconductor-nanostringnctools >=1.10.0,<1.11.0' - r-base - r-lme4 - r-matrix @@ -36,9 +37,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geomxtools >=3.4.0,<3.5.0' - - 'bioconductor-nanostringnctools >=1.8.0,<1.9.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geomxtools >=3.5.0,<3.6.0' + - 'bioconductor-nanostringnctools >=1.10.0,<1.11.0' - r-base - r-lme4 - r-matrix diff --git a/recipes/bioconductor-geoexplorer/meta.yaml b/recipes/bioconductor-geoexplorer/meta.yaml index 3bd3a3a3701cc..5002ad1d02b93 100644 --- a/recipes/bioconductor-geoexplorer/meta.yaml +++ b/recipes/bioconductor-geoexplorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "GEOexplorer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,64 +11,87 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e158f37de271fa9305fca41cf23b887a + md5: 213a1b499ce1d0640b267c8fb41e3204 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geoexplorer", max_pin="x.x") }}' noarch: generic -# Suggests: rmarkdown, knitr, usethis, testthat (>= 3.0.0) +# Suggests: rmarkdown, usethis, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base + - r-car - r-dt + - r-enrichr - r-factoextra - r-ggplot2 - r-heatmaply - r-htmltools - - r-maptools + - r-httr + - r-knitr + - r-markdown - r-pheatmap - r-plotly + - r-r.utils + - r-readxl - r-scales - r-shiny - - r-shinybs - r-shinybusy + - r-shinycssloaders - r-shinyheatmaply - r-stringr - r-umap + - r-xfun + - r-xml + - r-xml2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base + - r-car - r-dt + - r-enrichr - r-factoextra - r-ggplot2 - r-heatmaply - r-htmltools - - r-maptools + - r-httr + - r-knitr + - r-markdown - r-pheatmap - r-plotly + - r-r.utils + - r-readxl - r-scales - r-shiny - - r-shinybs - r-shinybusy + - r-shinycssloaders - r-shinyheatmaply - r-stringr - r-umap + - r-xfun + - r-xml + - r-xml2 test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'GEOexplorer: an R/Bioconductor package for gene expression analysis and visualisation' - description: 'GEOexplorer is a Shiny app that enables exploratory data analysis and differential gene expression of gene expression analysis on microarray gene expression datasets held on the GEO database. The outputs are interactive graphs that enable users to explore the results of the analysis. The development of GEOexplorer was made possible because of the excellent code provided by GEO2R (https: //www.ncbi.nlm.nih.gov/geo/geo2r/).' + summary: 'GEOexplorer: a webserver for gene expression analysis and visualisation' + description: 'GEOexplorer is a webserver and R/Bioconductor package and web application that enables users to perform gene expression analysis. The development of GEOexplorer was made possible because of the excellent code provided by GEO2R (https: //www.ncbi.nlm.nih.gov/geo/geo2r/).' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-geofastq/meta.yaml b/recipes/bioconductor-geofastq/meta.yaml index f15f6a8c9aab1..df5a172e6e81f 100644 --- a/recipes/bioconductor-geofastq/meta.yaml +++ b/recipes/bioconductor-geofastq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "GEOfastq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5c8bc6ae8926e6a803a5b1df7b3aa49 + md5: 339bd0c2f6a3f505457fc436997965a6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geofastq", max_pin="x.x") }}' noarch: generic # Suggests: BiocCheck, roxygen2, knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-geometadb/meta.yaml b/recipes/bioconductor-geometadb/meta.yaml index 7128400abbc16..dc42ecd5d1cfd 100644 --- a/recipes/bioconductor-geometadb/meta.yaml +++ b/recipes/bioconductor-geometadb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "GEOmetadb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4c6a5daf43e682620906dc428a4cb6cc + md5: 78e0bce3aa72836e1b126536221059c6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geometadb", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, dplyr, tm, wordcloud +# Suggests: knitr, rmarkdown, dplyr, dbplyr, tm, wordcloud requirements: host: - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base - r-rsqlite run: - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base - r-rsqlite test: diff --git a/recipes/bioconductor-geomxtools/meta.yaml b/recipes/bioconductor-geomxtools/meta.yaml index 754dd51f882eb..f8e4400a66844 100644 --- a/recipes/bioconductor-geomxtools/meta.yaml +++ b/recipes/bioconductor-geomxtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.0" %} +{% set version = "3.5.0" %} {% set name = "GeomxTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1977ed1034bb7ae33b6ac8ff3d18d896 + md5: 7ac9d92476a27e642927f906be2756db build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geomxtools", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-nanostringnctools >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-nanostringnctools >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr @@ -39,10 +40,10 @@ requirements: - r-seuratobject - r-stringr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-nanostringnctools >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-nanostringnctools >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-geoquery/meta.yaml b/recipes/bioconductor-geoquery/meta.yaml index 9282be967f594..d4246ec8b5641 100644 --- a/recipes/bioconductor-geoquery/meta.yaml +++ b/recipes/bioconductor-geoquery/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.68.0" %} +{% set version = "2.70.0" %} {% set name = "GEOquery" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 006c81971e10ad7dd94c875daa8a75af + md5: 5e8f233065ccb97c7cbb231479c936a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geoquery", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr, markdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-curl - r-data.table @@ -33,8 +34,8 @@ requirements: - r-tidyr - r-xml2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-curl - r-data.table @@ -61,4 +62,3 @@ extra: name: bioconductor-geoquery path: recipes/bioconductor-geoquery version: 2.48.0 - diff --git a/recipes/bioconductor-geosubmission/meta.yaml b/recipes/bioconductor-geosubmission/meta.yaml index b008d3688fa72..171c6416978eb 100644 --- a/recipes/bioconductor-geosubmission/meta.yaml +++ b/recipes/bioconductor-geosubmission/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "GEOsubmission" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 975c8bb07e646358a15315cdaf9665de + md5: 835a74433a1f0235676bf2d1012096af build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geosubmission", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-geotcgadata/meta.yaml b/recipes/bioconductor-geotcgadata/meta.yaml index 0571cea50acf6..4cba7f0dfdbe6 100644 --- a/recipes/bioconductor-geotcgadata/meta.yaml +++ b/recipes/bioconductor-geotcgadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.0" %} +{% set version = "2.2.0" %} {% set name = "GeoTcgaData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 463ef0f64e092337495a3f6da55b224a + md5: 653a353d37b0bcfbd892dfe12d420100 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geotcgadata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, DESeq2, S4Vectors, ChAMP, impute, tidyr, clusterProfiler, org.Hs.eg.db, edgeR, limma, quantreg, minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, dearseq, NOISeq, testthat (>= 3.0.0), CATT, TCGAbiolinks, enrichplot, GEOquery, BiocGenerics requirements: host: - - 'bioconductor-cqn >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topconfects >=1.16.0,<1.17.0' + - 'bioconductor-cqn >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topconfects >=1.18.0,<1.19.0' - r-base - r-data.table - r-plyr run: - - 'bioconductor-cqn >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topconfects >=1.16.0,<1.17.0' + - 'bioconductor-cqn >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topconfects >=1.18.0,<1.19.0' - r-base - r-data.table - r-plyr diff --git a/recipes/bioconductor-gep2pep/meta.yaml b/recipes/bioconductor-gep2pep/meta.yaml index d975a9a963484..8250b9d598084 100644 --- a/recipes/bioconductor-gep2pep/meta.yaml +++ b/recipes/bioconductor-gep2pep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "gep2pep" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 98994b580cde9a2d9431af735cf8c60c + md5: 0a8f1b44003eba297c44f8115f870df0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gep2pep", max_pin="x.x") }}' noarch: generic # Suggests: WriteXLS, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-digest - r-foreach @@ -31,9 +32,9 @@ requirements: - 'r-repo >=2.1.1' - r-xml run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-digest - r-foreach diff --git a/recipes/bioconductor-gesper/meta.yaml b/recipes/bioconductor-gesper/meta.yaml index 5604170a7054e..083aafb62aa77 100644 --- a/recipes/bioconductor-gesper/meta.yaml +++ b/recipes/bioconductor-gesper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.31.0" %} +{% set version = "1.34.0" %} {% set name = "gespeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71dc46d44b385b5443c76ae92caa659e + md5: b29c5440e5f853e993e3ca2df2eae3e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gesper", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-cellhts2 >=2.64.0,<2.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-cellhts2 >=2.66.0,<2.67.0' - r-base - r-doparallel - r-dplyr @@ -33,9 +34,9 @@ requirements: - r-matrix - r-reshape2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-cellhts2 >=2.64.0,<2.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-cellhts2 >=2.66.0,<2.67.0' - r-base - r-doparallel - r-dplyr diff --git a/recipes/bioconductor-getdee2/meta.yaml b/recipes/bioconductor-getdee2/meta.yaml index cae189ec65783..1ff51ddaf967c 100644 --- a/recipes/bioconductor-getdee2/meta.yaml +++ b/recipes/bioconductor-getdee2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "getDEE2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0afa472875b2b4ab0fa9805c79faa93e + md5: 5bae73105adbd3fba6517601379594c0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-getdee2", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-htm2txt run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-htm2txt test: diff --git a/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml b/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml index c17135a0cf002..6cda616d59429 100644 --- a/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml +++ b/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "GeuvadisTranscriptExpr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a37aba63d441f86e2b9eb68f34b92f0 + md5: 806de22bef0659a3b6f9db122d87a1d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geuvadistranscriptexpr", max_pin="x.x") }}' noarch: generic # Suggests: limma, rtracklayer, GenomicRanges, Rsamtools, VariantAnnotation, tools, BiocStyle, knitr, testthat requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh b/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh index f79467042f5fd..4723d360c3b55 100644 --- a/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh +++ b/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "geuvadistranscriptexpr-1.28.0" +installBiocDataPackage.sh "geuvadistranscriptexpr-1.30.0" diff --git a/recipes/bioconductor-geva/meta.yaml b/recipes/bioconductor-geva/meta.yaml index ff15ffe94bb29..05f850b06b2ec 100644 --- a/recipes/bioconductor-geva/meta.yaml +++ b/recipes/bioconductor-geva/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "geva" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aa42438cd413c4834920527e263b2549 + md5: ac06c7a9df29f5eb16fe102c81369ccb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geva", max_pin="x.x") }}' noarch: generic # Suggests: devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat (>= 3.0.0) requirements: diff --git a/recipes/bioconductor-gewist/meta.yaml b/recipes/bioconductor-gewist/meta.yaml index ae8837dbd5e53..5e0d3c2bb02e2 100644 --- a/recipes/bioconductor-gewist/meta.yaml +++ b/recipes/bioconductor-gewist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "GEWIST" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed8e6e450912a74621c1138d8e93d1b1 + md5: 3fe24d9c2f80cfc18dc41b37b118be6e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gewist", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-gg4way/build.sh b/recipes/bioconductor-gg4way/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gg4way/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gg4way/meta.yaml b/recipes/bioconductor-gg4way/meta.yaml new file mode 100644 index 0000000000000..835f32f2578c0 --- /dev/null +++ b/recipes/bioconductor-gg4way/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "1.0.0" %} +{% set name = "gg4way" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 500552b8ab9c3fc5cc58fcf56378a928 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gg4way", max_pin="x.x") }}' + noarch: generic +# Suggests: airway, BiocStyle, knitr, org.Hs.eg.db, rmarkdown, testthat +requirements: + host: + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - r-base + - r-dplyr + - r-ggplot2 + - r-ggrepel + - r-glue + - r-janitor + - r-magrittr + - r-purrr + - r-rlang + - r-scales + - r-stringr + - r-tibble + - r-tidyr + run: + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - r-base + - r-dplyr + - r-ggplot2 + - r-ggrepel + - r-glue + - r-janitor + - r-magrittr + - r-purrr + - r-rlang + - r-scales + - r-stringr + - r-tibble + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: '4way Plots of Differential Expression' + description: '4way plots enable a comparison of the logFC values from two contrasts of differential gene expression. The gg4way package creates 4way plots using the ggplot2 framework and supports popular Bioconductor objects. The package also provides information about the correlation between contrasts and significant genes of interest.' + license_file: LICENSE + diff --git a/recipes/bioconductor-ggbio/meta.yaml b/recipes/bioconductor-ggbio/meta.yaml index 006af33b86405..2ae0c837632c1 100644 --- a/recipes/bioconductor-ggbio/meta.yaml +++ b/recipes/bioconductor-ggbio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "ggbio" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7251a7fc9affae5f6ab3ea60c2446ecf + md5: de7ec73480f41c35fca2a8a758fbc7d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggbio", max_pin="x.x") }}' noarch: generic # Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggally - 'r-ggplot2 >=1.0.0' @@ -50,25 +51,25 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggally - 'r-ggplot2 >=1.0.0' diff --git a/recipes/bioconductor-ggcyto/meta.yaml b/recipes/bioconductor-ggcyto/meta.yaml index 910a8c1868c48..996e3aeda5742 100644 --- a/recipes/bioconductor-ggcyto/meta.yaml +++ b/recipes/bioconductor-ggcyto/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "ggcyto" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e01a55fb67a3cb3881d74e693049486b + md5: f50828f54e40b73d30aa3ac0ef06de21 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggcyto", max_pin="x.x") }}' noarch: generic # Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-ncdfflow >=2.46.0,<2.47.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' - r-base - r-data.table - - 'r-ggplot2 >=3.3.0' + - 'r-ggplot2 >=3.4.2' - r-gridextra - r-hexbin - r-plyr @@ -34,12 +35,12 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-ncdfflow >=2.46.0,<2.47.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' - r-base - r-data.table - - 'r-ggplot2 >=3.3.0' + - 'r-ggplot2 >=3.4.2' - r-gridextra - r-hexbin - r-plyr diff --git a/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml b/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml index 2ba9f67beb951..4bb5bc685c883 100644 --- a/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml +++ b/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.1" %} {% set name = "GGHumanMethCancerPanelv1.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,25 +13,26 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e8f4a37182b175fb33dd54f8093e6f52 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gghumanmethcancerpanelv1.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationforge >=1.42.0,<1.43.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationforge >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationforge >=1.42.0,<1.43.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationforge >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ggkegg/build.sh b/recipes/bioconductor-ggkegg/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ggkegg/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ggkegg/meta.yaml b/recipes/bioconductor-ggkegg/meta.yaml new file mode 100644 index 0000000000000..613b9acdc3d6a --- /dev/null +++ b/recipes/bioconductor-ggkegg/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.0.2" %} +{% set name = "ggkegg" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 747219ce420df145e10ee4b9243b17dc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggkegg", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, clusterProfiler, bnlearn, rmarkdown, BiocStyle, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - r-base + - r-cairo + - r-data.table + - r-dplyr + - r-getoptlong + - r-ggplot2 + - r-ggraph + - r-igraph + - r-magick + - r-patchwork + - r-shadowtext + - r-stringr + - r-tibble + - r-tidygraph + - r-xml + run: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - r-base + - r-cairo + - r-data.table + - r-dplyr + - r-getoptlong + - r-ggplot2 + - r-ggraph + - r-igraph + - r-magick + - r-patchwork + - r-shadowtext + - r-stringr + - r-tibble + - r-tidygraph + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'KEGG pathway visualization by ggplot2' + description: 'This package aims to import, parse, and analyze KEGG data such as KEGG PATHWAY and KEGG MODULE. The package supports visualizing KEGG information using ggplot2 and ggraph through using the grammar of graphics. The package enables the direct visualization of the results from various omics analysis packages.' + license_file: LICENSE + diff --git a/recipes/bioconductor-ggmanh/meta.yaml b/recipes/bioconductor-ggmanh/meta.yaml index 392707f7f661c..ab0bfd97963ec 100644 --- a/recipes/bioconductor-ggmanh/meta.yaml +++ b/recipes/bioconductor-ggmanh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "ggmanh" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d083b7129acff669ad41db946445336b + md5: dbbd8130e9ef70cb69c7e305af0c37d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggmanh", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0), markdown, GenomicRanges requirements: host: - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' - r-base - r-ggplot2 - r-ggrepel @@ -30,8 +31,8 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-ggmsa/meta.yaml b/recipes/bioconductor-ggmsa/meta.yaml index b45906c0af140..1ca7bf62799d6 100644 --- a/recipes/bioconductor-ggmsa/meta.yaml +++ b/recipes/bioconductor-ggmsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "ggmsa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 36c37e2d2e1f35d872621c6ff05af71a + md5: 1faea3aedc093bb7e151208c9a11b60c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggmsa", max_pin="x.x") }}' noarch: generic # Suggests: ggtreeExtra, ape, cowplot, knitr, BiocStyle, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-r4rna >=1.28.0,<1.29.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-r4rna >=1.30.0,<1.31.0' - r-aplot - r-base - r-dplyr @@ -36,9 +37,9 @@ requirements: - r-statebins - r-tidyr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-r4rna >=1.28.0,<1.29.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-r4rna >=1.30.0,<1.31.0' - r-aplot - r-base - r-dplyr diff --git a/recipes/bioconductor-ggpa/meta.yaml b/recipes/bioconductor-ggpa/meta.yaml index 5d4544485bfb5..5d4865bce21db 100644 --- a/recipes/bioconductor-ggpa/meta.yaml +++ b/recipes/bioconductor-ggpa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "GGPA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7d4034056bfd00a317aa0c6030422c9 + md5: 5c50ef4040a18ac94848d7c42484d28d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggpa", max_pin="x.x") }}' # Suggests: BiocStyle # SystemRequirements: GNU make requirements: diff --git a/recipes/bioconductor-ggsc/build.sh b/recipes/bioconductor-ggsc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ggsc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ggsc/meta.yaml b/recipes/bioconductor-ggsc/meta.yaml new file mode 100644 index 0000000000000..1441cbbb7e759 --- /dev/null +++ b/recipes/bioconductor-ggsc/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.0.2" %} +{% set name = "ggsc" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 4c0a1656e9943cadf436244c65b18242 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggsc", max_pin="x.x") }}' +# Suggests: aplot, BiocParallel, forcats, ggforce, ggnewscale, igraph, knitr, ks, Matrix, prettydoc, rmarkdown, scran, scater, scuttle, shadowtext, sf, SeuratObject, SpatialExperiment, STexampleData, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-cli + - r-dplyr + - r-ggplot2 + - r-rcpp + - r-rcpparmadillo + - r-rcppparallel + - r-rlang + - r-scattermore + - r-seurat + - r-tibble + - r-tidydr + - r-tidyr + - r-yulab.utils + - libblas + - liblapack + run: + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-cli + - r-dplyr + - r-ggplot2 + - r-rcpp + - r-rcpparmadillo + - r-rcppparallel + - r-rlang + - r-scattermore + - r-seurat + - r-tibble + - r-tidydr + - r-tidyr + - r-yulab.utils + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Visualizing Single Cell Data' + description: 'Useful functions to visualize single cell and spatial data. It supports both ''SingleCellExperiment'' and ''Seurat'' objects. It also supports visualizing the data using grammar of graphics implemented in ''ggplot2''.' + diff --git a/recipes/bioconductor-ggspavis/meta.yaml b/recipes/bioconductor-ggspavis/meta.yaml index a28c488446c59..eabd7d3e68766 100644 --- a/recipes/bioconductor-ggspavis/meta.yaml +++ b/recipes/bioconductor-ggspavis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "ggspavis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 94461bb1f26364b8f20a37ab49e8a4db + md5: c79337783dc059e449506a61c5579337 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggspavis", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix, scater, scran, uwot, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggside run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggside diff --git a/recipes/bioconductor-ggtree/meta.yaml b/recipes/bioconductor-ggtree/meta.yaml index 498ac6b1d2938..2a7d2de5144dc 100644 --- a/recipes/bioconductor-ggtree/meta.yaml +++ b/recipes/bioconductor-ggtree/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.8.0" %} +{% set version = "3.10.0" %} {% set name = "ggtree" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: efdbe433dc0a88c5582b0f69a0577865 + md5: 7e1894ce01245d811286b0ce1fbe8266 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggtree", max_pin="x.x") }}' noarch: generic # Suggests: emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, testthat, tibble, glue requirements: host: - - 'bioconductor-treeio >=1.24.0,<1.25.0' + - 'bioconductor-treeio >=1.26.0,<1.27.0' - r-ape - r-aplot - r-base @@ -34,10 +35,10 @@ requirements: - r-rlang - r-scales - r-tidyr - - 'r-tidytree >=0.3.9' + - 'r-tidytree >=0.4.5' - r-yulab.utils run: - - 'bioconductor-treeio >=1.24.0,<1.25.0' + - 'bioconductor-treeio >=1.26.0,<1.27.0' - r-ape - r-aplot - r-base @@ -50,7 +51,7 @@ requirements: - r-rlang - r-scales - r-tidyr - - 'r-tidytree >=0.3.9' + - 'r-tidytree >=0.4.5' - r-yulab.utils test: commands: diff --git a/recipes/bioconductor-ggtreedendro/meta.yaml b/recipes/bioconductor-ggtreedendro/meta.yaml index 7291d3ea96fcc..262bc36ce9821 100644 --- a/recipes/bioconductor-ggtreedendro/meta.yaml +++ b/recipes/bioconductor-ggtreedendro/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ggtreeDendro" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 426abd017dfad28e2752ee6943d1f345 + md5: e5839d466e08665eb2475a99fb74e833 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggtreedendro", max_pin="x.x") }}' noarch: generic # Suggests: aplot, cluster, knitr, MASS, mdendro, prettydoc, pvclust, rmarkdown, testthat (>= 3.0.0), treeio, yulab.utils requirements: host: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-base - r-ggplot2 - r-tidytree run: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-base - r-ggplot2 - r-tidytree diff --git a/recipes/bioconductor-ggtreeextra/meta.yaml b/recipes/bioconductor-ggtreeextra/meta.yaml index e16219e3ef5e3..43bbe1f1f6038 100644 --- a/recipes/bioconductor-ggtreeextra/meta.yaml +++ b/recipes/bioconductor-ggtreeextra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ggtreeExtra" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4c39f713cf930c99e6f7106cd96159a8 + md5: 0bfd8a30c6fbd323763722927d30296a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggtreeextra", max_pin="x.x") }}' noarch: generic # Suggests: treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc, markdown, testthat (>= 3.0.0), pillar requirements: host: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-base - r-cli - r-ggnewscale @@ -30,7 +31,7 @@ requirements: - r-rlang - 'r-tidytree >=0.3.9' run: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-base - r-cli - r-ggnewscale diff --git a/recipes/bioconductor-gigsea/meta.yaml b/recipes/bioconductor-gigsea/meta.yaml index f2495f207ccb8..0e0d6eec70f7b 100644 --- a/recipes/bioconductor-gigsea/meta.yaml +++ b/recipes/bioconductor-gigsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "GIGSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e98747c8ff218c3ef2d5590f055c1084 + md5: 1325b20f84be334e607b7ebec7db0d07 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gigsea", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-gigseadata/meta.yaml b/recipes/bioconductor-gigseadata/meta.yaml index caf5e26c0c2d1..6430624693d11 100644 --- a/recipes/bioconductor-gigseadata/meta.yaml +++ b/recipes/bioconductor-gigseadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "GIGSEAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad905645333890eafd314cdac44f793a + md5: 470cdb6073d9af3d23056b55e6b8c98d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gigseadata", max_pin="x.x") }}' noarch: generic # Suggests: GIGSEA, knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gigseadata/post-link.sh b/recipes/bioconductor-gigseadata/post-link.sh index 19ba27f282877..ee46d067c6e87 100644 --- a/recipes/bioconductor-gigseadata/post-link.sh +++ b/recipes/bioconductor-gigseadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gigseadata-1.18.0" +installBiocDataPackage.sh "gigseadata-1.20.0" diff --git a/recipes/bioconductor-girafe/meta.yaml b/recipes/bioconductor-girafe/meta.yaml index ca748fc02114f..8b2eb662a4fcf 100644 --- a/recipes/bioconductor-girafe/meta.yaml +++ b/recipes/bioconductor-girafe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "girafe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4d95b1c6c1147fd8833e62fbab42973b + md5: 4cf228e6d7f73cf97c923f1c349fb6c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-girafe", max_pin="x.x") }}' # Suggests: MASS, org.Mm.eg.db, RColorBrewer requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeintervals >=1.56.0,<1.57.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeintervals >=1.58.0,<1.59.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - 'r-intervals >=0.13.1' - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeintervals >=1.56.0,<1.57.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeintervals >=1.58.0,<1.59.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - 'r-intervals >=0.13.1' build: diff --git a/recipes/bioconductor-gispa/meta.yaml b/recipes/bioconductor-gispa/meta.yaml index 78995642ea117..7e2d4a3f793cc 100644 --- a/recipes/bioconductor-gispa/meta.yaml +++ b/recipes/bioconductor-gispa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "GISPA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e309fc9a17caf08ad92b993a0cdd90ad + md5: 012a529b5359b149705fa54cb75c1818 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gispa", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-changepoint - r-data.table @@ -33,9 +34,9 @@ requirements: - r-plyr - r-scatterplot3d run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-changepoint - r-data.table diff --git a/recipes/bioconductor-glad/build.sh b/recipes/bioconductor-glad/build.sh index 78ffa6cbcade8..c74d5641a31dc 100644 --- a/recipes/bioconductor-glad/build.sh +++ b/recipes/bioconductor-glad/build.sh @@ -8,5 +8,5 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -touch GLAD -$R CMD INSTALL --build . +sed -i.bak 's/^ac_unique_file="GLAD"/ac_unique_file="NAMESPACE"/' configure +$R CMD INSTALL --build --configure-vars='GSL_LIBS="-L$PREFIX/lib -lgsl -lgslcblas -lm"' . \ No newline at end of file diff --git a/recipes/bioconductor-glad/meta.yaml b/recipes/bioconductor-glad/meta.yaml index 28765c4e9b1b2..98a43342fbfd0 100644 --- a/recipes/bioconductor-glad/meta.yaml +++ b/recipes/bioconductor-glad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.64.0" %} +{% set version = "2.66.0" %} {% set name = "GLAD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a0dc76c1fc2b069084b16a9150611ba6 + md5: f222e07624fb8b1c4780a4960b0f2008 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-glad", max_pin="x.x") }}' # SystemRequirements: gsl. Note: users should have GSL installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. requirements: host: diff --git a/recipes/bioconductor-gladiatox/meta.yaml b/recipes/bioconductor-gladiatox/meta.yaml index 5290df2495cf9..75bf22493ac9e 100644 --- a/recipes/bioconductor-gladiatox/meta.yaml +++ b/recipes/bioconductor-gladiatox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "GladiaTOX" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b642344445e36310ab07ddd46285a9a + md5: a8affcce15bf1f5e9d03220e0de3fbe9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gladiatox", max_pin="x.x") }}' noarch: generic # Suggests: roxygen2, knitr, rmarkdown, testthat, BiocStyle requirements: @@ -31,7 +32,7 @@ requirements: - r-rcolorbrewer - r-rcurl - r-rjsonio - - r-rmysql + - r-rmariadb - r-rsqlite - r-stringr - r-tidyr @@ -48,7 +49,7 @@ requirements: - r-rcolorbrewer - r-rcurl - r-rjsonio - - r-rmysql + - r-rmariadb - r-rsqlite - r-stringr - r-tidyr diff --git a/recipes/bioconductor-glimma/meta.yaml b/recipes/bioconductor-glimma/meta.yaml index 7d696aad81cf4..32dc9bba1cbf7 100644 --- a/recipes/bioconductor-glimma/meta.yaml +++ b/recipes/bioconductor-glimma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "Glimma" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f127e3ae006335a13734d71ef7aa2640 + md5: bea9aeee00dca519586661d33ba8dc74 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-glimma", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle, IRanges, GenomicRanges, pryr, AnnotationHub, scRNAseq, scater, scran requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-htmlwidgets - r-jsonlite run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-htmlwidgets - r-jsonlite @@ -44,8 +45,8 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'Interactive HTML graphics' - description: 'This package generates interactive visualisations for analysis of RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an HTML page. The interactions are built on top of the popular static representations of analysis results in order to provide additional information.' + summary: 'Interactive visualizations for gene expression analysis' + description: 'This package produces interactive visualizations for RNA-seq data analysis, utilizing output from limma, edgeR, or DESeq2. It produces interactive htmlwidgets versions of popular RNA-seq analysis plots to enhance the exploration of analysis results by overlaying interactive features. The plots can be viewed in a web browser or embedded in notebook documents.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: identifiers: diff --git a/recipes/bioconductor-glmgampoi/meta.yaml b/recipes/bioconductor-glmgampoi/meta.yaml index d38b42353b0f4..68d5da5ce2f73 100644 --- a/recipes/bioconductor-glmgampoi/meta.yaml +++ b/recipes/bioconductor-glmgampoi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.2" %} +{% set version = "1.14.0" %} {% set name = "glmGamPoi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 299c9cff01d7696e4e6cb23db4c12920 + md5: ff74c3d78a7edc7d0a5f4521f7c5b9b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-glmgampoi", max_pin="x.x") }}' # Suggests: testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, beachmat, MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown, BiocStyle, TENxPBMCData, muscData, scran, Matrix, dplyr # SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrixstats - r-rcpp @@ -38,14 +39,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrixstats - r-rcpp diff --git a/recipes/bioconductor-glmsparsenet/meta.yaml b/recipes/bioconductor-glmsparsenet/meta.yaml index 039338c617606..b0bfedfe3022a 100644 --- a/recipes/bioconductor-glmsparsenet/meta.yaml +++ b/recipes/bioconductor-glmsparsenet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "glmSparseNet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 19e521eeaadf8bbfeda74bdb69d0297c + md5: b029a96bf3a653a8a3c24d764c841512 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-glmsparsenet", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, survival, survcomp, pROC, VennDiagram, BiocStyle, curatedTCGAData, TCGAutils requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-digest - r-dplyr @@ -40,9 +41,9 @@ requirements: - r-stringr - r-survminer run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-digest - r-dplyr diff --git a/recipes/bioconductor-globalancova/meta.yaml b/recipes/bioconductor-globalancova/meta.yaml index 60d2696f5ca30..84aa7d322bd84 100644 --- a/recipes/bioconductor-globalancova/meta.yaml +++ b/recipes/bioconductor-globalancova/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.18.0" %} +{% set version = "4.20.0" %} {% set name = "GlobalAncova" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6236d46ff193ab24e7ab0d85272b0ca3 + md5: 4fcc19ebc2bba1f610912cde1745b549 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-globalancova", max_pin="x.x") }}' # Suggests: GO.db, golubEsets, hu6800.db, vsn, Rgraphviz requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-globaltest >=5.54.0,<5.55.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-globaltest >=5.56.0,<5.57.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-corpcor - r-dendextend @@ -32,11 +33,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-globaltest >=5.54.0,<5.55.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-globaltest >=5.56.0,<5.57.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-corpcor - r-dendextend diff --git a/recipes/bioconductor-globalseq/meta.yaml b/recipes/bioconductor-globalseq/meta.yaml index f6cc742c6512c..0d5af193580c1 100644 --- a/recipes/bioconductor-globalseq/meta.yaml +++ b/recipes/bioconductor-globalseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "globalSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f1df637d4f75b814a55fc9025ea33769 + md5: 1b427214cf1345b8d75ba69dc02adb77 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-globalseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, SummarizedExperiment, S4Vectors requirements: diff --git a/recipes/bioconductor-globaltest/meta.yaml b/recipes/bioconductor-globaltest/meta.yaml index 7b419c131f313..7cd5098ec0714 100644 --- a/recipes/bioconductor-globaltest/meta.yaml +++ b/recipes/bioconductor-globaltest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "5.54.0" %} +{% set version = "5.56.0" %} {% set name = "globaltest" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0dee254d67879077ccb02fbe682eaed6 + md5: ca389a7105fc08bc6172ce755d842a31 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-globaltest", max_pin="x.x") }}' noarch: generic # Suggests: vsn, golubEsets, KEGGREST, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS, boot, rpart, mstate requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-survival run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-survival test: diff --git a/recipes/bioconductor-gloscope/build.sh b/recipes/bioconductor-gloscope/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gloscope/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gloscope/meta.yaml b/recipes/bioconductor-gloscope/meta.yaml new file mode 100644 index 0000000000000..c2c78a32218ab --- /dev/null +++ b/recipes/bioconductor-gloscope/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.0.0" %} +{% set name = "GloScope" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 00ab18ecdd0a5768690b841f2f2448e5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gloscope", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown, zellkonverter +requirements: + host: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - r-base + - r-fnn + - r-ggplot2 + - r-mass + - r-mclust + - r-mvnfast + - r-rann + - r-rlang + run: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - r-base + - r-fnn + - r-ggplot2 + - r-mass + - r-mclust + - r-mvnfast + - r-rann + - r-rlang +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Population-level Representation on scRNA-Seq data' + description: 'This package aims at representing and summarizing the entire single-cell profile of a sample. It allows researchers to perform important bioinformatic analyses at the sample-level such as visualization and quality control. The main functions Estimate sample distribution and calculate statistical divergence among samples, and visualize the distance matrix through MDS plots.' + diff --git a/recipes/bioconductor-gmapr/build.sh b/recipes/bioconductor-gmapr/build.sh index aa6ce291ac3aa..3c9546c924fe5 100644 --- a/recipes/bioconductor-gmapr/build.sh +++ b/recipes/bioconductor-gmapr/build.sh @@ -10,4 +10,4 @@ CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars # Remove object files (if present) that should not be in the source tarball rm -f src/samtools/*.[oa] -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gmapr/meta.yaml b/recipes/bioconductor-gmapr/meta.yaml index 862fc6f100cdd..45159a2ac666f 100644 --- a/recipes/bioconductor-gmapr/meta.yaml +++ b/recipes/bioconductor-gmapr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "gmapR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,47 +11,48 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dbe4da38f2fda8cbcef73cae97c1ee28 + md5: 3398b4dd3f0c05c2a748f9ecb0a28c41 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gmapr", max_pin="x.x") }}' # Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-gmicr/meta.yaml b/recipes/bioconductor-gmicr/meta.yaml index d7eb8e039cc91..9e030aeb49653 100644 --- a/recipes/bioconductor-gmicr/meta.yaml +++ b/recipes/bioconductor-gmicr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "GmicR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e089a259f66dcf368cf5bb49c102e1ea + md5: 13466f8e105c84116d73b39d38eed3cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gmicr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-ape - r-base - r-bnlearn @@ -40,12 +41,12 @@ requirements: - r-shiny - r-wgcna run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-ape - r-base - r-bnlearn diff --git a/recipes/bioconductor-gmoviz/meta.yaml b/recipes/bioconductor-gmoviz/meta.yaml index 22c92bf2ca7e9..1a7e6dd17007e 100644 --- a/recipes/bioconductor-gmoviz/meta.yaml +++ b/recipes/bioconductor-gmoviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "gmoviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,44 +11,45 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c48c8c41b980373fa3c764e4834ff8e3 + md5: 19164c63f0edf9ae927bef7bae0b1a12 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gmoviz", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle, BiocManager requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-circlize - r-colorspace - r-gridbase - r-pracma run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-circlize - r-colorspace diff --git a/recipes/bioconductor-gmrp/meta.yaml b/recipes/bioconductor-gmrp/meta.yaml index d320ffafc1366..b548aa45a5dea 100644 --- a/recipes/bioconductor-gmrp/meta.yaml +++ b/recipes/bioconductor-gmrp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "GMRP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2ee7fe352b10cf36aef04482614d7ac0 + md5: d33e226ce1134e0f16d4d531fadc7339 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gmrp", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BiocGenerics requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-diagram - r-plotrix run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-diagram - r-plotrix diff --git a/recipes/bioconductor-gnet2/meta.yaml b/recipes/bioconductor-gnet2/meta.yaml index 5c0d53071785b..c4a8c0c2f55e4 100644 --- a/recipes/bioconductor-gnet2/meta.yaml +++ b/recipes/bioconductor-gnet2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "GNET2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3764cd241d02bfc2308facf2cfdb800d + md5: 06382e36858e9d55d44aabba748d49b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gnet2", max_pin="x.x") }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-diagrammer - r-dplyr @@ -33,7 +34,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-diagrammer - r-dplyr diff --git a/recipes/bioconductor-gnosis/build.sh b/recipes/bioconductor-gnosis/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gnosis/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gnosis/meta.yaml b/recipes/bioconductor-gnosis/meta.yaml new file mode 100644 index 0000000000000..ed68757eb4d4d --- /dev/null +++ b/recipes/bioconductor-gnosis/meta.yaml @@ -0,0 +1,91 @@ +{% set version = "1.0.0" %} +{% set name = "GNOSIS" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e3cbf07a76da1ae0aa6e669bad2cb778 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gnosis", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-cbioportaldata >=2.14.0,<2.15.0' + - 'bioconductor-maftools >=2.18.0,<2.19.0' + - r-base + - r-car + - r-comparegroups + - r-dashboardthemes + - r-desctools + - r-dt + - r-fabricatr + - r-fontawesome + - r-magrittr + - r-operator.tools + - r-partykit + - r-rcolorbrewer + - r-reshape2 + - r-rpart + - r-rstatix + - r-shiny + - r-shinycssloaders + - r-shinydashboard + - r-shinydashboardplus + - r-shinyjs + - r-shinylogs + - r-shinymeta + - r-shinywidgets + - r-survival + - r-survminer + - r-tidyverse + run: + - 'bioconductor-cbioportaldata >=2.14.0,<2.15.0' + - 'bioconductor-maftools >=2.18.0,<2.19.0' + - r-base + - r-car + - r-comparegroups + - r-dashboardthemes + - r-desctools + - r-dt + - r-fabricatr + - r-fontawesome + - r-magrittr + - r-operator.tools + - r-partykit + - r-rcolorbrewer + - r-reshape2 + - r-rpart + - r-rstatix + - r-shiny + - r-shinycssloaders + - r-shinydashboard + - r-shinydashboardplus + - r-shinyjs + - r-shinylogs + - r-shinymeta + - r-shinywidgets + - r-survival + - r-survminer + - r-tidyverse +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Genomics explorer using statistical and survival analysis in R' + description: 'GNOSIS incorporates a range of R packages enabling users to efficiently explore and visualise clinical and genomic data obtained from cBioPortal. GNOSIS uses an intuitive GUI and multiple tab panels supporting a range of functionalities. These include data upload and initial exploration, data recoding and subsetting, multiple visualisations, survival analysis, statistical analysis and mutation analysis, in addition to facilitating reproducible research.' + license_file: LICENSE + diff --git a/recipes/bioconductor-go.db/meta.yaml b/recipes/bioconductor-go.db/meta.yaml index 3742220d4eb29..9311de2ff1dc9 100644 --- a/recipes/bioconductor-go.db/meta.yaml +++ b/recipes/bioconductor-go.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "GO.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f278f3cb015e04ead1cc3d982a3fd1b3 + md5: b23522167263afc45a9b115d01632cb1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-go.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-go.db/post-link.sh b/recipes/bioconductor-go.db/post-link.sh index 1a7bbea2aba0f..f1547533d3cd4 100644 --- a/recipes/bioconductor-go.db/post-link.sh +++ b/recipes/bioconductor-go.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "go.db-3.17.0" +installBiocDataPackage.sh "go.db-3.18.0" diff --git a/recipes/bioconductor-goexpress/meta.yaml b/recipes/bioconductor-goexpress/meta.yaml index 6bb8170489ffb..2ad3dd05dc553 100644 --- a/recipes/bioconductor-goexpress/meta.yaml +++ b/recipes/bioconductor-goexpress/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "GOexpress" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ecb2bcff2560c6f61a1da2407697903 + md5: b313b2555495c3d3fc5674120b7bb01b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-goexpress", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base - 'r-ggplot2 >=0.9.0' - 'r-gplots >=2.13.0' @@ -31,8 +32,8 @@ requirements: - 'r-rcurl >=1.95' - 'r-stringr >=0.6.2' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base - 'r-ggplot2 >=0.9.0' - 'r-gplots >=2.13.0' diff --git a/recipes/bioconductor-gofuncr/meta.yaml b/recipes/bioconductor-gofuncr/meta.yaml index 324860ad1e003..71d2d0bf7bc4f 100644 --- a/recipes/bioconductor-gofuncr/meta.yaml +++ b/recipes/bioconductor-gofuncr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GOfuncR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a81fecf10720e4ce20c7c4648b7fe1d + md5: d84c71ebda463871117ea00394d551ce build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gofuncr", max_pin="x.x") }}' # Suggests: Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-gtools >=3.5.0' - 'r-mapplots >=1.5' @@ -31,9 +32,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-gtools >=3.5.0' - 'r-mapplots >=1.5' diff --git a/recipes/bioconductor-golubesets/meta.yaml b/recipes/bioconductor-golubesets/meta.yaml index 181cf4e04483c..07b2c538aa5a1 100644 --- a/recipes/bioconductor-golubesets/meta.yaml +++ b/recipes/bioconductor-golubesets/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "golubEsets" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec7f4855c5a77d3ea3503a1102910a0c + md5: 49e3527c00f06c189a048a6b871f3d54 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-golubesets", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-golubesets/post-link.sh b/recipes/bioconductor-golubesets/post-link.sh index 9a15a0dca0cff..2a6d36332ced8 100644 --- a/recipes/bioconductor-golubesets/post-link.sh +++ b/recipes/bioconductor-golubesets/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "golubesets-1.42.0" +installBiocDataPackage.sh "golubesets-1.44.0" diff --git a/recipes/bioconductor-gopro/meta.yaml b/recipes/bioconductor-gopro/meta.yaml index 469642baa8eaf..28fc93fb2f3c8 100644 --- a/recipes/bioconductor-gopro/meta.yaml +++ b/recipes/bioconductor-gopro/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "GOpro" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b0112bd7b59baf1aae2c8bf7f3496600 + md5: c92dbcab08a7cdac3ee8ee6c28c6dc78 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gopro", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bh - r-dendextend @@ -35,12 +36,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bh - r-dendextend diff --git a/recipes/bioconductor-goprofiles/meta.yaml b/recipes/bioconductor-goprofiles/meta.yaml index 0d594871e1c39..f8cc90bc58c9f 100644 --- a/recipes/bioconductor-goprofiles/meta.yaml +++ b/recipes/bioconductor-goprofiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "goProfiles" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4da528658f42681fb65e8bc785b39804 + md5: ff2a664ff7284cf03e9caf932ad86d63 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-goprofiles", max_pin="x.x") }}' noarch: generic # Suggests: org.Hs.eg.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-compquadform - r-stringr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-compquadform - r-stringr diff --git a/recipes/bioconductor-gosemsim/meta.yaml b/recipes/bioconductor-gosemsim/meta.yaml index 028e3acfdbd90..186111722022f 100644 --- a/recipes/bioconductor-gosemsim/meta.yaml +++ b/recipes/bioconductor-gosemsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "GOSemSim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d6dc404ac64c03d0d12f932b2133411 + md5: ea9c9c6e25cc507a2b5cff51f268d848 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat, ROCR + run_exports: '{{ pin_subpackage("bioconductor-gosemsim", max_pin="x.x") }}' +# Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat, tidyr, tidyselect, ROCR requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-rcpp + - r-rlang - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-rcpp + - r-rlang build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-goseq/meta.yaml b/recipes/bioconductor-goseq/meta.yaml index 3ff69348277b8..ee94c1535f052 100644 --- a/recipes/bioconductor-goseq/meta.yaml +++ b/recipes/bioconductor-goseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "goseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4607e3167133fc26bacc97e215fe0138 + md5: 4c39d7fbb51594a70dd3e54b1bc10375 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-goseq", max_pin="x.x") }}' noarch: generic # Suggests: edgeR, org.Hs.eg.db, rtracklayer requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genelendatabase >=1.36.0,<1.37.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genelendatabase >=1.38.0,<1.39.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-biasedurn - r-mgcv run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genelendatabase >=1.36.0,<1.37.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genelendatabase >=1.38.0,<1.39.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-biasedurn - r-mgcv diff --git a/recipes/bioconductor-gosim/meta.yaml b/recipes/bioconductor-gosim/meta.yaml index a9cfe88fee26d..885c23bd98f98 100644 --- a/recipes/bioconductor-gosim/meta.yaml +++ b/recipes/bioconductor-gosim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "GOSim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02736c160f8b114ae80c27bd92d14dfc + md5: 2fb07a8f5ac4b386b5063f52486bb82b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gosim", max_pin="x.x") }}' requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-cluster - r-corpcor @@ -35,13 +36,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-cluster - r-corpcor diff --git a/recipes/bioconductor-gosorensen/meta.yaml b/recipes/bioconductor-gosorensen/meta.yaml index f882b2d957f27..a6ccadcbdd826 100644 --- a/recipes/bioconductor-gosorensen/meta.yaml +++ b/recipes/bioconductor-gosorensen/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "goSorensen" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3711f68b84fabd2730039daa4f81b38 + md5: 8fa5cc982341291dd857ab340abe4c73 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gosorensen", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-goprofiles >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-goprofiles >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base + - r-stringr run: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-goprofiles >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-goprofiles >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base + - r-stringr test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,6 +42,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)' - description: 'This package implements inferential methods to compare gene lists (in this first release, to prove equivalence) in terms of their biological meaning as expressed in the GO. The compared gene lists are characterized by cross-tabulation frequency tables of enriched GO items. Dissimilarity between gene lists is evaluated using the Sorensen-Dice index. The fundamental guiding principle is that two gene lists are taken as similar if they share a great proportion of common enriched GO items.' + description: 'This package implements inferential methods to compare gene lists in terms of their biological meaning as expressed in the GO. The compared gene lists are characterized by cross-tabulation frequency tables of enriched GO items. Dissimilarity between gene lists is evaluated using the Sorensen-Dice index. The fundamental guiding principle is that two gene lists are taken as similar if they share a great proportion of common enriched GO items.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-gostag/meta.yaml b/recipes/bioconductor-gostag/meta.yaml index f6e7a62697ff4..4ea3c9b583493 100644 --- a/recipes/bioconductor-gostag/meta.yaml +++ b/recipes/bioconductor-gostag/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "goSTAG" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7bc12d210ddda0a4b5f5edf28616fab7 + md5: 8d3245abbcc5813366a9393dc7bf79c7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gostag", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-memoise run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-memoise test: diff --git a/recipes/bioconductor-gostats/meta.yaml b/recipes/bioconductor-gostats/meta.yaml index 5ad536fd0eae2..d2f24d9217bbd 100644 --- a/recipes/bioconductor-gostats/meta.yaml +++ b/recipes/bioconductor-gostats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.66.0" %} +{% set version = "2.68.0" %} {% set name = "GOstats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9f2a76112093c47135db323a273405e2 + md5: 4489bff9142d2a3357ac2de0efc1b1b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gostats", max_pin="x.x") }}' noarch: generic # Suggests: hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics, BiocStyle, knitr requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationforge >=1.42.0,<1.43.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationforge >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationforge >=1.42.0,<1.43.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationforge >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-gosummaries/meta.yaml b/recipes/bioconductor-gosummaries/meta.yaml index f5121955778cb..6c26068237b8d 100644 --- a/recipes/bioconductor-gosummaries/meta.yaml +++ b/recipes/bioconductor-gosummaries/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.36.0" %} +{% set version = "2.37.0" %} {% set name = "GOsummaries" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e9b6d1a50cb877d24e9264a02023a79e + md5: e31e67ed4c66122dcf79a694096ef539 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gosummaries", max_pin="x.x") }}' # Suggests: vegan requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-gprofiler @@ -31,7 +32,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-gprofiler diff --git a/recipes/bioconductor-gothic/meta.yaml b/recipes/bioconductor-gothic/meta.yaml index 6779ef8846164..7651748e307e3 100644 --- a/recipes/bioconductor-gothic/meta.yaml +++ b/recipes/bioconductor-gothic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "GOTHiC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4f99fd13cc2e02957464e7b60647aeef + md5: 4674978396dedfc730c8ad85662dac8c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gothic", max_pin="x.x") }}' noarch: generic # Suggests: HiCDataLymphoblast requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-biocmanager - r-data.table - r-ggplot2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-biocmanager - r-data.table diff --git a/recipes/bioconductor-gotools/meta.yaml b/recipes/bioconductor-gotools/meta.yaml index 73f28508453af..0da93c1095d5d 100644 --- a/recipes/bioconductor-gotools/meta.yaml +++ b/recipes/bioconductor-gotools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "goTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 68377c0224a6e3f7bac808ec7c4ae70c + md5: a91344726dcce37779380a18f6e9bc1d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gotools", max_pin="x.x") }}' noarch: generic # Suggests: hgu133a.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base test: commands: diff --git a/recipes/bioconductor-gp53cdf/meta.yaml b/recipes/bioconductor-gp53cdf/meta.yaml index 14b16bade6051..8bdbd9cb32bf1 100644 --- a/recipes/bioconductor-gp53cdf/meta.yaml +++ b/recipes/bioconductor-gp53cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "gp53cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2887dd15d3fa29b5c13b068c8d641f61 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gp53cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gpa/meta.yaml b/recipes/bioconductor-gpa/meta.yaml index 5d901016355f6..c5e078dff7b47 100644 --- a/recipes/bioconductor-gpa/meta.yaml +++ b/recipes/bioconductor-gpa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "GPA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94cd599b75ea787687e4c66fbf54eb85 + md5: 2c1f0f3436c036a3e098d7780deb7282 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gpa", max_pin="x.x") }}' # Suggests: gpaExample # SystemRequirements: GNU make requirements: diff --git a/recipes/bioconductor-gpaexample/meta.yaml b/recipes/bioconductor-gpaexample/meta.yaml index b47ae952323c4..66694127c605d 100644 --- a/recipes/bioconductor-gpaexample/meta.yaml +++ b/recipes/bioconductor-gpaexample/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "gpaExample" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e5cd543667831a4996249fcc3dee8224 + md5: e989af58ed5bbc10573f7438b3ee7836 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gpaexample", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gpaexample/post-link.sh b/recipes/bioconductor-gpaexample/post-link.sh index efcb7585c143c..b48e9f2168532 100644 --- a/recipes/bioconductor-gpaexample/post-link.sh +++ b/recipes/bioconductor-gpaexample/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gpaexample-1.12.0" +installBiocDataPackage.sh "gpaexample-1.14.0" diff --git a/recipes/bioconductor-gpls/meta.yaml b/recipes/bioconductor-gpls/meta.yaml index e2e521ed427a1..a685bbc90fd0d 100644 --- a/recipes/bioconductor-gpls/meta.yaml +++ b/recipes/bioconductor-gpls/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "gpls" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c6d090f604af7c8c7b9f8478b7a7334f + md5: db6bc720156a5f7571a34e64b1189d3b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gpls", max_pin="x.x") }}' noarch: generic # Suggests: MASS requirements: diff --git a/recipes/bioconductor-gpumagic/meta.yaml b/recipes/bioconductor-gpumagic/meta.yaml index 378952cb58bfc..4aaa1e52b559b 100644 --- a/recipes/bioconductor-gpumagic/meta.yaml +++ b/recipes/bioconductor-gpumagic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "gpuMagic" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e9b10f314b0124f19525cc73763e9b15 + md5: b720e953b36ccc2db0c6b359f84b5c94 build: skip: True # [osx] - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gpumagic", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, BiocStyle # SystemRequirements: 1. C++11, 2. a graphic driver or a CPU SDK. 3. ICD loader For Windows user, an ICD loader is required at C:/windows/system32/OpenCL.dll (Usually it is installed by the graphic driver). For Linux user (Except mac): ocl-icd-opencl-dev package is required. For Mac user, no action is needed for the system has installed the dependency. 4. GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - ocl-icd # [linux] + - khronos-opencl-icd-loader # [osx] + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-deriv - r-desctools @@ -32,9 +35,8 @@ requirements: - r-stringr - libblas - liblapack - - ocl-icd run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-deriv - r-desctools @@ -42,7 +44,6 @@ requirements: - r-pryr - r-rcpp - r-stringr - - ocl-icd build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-granie/meta.yaml b/recipes/bioconductor-granie/meta.yaml index caaac3289b655..b29c58c558196 100644 --- a/recipes/bioconductor-granie/meta.yaml +++ b/recipes/bioconductor-granie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.1" %} {% set name = "GRaNIE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14f7e1ef111e181c602e29d04b07a36a + md5: d9db703063398ccd263ce6b54def9266 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-granie", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Mmulatta.UCSC.rheMac10, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn6.refGene, TxDb.Rnorvegicus.UCSC.rn7.refGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Mmulatta.UCSC.rheMac10.refGene, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, org.Mmu.eg.db, IHW, clusterProfiler, ReactomePA, DOSE, BiocFileCache, ChIPseeker, testthat (>= 3.0.0), BiocStyle, csaw, BiocParallel, WGCNA, variancePartition, purrr, EDASeq, JASPAR2022, TFBSTools, motifmatchr, rbioapi +# Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Mmulatta.UCSC.rheMac10, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn6.refGene, TxDb.Rnorvegicus.UCSC.rn7.refGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Mmulatta.UCSC.rheMac10.refGene, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, org.Mmu.eg.db, IHW, clusterProfiler, ReactomePA, DOSE, BiocFileCache, ChIPseeker, testthat (>= 3.0.0), BiocStyle, csaw, BiocParallel, WGCNA, variancePartition, purrr, EDASeq, JASPAR2022, TFBSTools, motifmatchr, rbioapi, LDlinkR requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-checkmate - r-circlize @@ -60,18 +61,18 @@ requirements: - r-tidyselect - r-viridis run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-checkmate - r-circlize diff --git a/recipes/bioconductor-granulator/meta.yaml b/recipes/bioconductor-granulator/meta.yaml index a25a11f292d22..1a7ce94a61265 100644 --- a/recipes/bioconductor-granulator/meta.yaml +++ b/recipes/bioconductor-granulator/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "granulator" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3dd49f32f5e06d8e71d2f9cf0061943b + md5: 05c4025460a33eb195280f676bd5695f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-granulator", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-graper/meta.yaml b/recipes/bioconductor-graper/meta.yaml index 36f59de7bbf4d..5f18d9093b48a 100644 --- a/recipes/bioconductor-graper/meta.yaml +++ b/recipes/bioconductor-graper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "graper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dfb81199dbe0b868891b0404ee6be865 + md5: e969608b591224df6c92d73194adea89 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-graper", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: diff --git a/recipes/bioconductor-graph/meta.yaml b/recipes/bioconductor-graph/meta.yaml index cdff1216b3f78..79a97be096508 100644 --- a/recipes/bioconductor-graph/meta.yaml +++ b/recipes/bioconductor-graph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "graph" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,7 +11,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cb2a06b2f76d5d7e1829110a2cac0790 + md5: 735b96df0f7c955806148170220b75b2 patches: - patch build: @@ -19,15 +19,16 @@ build: rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-graph", max_pin="x.x") }}' # Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-graphalignment/meta.yaml b/recipes/bioconductor-graphalignment/meta.yaml index c8feeee759960..29442eaaf9529 100644 --- a/recipes/bioconductor-graphalignment/meta.yaml +++ b/recipes/bioconductor-graphalignment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "GraphAlignment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e833670324045ba6e5faf80b0dbddaa6 + md5: 0bc71a4722d0771d97671e81103bc8bb build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-graphalignment", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-graphat/meta.yaml b/recipes/bioconductor-graphat/meta.yaml index 85bd95713a136..39efd6cd695cd 100644 --- a/recipes/bioconductor-graphat/meta.yaml +++ b/recipes/bioconductor-graphat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "GraphAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3024a1e165c2da03487c727786f4c69d + md5: 075a7ac1af3518ac6ef4b9087107b482 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-graphat", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-mcmcpack run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-mcmcpack test: diff --git a/recipes/bioconductor-graphite/meta.yaml b/recipes/bioconductor-graphite/meta.yaml index 08b2ce2c7d527..cbbc5f5590f62 100644 --- a/recipes/bioconductor-graphite/meta.yaml +++ b/recipes/bioconductor-graphite/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "graphite" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ee3a1dfe540fddb10caaf9dc89cb9244 + md5: 532e304cdb96a828c4b764bfd36cce85 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-graphite", max_pin="x.x") }}' noarch: generic -# Suggests: checkmate, a4Preproc, ALL, BiocStyle, clipper, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) +# Suggests: checkmate, a4Preproc, ALL, BiocStyle, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-httr - r-purrr - r-rappdirs - r-rlang run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-httr - r-purrr diff --git a/recipes/bioconductor-graphpac/meta.yaml b/recipes/bioconductor-graphpac/meta.yaml index 10cffce0ab041..c773413a30f97 100644 --- a/recipes/bioconductor-graphpac/meta.yaml +++ b/recipes/bioconductor-graphpac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "GraphPAC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a2ef8baf70be32173344ee1de04df841 + md5: 68794a35ae528c5cde68e7915611ace8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-graphpac", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-ipac >=1.44.0,<1.45.0' + - 'bioconductor-ipac >=1.46.0,<1.47.0' - r-base - r-igraph - r-rmallow - r-tsp run: - - 'bioconductor-ipac >=1.44.0,<1.45.0' + - 'bioconductor-ipac >=1.46.0,<1.47.0' - r-base - r-igraph - r-rmallow diff --git a/recipes/bioconductor-grasp2db/meta.yaml b/recipes/bioconductor-grasp2db/meta.yaml index 432e8571038f2..d1c3907d36ee0 100644 --- a/recipes/bioconductor-grasp2db/meta.yaml +++ b/recipes/bioconductor-grasp2db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "grasp2db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3fc90fc7c99e7da51dcbb687fd2d5515 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-grasp2db", max_pin="x.x") }}' noarch: generic # Suggests: gwascat, knitr requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base - r-dbplyr - r-digest - r-dplyr - r-rsqlite run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base - r-dbplyr - r-digest - r-dplyr - r-rsqlite - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-grenits/meta.yaml b/recipes/bioconductor-grenits/meta.yaml index 3cc7ca338509b..3625cf4b661d6 100644 --- a/recipes/bioconductor-grenits/meta.yaml +++ b/recipes/bioconductor-grenits/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.1" %} +{% set version = "1.54.0" %} {% set name = "GRENITS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: add877533a70243aba3429d02a1b9bd1 + md5: fd00e191f8c57c6ef54146263d21a089 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-grenits", max_pin="x.x") }}' # Suggests: network requirements: host: diff --git a/recipes/bioconductor-greylistchip/meta.yaml b/recipes/bioconductor-greylistchip/meta.yaml index 73198ac32ab4d..69807bd80c9c9 100644 --- a/recipes/bioconductor-greylistchip/meta.yaml +++ b/recipes/bioconductor-greylistchip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "GreyListChIP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ed3e5d046abc71c57b41dcd6d67ef41 + md5: 42fa9dbbc56cc2c4fdf511ce67ee234e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-greylistchip", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BiocGenerics, RUnit, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-mass run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-grmetrics/meta.yaml b/recipes/bioconductor-grmetrics/meta.yaml index 48850d9efee42..138a1f01df8f1 100644 --- a/recipes/bioconductor-grmetrics/meta.yaml +++ b/recipes/bioconductor-grmetrics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "GRmetrics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 26897f28f8310a63c26bfee3ef9aa5f1 + md5: 16b27cb79eafe9dbdbb84f0626c5f8da build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-grmetrics", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, tinytex requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-drc - r-ggplot2 - r-plotly run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-drc - r-ggplot2 diff --git a/recipes/bioconductor-grndata/meta.yaml b/recipes/bioconductor-grndata/meta.yaml index 4835bd51bcf00..19ec93513a47e 100644 --- a/recipes/bioconductor-grndata/meta.yaml +++ b/recipes/bioconductor-grndata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "grndata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e105a77f883593cbe67ddbdbe5ad91e3 + md5: 0ebac67277a5ca915f9a971d3659af5e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-grndata", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-grndata/post-link.sh b/recipes/bioconductor-grndata/post-link.sh index 5abbe76404e07..cc47b0a1e8a7f 100644 --- a/recipes/bioconductor-grndata/post-link.sh +++ b/recipes/bioconductor-grndata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "grndata-1.32.0" +installBiocDataPackage.sh "grndata-1.34.0" diff --git a/recipes/bioconductor-grohmm/meta.yaml b/recipes/bioconductor-grohmm/meta.yaml index e0cf197abaf2b..0861380ba58c9 100644 --- a/recipes/bioconductor-grohmm/meta.yaml +++ b/recipes/bioconductor-grohmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "groHMM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b485a920aa3764cdae9b4d49acbbe67 + md5: 0b1077948ddc9895c57188ca2560bc10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-grohmm", max_pin="x.x") }}' # Suggests: BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-mass - libblas - liblapack run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-mass build: diff --git a/recipes/bioconductor-gsalightning/meta.yaml b/recipes/bioconductor-gsalightning/meta.yaml index bc51010324050..f343d529a8d02 100644 --- a/recipes/bioconductor-gsalightning/meta.yaml +++ b/recipes/bioconductor-gsalightning/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "GSALightning" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 99107f0b7eb3b834af9628c73cdd2232 + md5: c6828603275d57045e613f1e7c0f143d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsalightning", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-gsar/meta.yaml b/recipes/bioconductor-gsar/meta.yaml index a49a1d187b976..294a6678158ba 100644 --- a/recipes/bioconductor-gsar/meta.yaml +++ b/recipes/bioconductor-gsar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "GSAR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 992d2824583ed572a43b035014d13681 + md5: 9828682d8721bde17ea31c9ed807174d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsar", max_pin="x.x") }}' noarch: generic # Suggests: MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate, org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR, BiocStyle requirements: diff --git a/recipes/bioconductor-gsbenchmark/meta.yaml b/recipes/bioconductor-gsbenchmark/meta.yaml index 0c3705cce95ea..562dacde1d6fc 100644 --- a/recipes/bioconductor-gsbenchmark/meta.yaml +++ b/recipes/bioconductor-gsbenchmark/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GSBenchMark" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67ad80e0d9aca2b2403031b8f5d79f57 + md5: bedfa52de1b414ae5fe9d5fc376380ba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsbenchmark", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gsbenchmark/post-link.sh b/recipes/bioconductor-gsbenchmark/post-link.sh index 639c923dcdb2d..7e75d49468c5e 100644 --- a/recipes/bioconductor-gsbenchmark/post-link.sh +++ b/recipes/bioconductor-gsbenchmark/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gsbenchmark-1.20.0" +installBiocDataPackage.sh "gsbenchmark-1.22.0" diff --git a/recipes/bioconductor-gsca/meta.yaml b/recipes/bioconductor-gsca/meta.yaml index 111c55efa76c6..a02a1031371d3 100644 --- a/recipes/bioconductor-gsca/meta.yaml +++ b/recipes/bioconductor-gsca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "GSCA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84486e7f5a9c1efb94dd0e8fd46347c1 + md5: 6cf569e7be20a330c190c8c3af6f0654 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsca", max_pin="x.x") }}' noarch: generic # Suggests: Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr requirements: host: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-ggplot2 - r-gplots @@ -30,7 +31,7 @@ requirements: - r-shiny - r-sp run: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-ggplot2 - r-gplots diff --git a/recipes/bioconductor-gse103322/meta.yaml b/recipes/bioconductor-gse103322/meta.yaml index 9d5041b4df503..78cde2aa8566a 100644 --- a/recipes/bioconductor-gse103322/meta.yaml +++ b/recipes/bioconductor-gse103322/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "GSE103322" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f0ae42096e6851fc40f3c45831d38c7 + md5: 3816b430b716edaaa0ef22dba38cf58e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gse103322", max_pin="x.x") }}' noarch: generic # Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown, SummarizedExperiment, SingleCellExperiment requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gse103322/post-link.sh b/recipes/bioconductor-gse103322/post-link.sh index 400e8f8c47a7d..719c9773297fe 100644 --- a/recipes/bioconductor-gse103322/post-link.sh +++ b/recipes/bioconductor-gse103322/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gse103322-1.6.0" +installBiocDataPackage.sh "gse103322-1.8.0" diff --git a/recipes/bioconductor-gse13015/meta.yaml b/recipes/bioconductor-gse13015/meta.yaml index ad1dd80f10e5c..f6b004027246e 100644 --- a/recipes/bioconductor-gse13015/meta.yaml +++ b/recipes/bioconductor-gse13015/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "GSE13015" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 749148d0e8ddb719e43d6513e340e8b6 + md5: 99fae6872abf6820842a1340f7fd6b4e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gse13015", max_pin="x.x") }}' noarch: generic # Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gse13015/post-link.sh b/recipes/bioconductor-gse13015/post-link.sh index dcba32af32068..03e9a7afbddbe 100644 --- a/recipes/bioconductor-gse13015/post-link.sh +++ b/recipes/bioconductor-gse13015/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gse13015-1.8.0" +installBiocDataPackage.sh "gse13015-1.10.0" diff --git a/recipes/bioconductor-gse159526/meta.yaml b/recipes/bioconductor-gse159526/meta.yaml index 41485e8f1644d..abca80d825751 100644 --- a/recipes/bioconductor-gse159526/meta.yaml +++ b/recipes/bioconductor-gse159526/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "GSE159526" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 930aac8c4e8b481b62e489d6e5d94487 + md5: d89442c94cb87f0760a9f0f85426a8fa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gse159526", max_pin="x.x") }}' noarch: generic # Suggests: ExperimentHub, BiocStyle, RefManageR, knitr, rmarkdown, testthat, minfi, tibble, sessioninfo requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gse159526/post-link.sh b/recipes/bioconductor-gse159526/post-link.sh index 7caa9a6ed0578..70558b3f8c891 100644 --- a/recipes/bioconductor-gse159526/post-link.sh +++ b/recipes/bioconductor-gse159526/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gse159526-1.6.0" +installBiocDataPackage.sh "gse159526-1.8.0" diff --git a/recipes/bioconductor-gse62944/meta.yaml b/recipes/bioconductor-gse62944/meta.yaml index 4bd7db2ce4430..925d457637f38 100644 --- a/recipes/bioconductor-gse62944/meta.yaml +++ b/recipes/bioconductor-gse62944/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "GSE62944" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8759202f2247d2a60d0bb17acfffad6a + md5: 5b6c58aaee948c9cd0e0d52b5adcf264 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gse62944", max_pin="x.x") }}' noarch: generic # Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown, DESeq2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gse62944/post-link.sh b/recipes/bioconductor-gse62944/post-link.sh index 49a2bf82549c1..35edd4d1cec52 100644 --- a/recipes/bioconductor-gse62944/post-link.sh +++ b/recipes/bioconductor-gse62944/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gse62944-1.28.1" +installBiocDataPackage.sh "gse62944-1.30.0" diff --git a/recipes/bioconductor-gseabase/meta.yaml b/recipes/bioconductor-gseabase/meta.yaml index f7a33aceccb03..87db5ecfad250 100644 --- a/recipes/bioconductor-gseabase/meta.yaml +++ b/recipes/bioconductor-gseabase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "GSEABase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ac49fd7057e13a7485d3fcd18036e2f8 + md5: a9d4d48654c9a05cdec2f09f8f805c4e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gseabase", max_pin="x.x") }}' noarch: generic # Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools, testthat, BiocStyle, knitr, RUnit requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-xml run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-xml test: diff --git a/recipes/bioconductor-gseabenchmarker/meta.yaml b/recipes/bioconductor-gseabenchmarker/meta.yaml index 2c863dcc8f95f..d3a50bed81819 100644 --- a/recipes/bioconductor-gseabenchmarker/meta.yaml +++ b/recipes/bioconductor-gseabenchmarker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GSEABenchmarkeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,42 +11,43 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 34229c527aba8c7025fa9d310f3f2d16 + md5: 9f297d155b3c254f091eb70a180ea9fa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gseabenchmarker", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, GSE62944, knitr, rappdirs, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-enrichmentbrowser >=2.30.0,<2.31.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-keggandmetacoredzpathwaysgeo >=1.20.0,<1.21.0' - - 'bioconductor-keggdzpathwaysgeo >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-enrichmentbrowser >=2.32.0,<2.33.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-keggandmetacoredzpathwaysgeo >=1.22.0,<1.23.0' + - 'bioconductor-keggdzpathwaysgeo >=1.40.0,<1.41.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-enrichmentbrowser >=2.30.0,<2.31.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-keggandmetacoredzpathwaysgeo >=1.20.0,<1.21.0' - - 'bioconductor-keggdzpathwaysgeo >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-enrichmentbrowser >=2.32.0,<2.33.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-keggandmetacoredzpathwaysgeo >=1.22.0,<1.23.0' + - 'bioconductor-keggdzpathwaysgeo >=1.40.0,<1.41.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-gsealm/meta.yaml b/recipes/bioconductor-gsealm/meta.yaml index e0da1b02b43b4..502e5017b9cf4 100644 --- a/recipes/bioconductor-gsealm/meta.yaml +++ b/recipes/bioconductor-gsealm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "GSEAlm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2df157d143a03b871109690f6b4769c7 + md5: b88623d080b75bb6775026e9e6c4dd9e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsealm", max_pin="x.x") }}' noarch: generic # Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-gseamining/meta.yaml b/recipes/bioconductor-gseamining/meta.yaml index 2ade682c1a61e..bff37cad1e697 100644 --- a/recipes/bioconductor-gseamining/meta.yaml +++ b/recipes/bioconductor-gseamining/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "GSEAmining" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,14 +11,15 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 473b3365763356450a2e7820736ca4dd + md5: 703f12fed97e95761b2cd41894da0645 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gseamining", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, BiocStyle, clusterProfiler, testthat +# Suggests: knitr, rmarkdown, BiocStyle, clusterProfiler, testthat, tm requirements: host: - r-base diff --git a/recipes/bioconductor-gsean/meta.yaml b/recipes/bioconductor-gsean/meta.yaml index 699c899ca2f21..56e88aeaa6ee8 100644 --- a/recipes/bioconductor-gsean/meta.yaml +++ b/recipes/bioconductor-gsean/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.2" %} +{% set version = "1.22.0" %} {% set name = "gsean" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 86ad318c3f149e10fc6561c415b1ca96 + md5: 501dfe30896b53197345abe9d1600247 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsean", max_pin="x.x") }}' # Suggests: SummarizedExperiment, pasilla, org.Dm.eg.db, AnnotationDbi, knitr, plotly, WGCNA, rmarkdown requirements: host: - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-ppinfer >=1.26.0,<1.27.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-ppinfer >=1.28.0,<1.29.0' - r-base - libblas - liblapack run: - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-ppinfer >=1.26.0,<1.27.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-ppinfer >=1.28.0,<1.29.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-gsgalgor/meta.yaml b/recipes/bioconductor-gsgalgor/meta.yaml index 13bc612d97a4a..cf311c036c026 100644 --- a/recipes/bioconductor-gsgalgor/meta.yaml +++ b/recipes/bioconductor-gsgalgor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "GSgalgoR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f05f9acb6cf8bdc69944006f950d689 + md5: 09d5b90490f44ee7384c71762228244d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsgalgor", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp, Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP, iC10TrainingData, pamr, testthat requirements: diff --git a/recipes/bioconductor-gsreg/meta.yaml b/recipes/bioconductor-gsreg/meta.yaml index 44f757afe803f..42f7a252d92c8 100644 --- a/recipes/bioconductor-gsreg/meta.yaml +++ b/recipes/bioconductor-gsreg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "GSReg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5c4d1a7a4a517c6c05a30694549f144f + md5: 631e2589b571bfcdf38b5673ba0693d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsreg", max_pin="x.x") }}' # Suggests: GenomicRanges, GSBenchMark requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-gsri/meta.yaml b/recipes/bioconductor-gsri/meta.yaml index 1d0bb1fb961a6..80acc691c0711 100644 --- a/recipes/bioconductor-gsri/meta.yaml +++ b/recipes/bioconductor-gsri/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.48.0" %} +{% set version = "2.50.0" %} {% set name = "GSRI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: be540e94ade102397a842e6857d772d4 + md5: 686ab91e4ee0adeb4828a5b2ac2f6943 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsri", max_pin="x.x") }}' noarch: generic # Suggests: limma, hgu95av2.db requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-les >=1.50.0,<1.51.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-les >=1.52.0,<1.53.0' - r-base - r-fdrtool run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-les >=1.50.0,<1.51.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-les >=1.52.0,<1.53.0' - r-base - r-fdrtool test: diff --git a/recipes/bioconductor-gsva/meta.yaml b/recipes/bioconductor-gsva/meta.yaml index 4d6b781e794e2..b921c6e030815 100644 --- a/recipes/bioconductor-gsva/meta.yaml +++ b/recipes/bioconductor-gsva/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.2" %} +{% set version = "1.50.0" %} {% set name = "GSVA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,44 +11,45 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4732baaf15d6d75e98374e143039d541 + md5: e21af1ab9dabfa5801fb978b50f992e2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsva", max_pin="x.x") }}' # Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinydashboard, ggplot2, data.table, plotly, future, promises, shinybusy, shinyjs requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-matrix >=1.5-0' - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-matrix >=1.5-0' build: @@ -60,7 +61,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'Gene Set Variation Analysis for microarray and RNA-seq data' + summary: 'Gene Set Variation Analysis for Microarray and RNA-Seq Data' description: 'Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: diff --git a/recipes/bioconductor-gsvadata/meta.yaml b/recipes/bioconductor-gsvadata/meta.yaml index 7c0fcff56d32d..b4a138b0bd959 100644 --- a/recipes/bioconductor-gsvadata/meta.yaml +++ b/recipes/bioconductor-gsvadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "GSVAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 745225b064d2d82499906b03543ee0ac + md5: 3c2d6a66967ab8c3c2545fc3323282b3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsvadata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - 'bioconductor-hgu95a.db >=3.13.0,<3.14.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - 'bioconductor-hgu95a.db >=3.13.0,<3.14.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gsvadata/post-link.sh b/recipes/bioconductor-gsvadata/post-link.sh index 7f3de7e3f402e..47efe8a70a147 100644 --- a/recipes/bioconductor-gsvadata/post-link.sh +++ b/recipes/bioconductor-gsvadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gsvadata-1.36.0" +installBiocDataPackage.sh "gsvadata-1.38.0" diff --git a/recipes/bioconductor-gtrellis/meta.yaml b/recipes/bioconductor-gtrellis/meta.yaml index 6eb24455fff17..161c476c7d085 100644 --- a/recipes/bioconductor-gtrellis/meta.yaml +++ b/recipes/bioconductor-gtrellis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "gtrellis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b3e1e7fce6888cb1ead8c1ad4f637708 + md5: 795b74d96310e3cd9a5771bd8695cf64 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gtrellis", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 1.0.0), knitr, RColorBrewer, markdown, rmarkdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-circlize >=0.4.8' - r-getoptlong run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-circlize >=0.4.8' - r-getoptlong diff --git a/recipes/bioconductor-guideseq/meta.yaml b/recipes/bioconductor-guideseq/meta.yaml index 0ada362630533..b3a7b618ced7e 100644 --- a/recipes/bioconductor-guideseq/meta.yaml +++ b/recipes/bioconductor-guideseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "GUIDEseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9005588165cf4614cf71fefb7fa0e42d + md5: fe01afa9546bc7bdc1fbeea8c8bda8db build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-guideseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-crisprseek >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-crisprseek >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr @@ -49,20 +50,20 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-crisprseek >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-crisprseek >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-guitar/meta.yaml b/recipes/bioconductor-guitar/meta.yaml index 282ac72e4515c..5ead73d849ee9 100644 --- a/recipes/bioconductor-guitar/meta.yaml +++ b/recipes/bioconductor-guitar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "Guitar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a2c085559ba2fd466f795f3ae5877db7 + md5: e62e4238e3e3b939a2195eb384079bb3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-guitar", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-dplyr - r-ggplot2 - r-knitr - r-magrittr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-gviz/meta.yaml b/recipes/bioconductor-gviz/meta.yaml index 49cf722385529..e0c413f6a6708 100644 --- a/recipes/bioconductor-gviz/meta.yaml +++ b/recipes/bioconductor-gviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.1" %} {% set name = "Gviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea2e7a3016f67158d00b4d116482da04 + md5: 2e1eba2ac7cb0d1178f17bba471b0a62 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gviz", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19, xml2, BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-digest >=0.6.8' - r-lattice @@ -45,23 +46,23 @@ requirements: - 'r-matrixstats >=0.8.14' - r-rcolorbrewer run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-digest >=0.6.8' - r-lattice diff --git a/recipes/bioconductor-gwas.bayes/meta.yaml b/recipes/bioconductor-gwas.bayes/meta.yaml index c0cf1fbc23391..e00fe8aad9e30 100644 --- a/recipes/bioconductor-gwas.bayes/meta.yaml +++ b/recipes/bioconductor-gwas.bayes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "GWAS.BAYES" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e8733509e3803574f9b92e9902010d8 + md5: cf62f1d1c5f69ef4051bf659da548b1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gwas.bayes", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - 'r-caret >=6.0-86' - 'r-ga >=3.2' @@ -29,7 +30,7 @@ requirements: - 'r-matrix >=1.2-18' - 'r-memoise >=1.1.0' run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - 'r-caret >=6.0-86' - 'r-ga >=3.2' diff --git a/recipes/bioconductor-gwascat/meta.yaml b/recipes/bioconductor-gwascat/meta.yaml index 8458e47b680fb..fd05265aa675a 100644 --- a/recipes/bioconductor-gwascat/meta.yaml +++ b/recipes/bioconductor-gwascat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "gwascat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 47e8a78f635d5137f6ce804a50edfb9f + md5: a7cbd1d5ac4b3d4fbb8d1fbd77269e44 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gwascat", max_pin="x.x") }}' noarch: generic # Suggests: DO.db, DT, knitr, RBGL, testthat, rmarkdown, dplyr, Gviz, Rsamtools, rtracklayer, graph, ggbio, DelayedArray, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-readr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-readr test: diff --git a/recipes/bioconductor-gwascatdata/meta.yaml b/recipes/bioconductor-gwascatdata/meta.yaml index 44fc9e5897fe5..993381303c0d2 100644 --- a/recipes/bioconductor-gwascatdata/meta.yaml +++ b/recipes/bioconductor-gwascatdata/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.6" %} {% set name = "gwascatData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fa09db539ac0a16ba136e810a5b9970a build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gwascatdata", max_pin="x.x") }}' noarch: generic # Suggests: testthat, AnnotationHub, rmarkdown, knitr requirements: @@ -27,7 +28,7 @@ requirements: - r-base - r-data.table - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gwasdata/meta.yaml b/recipes/bioconductor-gwasdata/meta.yaml index f81ccc89c6f9b..f30c72237cf4e 100644 --- a/recipes/bioconductor-gwasdata/meta.yaml +++ b/recipes/bioconductor-gwasdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.1" %} +{% set version = "1.40.0" %} {% set name = "GWASdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f613097e6cc22f457d1de41f8e677aa6 + md5: 57fec70f980b9e476f0c59d397797815 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gwasdata", max_pin="x.x") }}' noarch: generic # Suggests: ncdf4 requirements: host: - - 'bioconductor-gwastools >=1.46.0,<1.47.0' + - 'bioconductor-gwastools >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-gwastools >=1.46.0,<1.47.0' + - 'bioconductor-gwastools >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gwasdata/post-link.sh b/recipes/bioconductor-gwasdata/post-link.sh index 691a1bc8e0e26..11e8192ddace6 100644 --- a/recipes/bioconductor-gwasdata/post-link.sh +++ b/recipes/bioconductor-gwasdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gwasdata-1.38.1" +installBiocDataPackage.sh "gwasdata-1.40.0" diff --git a/recipes/bioconductor-gwastools/meta.yaml b/recipes/bioconductor-gwastools/meta.yaml index 5e09816c4bd28..1607a30635493 100644 --- a/recipes/bioconductor-gwastools/meta.yaml +++ b/recipes/bioconductor-gwastools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "GWASTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71908b60ba4de5563bc3729ee64193cb + md5: af968b8e8a3e4a1981cae02cb2a781ec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gwastools", max_pin="x.x") }}' noarch: generic -# Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel +# Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel, BiocStyle, knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-quantsmooth >=1.66.0,<1.67.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-quantsmooth >=1.68.0,<1.69.0' - r-base - r-data.table - r-dbi @@ -35,10 +36,10 @@ requirements: - r-sandwich - r-survival run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-quantsmooth >=1.66.0,<1.67.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-quantsmooth >=1.68.0,<1.69.0' - r-base - r-data.table - r-dbi diff --git a/recipes/bioconductor-gwasurvivr/meta.yaml b/recipes/bioconductor-gwasurvivr/meta.yaml index 87a442730f93c..c62748b8cba02 100644 --- a/recipes/bioconductor-gwasurvivr/meta.yaml +++ b/recipes/bioconductor-gwasurvivr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "gwasurvivr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 53493a3fa552b7a0d357cfb2a459a6aa + md5: 699843eb7ff1528732a6a2e093600aef build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gwasurvivr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-gwastools >=1.46.0,<1.47.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-gwastools >=1.48.0,<1.49.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-matrixstats - r-survival run: - - 'bioconductor-gwastools >=1.46.0,<1.47.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-gwastools >=1.48.0,<1.49.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-matrixstats - r-survival diff --git a/recipes/bioconductor-gwena/meta.yaml b/recipes/bioconductor-gwena/meta.yaml index c0772b6ce57ac..9ded48032ed13 100644 --- a/recipes/bioconductor-gwena/meta.yaml +++ b/recipes/bioconductor-gwena/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "GWENA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7db0c32d0fd31879561c5325e0f5b571 + md5: 8f1bd435deae9546d0ec3f8605a0b682 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gwena", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), knitr (>= 1.25), rmarkdown (>= 1.16), prettydoc (>= 0.3.0), httr (>= 1.4.1), S4Vectors (>= 0.22.1), BiocStyle (>= 2.15.8) requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-cluster >=2.1.0' - 'r-dplyr >=0.8.3' @@ -40,7 +41,7 @@ requirements: - 'r-tidyr >=1.0.0' - 'r-wgcna >=1.67' run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-cluster >=2.1.0' - 'r-dplyr >=0.8.3' diff --git a/recipes/bioconductor-h10kcod.db/meta.yaml b/recipes/bioconductor-h10kcod.db/meta.yaml index 4ca070938e6ba..c4c1dfaeef710 100644 --- a/recipes/bioconductor-h10kcod.db/meta.yaml +++ b/recipes/bioconductor-h10kcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "h10kcod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a555739cea229f286953c3297c145e9c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-h10kcod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-h20kcod.db/meta.yaml b/recipes/bioconductor-h20kcod.db/meta.yaml index 36fa342084d4d..8427bc3859258 100644 --- a/recipes/bioconductor-h20kcod.db/meta.yaml +++ b/recipes/bioconductor-h20kcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "h20kcod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3647facb272f58424f4c94ef92e8ee45 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-h20kcod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-h5vc/meta.yaml b/recipes/bioconductor-h5vc/meta.yaml index b0e9d79f7de3e..d5c396bb578ac 100644 --- a/recipes/bioconductor-h5vc/meta.yaml +++ b/recipes/bioconductor-h5vc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "h5vc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8322cd34695b64b550a28eac35740c63 + md5: 2d827ac4606ef723005e479de8540b7a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-h5vc", max_pin="x.x") }}' # Suggests: knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics, rmarkdown # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-h5vcdata >=2.20.0,<2.21.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-h5vcdata >=2.22.0,<2.23.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-abind - r-base - r-batchjobs @@ -40,16 +41,16 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-h5vcdata >=2.20.0,<2.21.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-h5vcdata >=2.22.0,<2.23.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-abind - r-base - r-batchjobs diff --git a/recipes/bioconductor-h5vcdata/meta.yaml b/recipes/bioconductor-h5vcdata/meta.yaml index 3b31e5f911d04..7edd272d4b3ef 100644 --- a/recipes/bioconductor-h5vcdata/meta.yaml +++ b/recipes/bioconductor-h5vcdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "h5vcData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e233ff9873648c459591fda6942a8790 + md5: c251316e2d6dc6cb90e8faad0015103b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-h5vcdata", max_pin="x.x") }}' noarch: generic # Suggests: h5vc requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-h5vcdata/post-link.sh b/recipes/bioconductor-h5vcdata/post-link.sh index f44cf91b76794..1962bfe15c1eb 100644 --- a/recipes/bioconductor-h5vcdata/post-link.sh +++ b/recipes/bioconductor-h5vcdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "h5vcdata-2.20.0" +installBiocDataPackage.sh "h5vcdata-2.22.0" diff --git a/recipes/bioconductor-hapfabia/meta.yaml b/recipes/bioconductor-hapfabia/meta.yaml index f317c897e36cc..ff56c6ea7dada 100644 --- a/recipes/bioconductor-hapfabia/meta.yaml +++ b/recipes/bioconductor-hapfabia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "hapFabia" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43b510f5d1b6e18ad523e0429a84618b + md5: a14370aec9e86245541aea68b90c3812 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hapfabia", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-fabia >=2.46.0,<2.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-fabia >=2.48.0,<2.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-fabia >=2.46.0,<2.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-fabia >=2.48.0,<2.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-hapmap100khind/meta.yaml b/recipes/bioconductor-hapmap100khind/meta.yaml index bc6cd30450d6f..3b61d5d83e55f 100644 --- a/recipes/bioconductor-hapmap100khind/meta.yaml +++ b/recipes/bioconductor-hapmap100khind/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "hapmap100khind" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ec3213b4ced09f678386a981176e3410 + md5: 0168028295626d811e305d4008ce9996 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hapmap100khind", max_pin="x.x") }}' noarch: generic # Suggests: oligo requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmap100khind/post-link.sh b/recipes/bioconductor-hapmap100khind/post-link.sh index 0a039b707cc55..d9f5a26dbbc86 100644 --- a/recipes/bioconductor-hapmap100khind/post-link.sh +++ b/recipes/bioconductor-hapmap100khind/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hapmap100khind-1.42.0" +installBiocDataPackage.sh "hapmap100khind-1.44.0" diff --git a/recipes/bioconductor-hapmap100kxba/meta.yaml b/recipes/bioconductor-hapmap100kxba/meta.yaml index 0191502c36e6b..50530871601de 100644 --- a/recipes/bioconductor-hapmap100kxba/meta.yaml +++ b/recipes/bioconductor-hapmap100kxba/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "hapmap100kxba" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 46a995b0ad38d46aebdf89c52678c587 + md5: b4a619fb108a36920109307fbf63985b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hapmap100kxba", max_pin="x.x") }}' noarch: generic # Suggests: oligo requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmap100kxba/post-link.sh b/recipes/bioconductor-hapmap100kxba/post-link.sh index 6f5564a5a776c..e71f400872e77 100644 --- a/recipes/bioconductor-hapmap100kxba/post-link.sh +++ b/recipes/bioconductor-hapmap100kxba/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hapmap100kxba-1.42.0" +installBiocDataPackage.sh "hapmap100kxba-1.44.0" diff --git a/recipes/bioconductor-hapmap370k/meta.yaml b/recipes/bioconductor-hapmap370k/meta.yaml index cb3865a809e87..4711fa3319d8d 100644 --- a/recipes/bioconductor-hapmap370k/meta.yaml +++ b/recipes/bioconductor-hapmap370k/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "hapmap370k" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 569556341a45da799372aaf1012be72e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hapmap370k", max_pin="x.x") }}' noarch: generic # Suggests: crlmm requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmap500knsp/meta.yaml b/recipes/bioconductor-hapmap500knsp/meta.yaml index 63f11361b25e2..379eb3e96b54a 100644 --- a/recipes/bioconductor-hapmap500knsp/meta.yaml +++ b/recipes/bioconductor-hapmap500knsp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "hapmap500knsp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c54725a8ec3607d9db051ef7dfb8b16f + md5: 15b799bba4a395ccf715acfc7bbdae04 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hapmap500knsp", max_pin="x.x") }}' noarch: generic # Suggests: oligo requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmap500knsp/post-link.sh b/recipes/bioconductor-hapmap500knsp/post-link.sh index f7cfbfd4b45a1..1d91347c61c09 100644 --- a/recipes/bioconductor-hapmap500knsp/post-link.sh +++ b/recipes/bioconductor-hapmap500knsp/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hapmap500knsp-1.42.0" +installBiocDataPackage.sh "hapmap500knsp-1.44.0" diff --git a/recipes/bioconductor-hapmap500ksty/meta.yaml b/recipes/bioconductor-hapmap500ksty/meta.yaml index c9e4a88c27127..d4b94cf67c00c 100644 --- a/recipes/bioconductor-hapmap500ksty/meta.yaml +++ b/recipes/bioconductor-hapmap500ksty/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "hapmap500ksty" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b283985ebfd5c8eace1e5f436fb1d07c + md5: 7a1d4983ac3e411dadedc130d85c2557 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hapmap500ksty", max_pin="x.x") }}' noarch: generic # Suggests: oligo requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmap500ksty/post-link.sh b/recipes/bioconductor-hapmap500ksty/post-link.sh index ce7389adcc9e4..fe55de17a68f4 100644 --- a/recipes/bioconductor-hapmap500ksty/post-link.sh +++ b/recipes/bioconductor-hapmap500ksty/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hapmap500ksty-1.42.0" +installBiocDataPackage.sh "hapmap500ksty-1.44.0" diff --git a/recipes/bioconductor-hapmapsnp5/meta.yaml b/recipes/bioconductor-hapmapsnp5/meta.yaml index a9c280b8ca83e..d3d9f4de67114 100644 --- a/recipes/bioconductor-hapmapsnp5/meta.yaml +++ b/recipes/bioconductor-hapmapsnp5/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "hapmapsnp5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ccc4fe2a3fcb840365fb2b3bdec3cfd8 + md5: 2f14e60f39cf94c43f2dd0e5aa5a48e2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hapmapsnp5", max_pin="x.x") }}' noarch: generic # Suggests: oligo requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmapsnp5/post-link.sh b/recipes/bioconductor-hapmapsnp5/post-link.sh index b4eb52c418b84..de833d94f68c6 100644 --- a/recipes/bioconductor-hapmapsnp5/post-link.sh +++ b/recipes/bioconductor-hapmapsnp5/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hapmapsnp5-1.42.0" +installBiocDataPackage.sh "hapmapsnp5-1.44.0" diff --git a/recipes/bioconductor-hapmapsnp6/meta.yaml b/recipes/bioconductor-hapmapsnp6/meta.yaml index 499bcbdbecc09..17aec4ff0bb9d 100644 --- a/recipes/bioconductor-hapmapsnp6/meta.yaml +++ b/recipes/bioconductor-hapmapsnp6/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "hapmapsnp6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a6ca8fb7d228e64ba1567d4cb7bcd81e + md5: 2635c012a513343484177db2070209e9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hapmapsnp6", max_pin="x.x") }}' noarch: generic # Suggests: oligo, oligoClasses requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmapsnp6/post-link.sh b/recipes/bioconductor-hapmapsnp6/post-link.sh index eb074feda8ad7..44c99a5802936 100644 --- a/recipes/bioconductor-hapmapsnp6/post-link.sh +++ b/recipes/bioconductor-hapmapsnp6/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hapmapsnp6-1.42.0" +installBiocDataPackage.sh "hapmapsnp6-1.44.0" diff --git a/recipes/bioconductor-harbchip/meta.yaml b/recipes/bioconductor-harbchip/meta.yaml index 7ef59a1f169ca..ee6acbfff7d6f 100644 --- a/recipes/bioconductor-harbchip/meta.yaml +++ b/recipes/bioconductor-harbchip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "harbChIP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5713ddec61a7771a7c8be36ced779ef1 + md5: f5948fc0f4c1ced0a43e85c1885f5d9e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-harbchip", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-harbchip/post-link.sh b/recipes/bioconductor-harbchip/post-link.sh index 0300d3a1f20b5..d2133dee6fc33 100644 --- a/recipes/bioconductor-harbchip/post-link.sh +++ b/recipes/bioconductor-harbchip/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "harbchip-1.38.0" +installBiocDataPackage.sh "harbchip-1.40.0" diff --git a/recipes/bioconductor-harman/meta.yaml b/recipes/bioconductor-harman/meta.yaml index 64348ff3cf2d6..aa06daaaff680 100644 --- a/recipes/bioconductor-harman/meta.yaml +++ b/recipes/bioconductor-harman/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "Harman" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c60199c4fb9c66f65597ea11d926f410 + md5: aaec4256c0cb2949d553ff81d94e48d2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-harman", max_pin="x.x") }}' # Suggests: HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva requirements: host: diff --git a/recipes/bioconductor-harmandata/meta.yaml b/recipes/bioconductor-harmandata/meta.yaml index ab52d0029ec7c..f0076f4ffdd6a 100644 --- a/recipes/bioconductor-harmandata/meta.yaml +++ b/recipes/bioconductor-harmandata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "HarmanData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43bca3e57aee5603fda4b7be1cb9c738 + md5: 7df1447aff75abdf025678b51a0ee8fb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-harmandata", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, knitr, rmarkdown, Harman (>= 1.23.3) requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-harmandata/post-link.sh b/recipes/bioconductor-harmandata/post-link.sh index f61d2ad4aff59..bfce705eabe09 100644 --- a/recipes/bioconductor-harmandata/post-link.sh +++ b/recipes/bioconductor-harmandata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "harmandata-1.28.0" +installBiocDataPackage.sh "harmandata-1.30.0" diff --git a/recipes/bioconductor-harmonizedtcgadata/meta.yaml b/recipes/bioconductor-harmonizedtcgadata/meta.yaml index 38b5ec17a9e77..c421c5e1b4ec4 100644 --- a/recipes/bioconductor-harmonizedtcgadata/meta.yaml +++ b/recipes/bioconductor-harmonizedtcgadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "HarmonizedTCGAData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c615eb02dbda3204fb5f3d9308a0115c + md5: f6e8f685a67152c6f382089c0e6aae01 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-harmonizedtcgadata", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationHub, knitr, rmarkdown, igraph, survival, ANF, stats, testthat requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-harmonizedtcgadata/post-link.sh b/recipes/bioconductor-harmonizedtcgadata/post-link.sh index a524f01cbd414..dbe5eabb855e7 100644 --- a/recipes/bioconductor-harmonizedtcgadata/post-link.sh +++ b/recipes/bioconductor-harmonizedtcgadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "harmonizedtcgadata-1.22.0" +installBiocDataPackage.sh "harmonizedtcgadata-1.24.0" diff --git a/recipes/bioconductor-harmonizr/build.sh b/recipes/bioconductor-harmonizr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-harmonizr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-harmonizr/meta.yaml b/recipes/bioconductor-harmonizr/meta.yaml new file mode 100644 index 0000000000000..ee8a16ab953cf --- /dev/null +++ b/recipes/bioconductor-harmonizr/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.0.0" %} +{% set name = "HarmonizR" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6e81c009fe8678273d8091378ae2f8e3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-harmonizr", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' + - r-base + - 'r-doparallel >=1.0.16' + - 'r-foreach >=1.5.1' + - 'r-janitor >=2.1.0' + - 'r-plyr >=1.8.6' + - 'r-seriation >=1.3.5' + run: + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' + - r-base + - 'r-doparallel >=1.0.16' + - 'r-foreach >=1.5.1' + - 'r-janitor >=2.1.0' + - 'r-plyr >=1.8.6' + - 'r-seriation >=1.3.5' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Handles missing values and makes more data available' + description: 'An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma. The implementation appropriately handles missing values by dissecting the input matrix into smaller matrices with sufficient data to feed the ComBat or limma algorithm. The adjusted data is returned to the user as a rebuild matrix. The implementation is meant to make as much data available as possible with minimal data loss.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-harshlight/meta.yaml b/recipes/bioconductor-harshlight/meta.yaml index 023d6e9ae198e..2a5a3f49a1f5e 100644 --- a/recipes/bioconductor-harshlight/meta.yaml +++ b/recipes/bioconductor-harshlight/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "Harshlight" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6e7e404fef55917ab6b589f77430a8ec + md5: 36adabb3111ae035069431431dd9434a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-harshlight", max_pin="x.x") }}' requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-altcdfenvs >=2.62.0,<2.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-altcdfenvs >=2.64.0,<2.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-altcdfenvs >=2.62.0,<2.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-altcdfenvs >=2.64.0,<2.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-hca/meta.yaml b/recipes/bioconductor-hca/meta.yaml index ed97a3695a444..0d284f48c3444 100644 --- a/recipes/bioconductor-hca/meta.yaml +++ b/recipes/bioconductor-hca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "hca" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0bad76d71df17bd87e1f256b1ece6bfc + md5: 8a1c812efb51ab7e30a7d419bdf918a3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hca", max_pin="x.x") }}' noarch: generic # Suggests: LoomExperiment, SummarizedExperiment, SingleCellExperiment, S4Vectors, methods, testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-digest - r-dplyr @@ -34,7 +35,7 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-digest - r-dplyr diff --git a/recipes/bioconductor-hcadata/meta.yaml b/recipes/bioconductor-hcadata/meta.yaml index 510ec4f2806c0..de0348abe7497 100644 --- a/recipes/bioconductor-hcadata/meta.yaml +++ b/recipes/bioconductor-hcadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "HCAData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8a2e18f3a29f80ba013759f6c87619e + md5: 4f16bf5904ca21c0fb0bd6515d7ab4d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hcadata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, scran (>= 1.11.4), BiocSingular, scater, scuttle, Rtsne, igraph, iSEE, testthat requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hcadata/post-link.sh b/recipes/bioconductor-hcadata/post-link.sh index a7d7e277e5273..66d5690d2efbb 100644 --- a/recipes/bioconductor-hcadata/post-link.sh +++ b/recipes/bioconductor-hcadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hcadata-1.16.0" +installBiocDataPackage.sh "hcadata-1.18.0" diff --git a/recipes/bioconductor-hcatonsildata/meta.yaml b/recipes/bioconductor-hcatonsildata/meta.yaml new file mode 100644 index 0000000000000..c329508ef650e --- /dev/null +++ b/recipes/bioconductor-hcatonsildata/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.0.0" %} +{% set name = "HCATonsilData" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dda9d216f608690d05bd5ffbcb73bb05 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hcatonsildata", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, ggplot2, testthat (>= 3.0.0), scater, Seurat, Signac, zellkonverter, iSEE, ggspavis, kableExtra, BiocStyle +requirements: + host: + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-base64enc + - r-htmltools + - r-rmarkdown + run: + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-base64enc + - r-htmltools + - r-rmarkdown + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Provide programmatic access to the tonsil cell atlas datasets' + description: 'This package provides access to the scRNA-seq, scATAC-seq, multiome, CITE-seq and spatial transcriptomics (Visium) data generated by the tonsil cell atlas in the context of the Human Cell Atlas (HCA). The data is provided via the Bioconductor project in the form of SingleCellExperiments. Additionally, information on the whole compendium of identified cell types is provided in form of a glossary.' + license_file: LICENSE + diff --git a/recipes/bioconductor-hcatonsildata/post-link.sh b/recipes/bioconductor-hcatonsildata/post-link.sh new file mode 100644 index 0000000000000..55f8721ee344a --- /dev/null +++ b/recipes/bioconductor-hcatonsildata/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "hcatonsildata-1.0.0" diff --git a/recipes/bioconductor-hcatonsildata/pre-unlink.sh b/recipes/bioconductor-hcatonsildata/pre-unlink.sh new file mode 100644 index 0000000000000..7b67c6f0a09f6 --- /dev/null +++ b/recipes/bioconductor-hcatonsildata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HCATonsilData diff --git a/recipes/bioconductor-hcg110.db/meta.yaml b/recipes/bioconductor-hcg110.db/meta.yaml index 11261857c2e11..c77a258d0c61b 100644 --- a/recipes/bioconductor-hcg110.db/meta.yaml +++ b/recipes/bioconductor-hcg110.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hcg110.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4c536c3539a61d7f1f67dac149f10b11 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hcg110.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hcg110cdf/meta.yaml b/recipes/bioconductor-hcg110cdf/meta.yaml index 7e24db7b745c9..6460e345d15fd 100644 --- a/recipes/bioconductor-hcg110cdf/meta.yaml +++ b/recipes/bioconductor-hcg110cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hcg110cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b53167876217ddb301204719da23eafc build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hcg110cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hcg110probe/meta.yaml b/recipes/bioconductor-hcg110probe/meta.yaml index 28ac1ca33e9d9..43ac0da0bf42d 100644 --- a/recipes/bioconductor-hcg110probe/meta.yaml +++ b/recipes/bioconductor-hcg110probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hcg110probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 51af8d6a7090ea7c5fe630dcea68bfb3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hcg110probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hd2013sgi/meta.yaml b/recipes/bioconductor-hd2013sgi/meta.yaml index c9386c47fc272..bfee69a492903 100644 --- a/recipes/bioconductor-hd2013sgi/meta.yaml +++ b/recipes/bioconductor-hd2013sgi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "HD2013SGI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4cc03451c32df17e2a946ab45d32659e + md5: f8c7020a4fbfcb5c4026cea93e5a5bc6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hd2013sgi", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle # SystemRequirements: GNU make requirements: host: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-splots >=1.66.0,<1.67.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-splots >=1.68.0,<1.69.0' - r-base - r-gplots - r-lsd - r-rcolorbrewer - r-vcd run: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-splots >=1.66.0,<1.67.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-splots >=1.68.0,<1.69.0' - r-base - r-gplots - r-lsd - r-rcolorbrewer - r-vcd - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hd2013sgi/post-link.sh b/recipes/bioconductor-hd2013sgi/post-link.sh index ec3b2ce7c28e1..498c6fc12a428 100644 --- a/recipes/bioconductor-hd2013sgi/post-link.sh +++ b/recipes/bioconductor-hd2013sgi/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hd2013sgi-1.40.0" +installBiocDataPackage.sh "hd2013sgi-1.42.0" diff --git a/recipes/bioconductor-hdcytodata/meta.yaml b/recipes/bioconductor-hdcytodata/meta.yaml index b4b799a8de2e3..45497fcf65184 100644 --- a/recipes/bioconductor-hdcytodata/meta.yaml +++ b/recipes/bioconductor-hdcytodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "HDCytoData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ab01564970b77ca4d62db12c07a1ed4 + md5: 8f962c6124539fea7a4a02a30e776de8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hdcytodata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM, mclust requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hdcytodata/post-link.sh b/recipes/bioconductor-hdcytodata/post-link.sh index 8b22d0b2aedcd..d0ac96449fd70 100644 --- a/recipes/bioconductor-hdcytodata/post-link.sh +++ b/recipes/bioconductor-hdcytodata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hdcytodata-1.20.0" +installBiocDataPackage.sh "hdcytodata-1.22.0" diff --git a/recipes/bioconductor-hdf5array/meta.yaml b/recipes/bioconductor-hdf5array/meta.yaml index 9a96452b591ca..6f725cd98876b 100644 --- a/recipes/bioconductor-hdf5array/meta.yaml +++ b/recipes/bioconductor-hdf5array/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "HDF5Array" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 13cc3879d4e7ef05ed4ffaa9c0e80429 + md5: c59fcd283e0f9877f68457524b9d86bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hdf5array", max_pin="x.x") }}' # Suggests: BiocParallel, GenomicRanges, SummarizedExperiment (>= 1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter, GenomicFeatures, RUnit, SingleCellExperiment # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5filters >=1.12.0,<1.13.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-s4arrays >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5filters >=1.14.0,<1.15.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4arrays >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5filters >=1.12.0,<1.13.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-s4arrays >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5filters >=1.14.0,<1.15.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4arrays >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix build: diff --git a/recipes/bioconductor-hdo.db/meta.yaml b/recipes/bioconductor-hdo.db/meta.yaml index 28a3ad127fb79..451b87e2c1add 100644 --- a/recipes/bioconductor-hdo.db/meta.yaml +++ b/recipes/bioconductor-hdo.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.1" %} {% set name = "HDO.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 007a50523f1de27048dfc97f4d458f59 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hdo.db", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hdtd/meta.yaml b/recipes/bioconductor-hdtd/meta.yaml index d01a3252b7342..f9eedc12bc226 100644 --- a/recipes/bioconductor-hdtd/meta.yaml +++ b/recipes/bioconductor-hdtd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.1" %} +{% set version = "1.36.0" %} {% set name = "HDTD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c3037443550f72d6e196587d5b8af94 + md5: c990bac6152195272ae3aa3557f8b82b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hdtd", max_pin="x.x") }}' # Suggests: knitr, rmarkdown requirements: host: diff --git a/recipes/bioconductor-healthycontrolspresencechecker/meta.yaml b/recipes/bioconductor-healthycontrolspresencechecker/meta.yaml index 56d07db97bf39..e9081da4b5fd8 100644 --- a/recipes/bioconductor-healthycontrolspresencechecker/meta.yaml +++ b/recipes/bioconductor-healthycontrolspresencechecker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "healthyControlsPresenceChecker" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cc422930fe0cf3237bc707d107517381 + md5: 50ba7cea9e361d43c78d64ce1c89ba1a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-healthycontrolspresencechecker", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, markdown, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base - r-geneexpressionfromgeo - r-magrittr - r-xml2 run: - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base - r-geneexpressionfromgeo - r-magrittr - r-xml2 - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-healthycontrolspresencechecker/post-link.sh b/recipes/bioconductor-healthycontrolspresencechecker/post-link.sh index 9d5fddf3a957a..a259bb6b38c3a 100644 --- a/recipes/bioconductor-healthycontrolspresencechecker/post-link.sh +++ b/recipes/bioconductor-healthycontrolspresencechecker/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "healthycontrolspresencechecker-1.4.0" +installBiocDataPackage.sh "healthycontrolspresencechecker-1.6.0" diff --git a/recipes/bioconductor-healthyflowdata/meta.yaml b/recipes/bioconductor-healthyflowdata/meta.yaml index fac084e69c483..8797dd046a6e7 100644 --- a/recipes/bioconductor-healthyflowdata/meta.yaml +++ b/recipes/bioconductor-healthyflowdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "healthyFlowData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 478453f16b73527c4f1a9c5697d0b576 + md5: ed0a9c99295e278a8445368a2cb226df build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-healthyflowdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-healthyflowdata/post-link.sh b/recipes/bioconductor-healthyflowdata/post-link.sh index a0537a8057659..0e206a9e263b2 100644 --- a/recipes/bioconductor-healthyflowdata/post-link.sh +++ b/recipes/bioconductor-healthyflowdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "healthyflowdata-1.38.0" +installBiocDataPackage.sh "healthyflowdata-1.40.0" diff --git a/recipes/bioconductor-heatmaps/meta.yaml b/recipes/bioconductor-heatmaps/meta.yaml index 95d30caecdb5e..5e3b7691db75b 100644 --- a/recipes/bioconductor-heatmaps/meta.yaml +++ b/recipes/bioconductor-heatmaps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "heatmaps" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d94b93fd4532100c3d31e9cb7985c6c5 + md5: 68b0a507dd5b2bcdfef2106195429dc2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-heatmaps", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Drerio.UCSC.danRer7, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-kernsmooth - r-matrix - r-plotrix - r-rcolorbrewer run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-kernsmooth - r-matrix diff --git a/recipes/bioconductor-heatplus/meta.yaml b/recipes/bioconductor-heatplus/meta.yaml index d2c6de8674d1f..2e65c161b133c 100644 --- a/recipes/bioconductor-heatplus/meta.yaml +++ b/recipes/bioconductor-heatplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.8.0" %} +{% set version = "3.10.0" %} {% set name = "Heatplus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ffa5d82b6d75383ab65c286ff8b9d707 + md5: 459fb0dbd1242699e9f394f156a7e0c1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-heatplus", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, hgu95av2.db, limma requirements: diff --git a/recipes/bioconductor-heebodata/meta.yaml b/recipes/bioconductor-heebodata/meta.yaml index ad3e7a9b3d12a..b2bccf7c7e017 100644 --- a/recipes/bioconductor-heebodata/meta.yaml +++ b/recipes/bioconductor-heebodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "HEEBOdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf931bc3409e110143d9090c8cb37c9a + md5: 885df0689d6663e079e952ea297ee777 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-heebodata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-heebodata/post-link.sh b/recipes/bioconductor-heebodata/post-link.sh index 9fe644ff2fb14..af9b31ef9b0a2 100644 --- a/recipes/bioconductor-heebodata/post-link.sh +++ b/recipes/bioconductor-heebodata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "heebodata-1.38.0" +installBiocDataPackage.sh "heebodata-1.40.0" diff --git a/recipes/bioconductor-helloranges/meta.yaml b/recipes/bioconductor-helloranges/meta.yaml index 3d920b2f06697..5e449934f1360 100644 --- a/recipes/bioconductor-helloranges/meta.yaml +++ b/recipes/bioconductor-helloranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "HelloRanges" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,47 +11,48 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ab315f2b6ce576e79f3c00634c2ad24 + md5: a83b42b9a323f3f3e356bfa8bbc0fd85 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-helloranges", max_pin="x.x") }}' noarch: generic -# Suggests: HelloRangesData, BiocStyle +# Suggests: HelloRangesData, BiocStyle, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-docopt run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-docopt test: diff --git a/recipes/bioconductor-hellorangesdata/meta.yaml b/recipes/bioconductor-hellorangesdata/meta.yaml index 5abcb2471cc13..4b189bec162c2 100644 --- a/recipes/bioconductor-hellorangesdata/meta.yaml +++ b/recipes/bioconductor-hellorangesdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "HelloRangesData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 34dbe70ca5ea008e5a17803388bed705 + md5: 6ae6ac65f3af7f41136eb6fb3558eb2a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hellorangesdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hellorangesdata/post-link.sh b/recipes/bioconductor-hellorangesdata/post-link.sh index 242daf849104e..3a9fee9bcee90 100644 --- a/recipes/bioconductor-hellorangesdata/post-link.sh +++ b/recipes/bioconductor-hellorangesdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hellorangesdata-1.26.0" +installBiocDataPackage.sh "hellorangesdata-1.28.0" diff --git a/recipes/bioconductor-help/meta.yaml b/recipes/bioconductor-help/meta.yaml index 819de68209db2..02757fe4dc641 100644 --- a/recipes/bioconductor-help/meta.yaml +++ b/recipes/bioconductor-help/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "HELP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e664628988f8c6e0b63403618256654 + md5: d7a1038ee6eb5ec01393b39e30e028fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-help", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-hem/meta.yaml b/recipes/bioconductor-hem/meta.yaml index 9e13985e30272..d6fe622e155cb 100644 --- a/recipes/bioconductor-hem/meta.yaml +++ b/recipes/bioconductor-hem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "HEM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5099d4d170fe1738efbb549fabbf70a1 + md5: 3ad1825d95504eaf9e2bcad8438816f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hem", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-hermes/meta.yaml b/recipes/bioconductor-hermes/meta.yaml index cb190ad49ec97..628da60c967f4 100644 --- a/recipes/bioconductor-hermes/meta.yaml +++ b/recipes/bioconductor-hermes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "hermes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7a2aabc5a9a77c759a57a56683e6e351 + md5: af1e1dd4bab597cfb7b0bd12a1e9e7dd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hermes", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, DelayedArray, DT, grid, httr, knitr, rmarkdown, statmod, testthat (>= 2.0), vdiffr, withr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - 'r-checkmate >=2.1' @@ -52,18 +53,18 @@ requirements: - r-rlang - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - 'r-checkmate >=2.1' diff --git a/recipes/bioconductor-heron/build.sh b/recipes/bioconductor-heron/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-heron/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-heron/meta.yaml b/recipes/bioconductor-heron/meta.yaml new file mode 100644 index 0000000000000..abc4916803605 --- /dev/null +++ b/recipes/bioconductor-heron/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.0.0" %} +{% set name = "HERON" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9c146a8d99bada338098732e1de5a5e2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-heron", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-cluster + - r-data.table + - r-harmonicmeanp + - r-matrix + - r-matrixstats + - r-metap + - r-spdep + run: + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-cluster + - r-data.table + - r-harmonicmeanp + - r-matrix + - r-matrixstats + - r-metap + - r-spdep +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'Hierarchical Epitope pROtein biNding' + description: 'HERON is a software package for analyzing peptide binding array data. In addition to identifying significant binding probes, HERON also provides functions for finding epitopes (string of consecutive peptides within a protein). HERON also calculates significance on the probe, epitope, and protein level by employing meta p-value methods. HERON is designed for obtaining calls on the sample level and calculates fractions of hits for different conditions.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-herper/meta.yaml b/recipes/bioconductor-herper/meta.yaml index a315614ff78d6..1ec27237788bd 100644 --- a/recipes/bioconductor-herper/meta.yaml +++ b/recipes/bioconductor-herper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "Herper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a83b6c90414e5508e93fea96042b9b2 + md5: dad437a472cae186246d3cf0f6b44964 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-herper", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown, seqCNA requirements: diff --git a/recipes/bioconductor-hgc/meta.yaml b/recipes/bioconductor-hgc/meta.yaml index 51b48cf81af8b..415c8beba464a 100644 --- a/recipes/bioconductor-hgc/meta.yaml +++ b/recipes/bioconductor-hgc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "HGC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cac848972223a04ae6d10ba3599b4bcf + md5: 7a8ac62af3106b62952c79c162937a3c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgc", max_pin="x.x") }}' # Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) # SystemRequirements: C++11 requirements: diff --git a/recipes/bioconductor-hgfocus.db/meta.yaml b/recipes/bioconductor-hgfocus.db/meta.yaml index af9be261c0a2e..7aed356288bfa 100644 --- a/recipes/bioconductor-hgfocus.db/meta.yaml +++ b/recipes/bioconductor-hgfocus.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgfocus.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a6bee48c0aa947d3c7d25ef2c5a4d485 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgfocus.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgfocuscdf/meta.yaml b/recipes/bioconductor-hgfocuscdf/meta.yaml index 38c059916b7e8..eff511fe7d21c 100644 --- a/recipes/bioconductor-hgfocuscdf/meta.yaml +++ b/recipes/bioconductor-hgfocuscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgfocuscdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9883e53bfd9ddb9ad5f3a9c2e47bbd2c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgfocuscdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgfocusprobe/meta.yaml b/recipes/bioconductor-hgfocusprobe/meta.yaml index b8d1a35b27883..778b13ab99e1f 100644 --- a/recipes/bioconductor-hgfocusprobe/meta.yaml +++ b/recipes/bioconductor-hgfocusprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgfocusprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0a399ed276b89e3d80946b6cbbf167b4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgfocusprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133a.db/meta.yaml b/recipes/bioconductor-hgu133a.db/meta.yaml index 4ead650e6e28e..7f4d6907ae274 100644 --- a/recipes/bioconductor-hgu133a.db/meta.yaml +++ b/recipes/bioconductor-hgu133a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu133a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 97675c27b13624bdfd760460dbca6bf0 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133a2.db/meta.yaml b/recipes/bioconductor-hgu133a2.db/meta.yaml index 5451366bc530a..4d8b4ac0c42dd 100644 --- a/recipes/bioconductor-hgu133a2.db/meta.yaml +++ b/recipes/bioconductor-hgu133a2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu133a2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e3bf9c5c9941f5f378cbc3dbeb9919ee build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133a2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133a2cdf/meta.yaml b/recipes/bioconductor-hgu133a2cdf/meta.yaml index 2c72bc37d575d..f9a09d9b3bf33 100644 --- a/recipes/bioconductor-hgu133a2cdf/meta.yaml +++ b/recipes/bioconductor-hgu133a2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133a2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 566bc70f0bb94a376bf88f191a2f067e build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133a2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133a2frmavecs/meta.yaml b/recipes/bioconductor-hgu133a2frmavecs/meta.yaml index af2cc6fcc3608..94e507f7794fa 100644 --- a/recipes/bioconductor-hgu133a2frmavecs/meta.yaml +++ b/recipes/bioconductor-hgu133a2frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.2.0" %} {% set name = "hgu133a2frmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4bf8cf5cbaf288ce0a9618d764c87044 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133a2frmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133a2probe/meta.yaml b/recipes/bioconductor-hgu133a2probe/meta.yaml index d6bb19c287baf..6ee5643b2e00d 100644 --- a/recipes/bioconductor-hgu133a2probe/meta.yaml +++ b/recipes/bioconductor-hgu133a2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133a2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 736b43cfc37a297ccc0d30cb75fcc95a build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133a2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133abarcodevecs/meta.yaml b/recipes/bioconductor-hgu133abarcodevecs/meta.yaml index 47b87218b5752..c86306fc1565e 100644 --- a/recipes/bioconductor-hgu133abarcodevecs/meta.yaml +++ b/recipes/bioconductor-hgu133abarcodevecs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "hgu133abarcodevecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: af366465c10e3dbc799cdedab97d179d + md5: 4a6ec67e649f7ca004242fd860f79521 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133abarcodevecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133abarcodevecs/post-link.sh b/recipes/bioconductor-hgu133abarcodevecs/post-link.sh index b1a041adb2aa2..fba77b0ea4940 100644 --- a/recipes/bioconductor-hgu133abarcodevecs/post-link.sh +++ b/recipes/bioconductor-hgu133abarcodevecs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hgu133abarcodevecs-1.38.0" +installBiocDataPackage.sh "hgu133abarcodevecs-1.40.0" diff --git a/recipes/bioconductor-hgu133acdf/meta.yaml b/recipes/bioconductor-hgu133acdf/meta.yaml index badb6b318aba0..d4d21cf580157 100644 --- a/recipes/bioconductor-hgu133acdf/meta.yaml +++ b/recipes/bioconductor-hgu133acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133acdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d3e0e22b2d3943d26c94e7c01b91035c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133acdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133afrmavecs/meta.yaml b/recipes/bioconductor-hgu133afrmavecs/meta.yaml index 55c69a277dee1..97d6ef809ddbb 100644 --- a/recipes/bioconductor-hgu133afrmavecs/meta.yaml +++ b/recipes/bioconductor-hgu133afrmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "hgu133afrmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 85034ab02491f5b3699d210cef50812d build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133afrmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133aprobe/meta.yaml b/recipes/bioconductor-hgu133aprobe/meta.yaml index 333427025e466..289e639bf7daa 100644 --- a/recipes/bioconductor-hgu133aprobe/meta.yaml +++ b/recipes/bioconductor-hgu133aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133aprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 76cd9c54b0a8a0240dbb0fc758959d62 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133aprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133atagcdf/meta.yaml b/recipes/bioconductor-hgu133atagcdf/meta.yaml index 7e52e847c7760..96ad110b6ed05 100644 --- a/recipes/bioconductor-hgu133atagcdf/meta.yaml +++ b/recipes/bioconductor-hgu133atagcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133atagcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 01f8809e0deb5b83f3f0decec881a1d8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133atagcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133atagprobe/meta.yaml b/recipes/bioconductor-hgu133atagprobe/meta.yaml index cac2c3028f5e8..26c2b3d196144 100644 --- a/recipes/bioconductor-hgu133atagprobe/meta.yaml +++ b/recipes/bioconductor-hgu133atagprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133atagprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 97aeaf9ac9450369cf030581b8ec5a53 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133atagprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133b.db/meta.yaml b/recipes/bioconductor-hgu133b.db/meta.yaml index ffedbcc4e1d0b..1667653d2b6b0 100644 --- a/recipes/bioconductor-hgu133b.db/meta.yaml +++ b/recipes/bioconductor-hgu133b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu133b.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ff7930c99300c1022fde06ebe5c4a8cc build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133b.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133bcdf/meta.yaml b/recipes/bioconductor-hgu133bcdf/meta.yaml index 5fe9e5a76a972..0d9eb06173948 100644 --- a/recipes/bioconductor-hgu133bcdf/meta.yaml +++ b/recipes/bioconductor-hgu133bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133bcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 649aaa5e6275be6ee4d24d80ca390ea5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133bcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133bprobe/meta.yaml b/recipes/bioconductor-hgu133bprobe/meta.yaml index 92c0cd13bbe02..ea232fc9d19a3 100644 --- a/recipes/bioconductor-hgu133bprobe/meta.yaml +++ b/recipes/bioconductor-hgu133bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133bprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 203750510e51450e1267e08c241151c4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133bprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133plus2.db/meta.yaml b/recipes/bioconductor-hgu133plus2.db/meta.yaml index 08cb39b045275..cf1fe96b56771 100644 --- a/recipes/bioconductor-hgu133plus2.db/meta.yaml +++ b/recipes/bioconductor-hgu133plus2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu133plus2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 459fcf4880a9eaa25b373c5635fede3d build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133plus2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml b/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml index 22db1c1b61c76..cb5e8dfdb2d01 100644 --- a/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml +++ b/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "hgu133plus2barcodevecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a30a110289e8dff08599c97adb71adb0 + md5: 624bad8617d806474bc9406dc3c22384 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133plus2barcodevecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh b/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh index b08192bf7142d..f44c331060ecf 100644 --- a/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh +++ b/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hgu133plus2barcodevecs-1.38.0" +installBiocDataPackage.sh "hgu133plus2barcodevecs-1.40.0" diff --git a/recipes/bioconductor-hgu133plus2cdf/meta.yaml b/recipes/bioconductor-hgu133plus2cdf/meta.yaml index 98627976fb3e1..9e57c07dda204 100644 --- a/recipes/bioconductor-hgu133plus2cdf/meta.yaml +++ b/recipes/bioconductor-hgu133plus2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133plus2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 284fef2f0b777d7b53451538ddd53de3 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133plus2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133plus2cellscore/meta.yaml b/recipes/bioconductor-hgu133plus2cellscore/meta.yaml index b37309c611db0..8d4b60ba2ced3 100644 --- a/recipes/bioconductor-hgu133plus2cellscore/meta.yaml +++ b/recipes/bioconductor-hgu133plus2cellscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "hgu133plus2CellScore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 348bb596918ca6f6a51d72d20003545c + md5: 486b7084ad0056c1031545af9c6dd515 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133plus2cellscore", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133plus2cellscore/post-link.sh b/recipes/bioconductor-hgu133plus2cellscore/post-link.sh index f327ced153ca1..5db37f89ca4fd 100644 --- a/recipes/bioconductor-hgu133plus2cellscore/post-link.sh +++ b/recipes/bioconductor-hgu133plus2cellscore/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hgu133plus2cellscore-1.20.0" +installBiocDataPackage.sh "hgu133plus2cellscore-1.22.0" diff --git a/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml b/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml index c749cf9021e82..a4180048a8637 100644 --- a/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml +++ b/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "hgu133plus2frmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a4781cbcccc1ee17dfd16259f1c7bebc build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133plus2frmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133plus2probe/meta.yaml b/recipes/bioconductor-hgu133plus2probe/meta.yaml index 57d9103819acc..15f9e2c0e4cd0 100644 --- a/recipes/bioconductor-hgu133plus2probe/meta.yaml +++ b/recipes/bioconductor-hgu133plus2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133plus2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7a244787a0269bc72732ac3d830f34dd build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133plus2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu219.db/meta.yaml b/recipes/bioconductor-hgu219.db/meta.yaml index 394a442bf04bf..6207dd4fbfcc9 100644 --- a/recipes/bioconductor-hgu219.db/meta.yaml +++ b/recipes/bioconductor-hgu219.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgu219.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a4a0fd2ac170a75d8b17618615fcd7a0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu219.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu219cdf/meta.yaml b/recipes/bioconductor-hgu219cdf/meta.yaml index 63ab00e91e157..b692201bd81cd 100644 --- a/recipes/bioconductor-hgu219cdf/meta.yaml +++ b/recipes/bioconductor-hgu219cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu219cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 157a4280a9de960902260ab18f678949 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu219cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu219probe/meta.yaml b/recipes/bioconductor-hgu219probe/meta.yaml index 1e63c73163662..ce6e47caba3dd 100644 --- a/recipes/bioconductor-hgu219probe/meta.yaml +++ b/recipes/bioconductor-hgu219probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu219probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c5bb2f7b2e0f8fa89e6a30befaee6497 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu219probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu2beta7/meta.yaml b/recipes/bioconductor-hgu2beta7/meta.yaml index 1f6449fe5fdfd..e96e80fe95558 100644 --- a/recipes/bioconductor-hgu2beta7/meta.yaml +++ b/recipes/bioconductor-hgu2beta7/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "hgu2beta7" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2f1a9cc48f2608678e7349d6671a4949 + md5: 0643f49d27bf1dd6b73fb9192b23ebaa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu2beta7", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu2beta7/post-link.sh b/recipes/bioconductor-hgu2beta7/post-link.sh index 3d43283a70466..344f6120b8df6 100644 --- a/recipes/bioconductor-hgu2beta7/post-link.sh +++ b/recipes/bioconductor-hgu2beta7/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hgu2beta7-1.40.0" +installBiocDataPackage.sh "hgu2beta7-1.42.0" diff --git a/recipes/bioconductor-hgu95a.db/meta.yaml b/recipes/bioconductor-hgu95a.db/meta.yaml index c753b74895da7..304c7640fc879 100644 --- a/recipes/bioconductor-hgu95a.db/meta.yaml +++ b/recipes/bioconductor-hgu95a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu95a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b228ec0eded3ba9bccf033c2fff8f7b8 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95acdf/meta.yaml b/recipes/bioconductor-hgu95acdf/meta.yaml index 5d2431beba4fa..1b49083b8669c 100644 --- a/recipes/bioconductor-hgu95acdf/meta.yaml +++ b/recipes/bioconductor-hgu95acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95acdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: afc999d77b1532154d45911ad15a5897 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95acdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95aprobe/meta.yaml b/recipes/bioconductor-hgu95aprobe/meta.yaml index 2ccd8e5b546e5..0d469c84c6f9b 100644 --- a/recipes/bioconductor-hgu95aprobe/meta.yaml +++ b/recipes/bioconductor-hgu95aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95aprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 67d94ecdc1889acc19dafd19d26700a2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95aprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95av2.db/meta.yaml b/recipes/bioconductor-hgu95av2.db/meta.yaml index 010ebe9638fc3..3ff766aa5fb19 100644 --- a/recipes/bioconductor-hgu95av2.db/meta.yaml +++ b/recipes/bioconductor-hgu95av2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu95av2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0ada3f3c2507992b94d2daa7de8b7fbf build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95av2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95av2/meta.yaml b/recipes/bioconductor-hgu95av2/meta.yaml index ef089c5177fb9..78e1d0a7807fd 100644 --- a/recipes/bioconductor-hgu95av2/meta.yaml +++ b/recipes/bioconductor-hgu95av2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.2.0" %} {% set name = "hgu95av2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b92585c0f43e91bd1abd234b9465a6a7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95av2", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95av2cdf/meta.yaml b/recipes/bioconductor-hgu95av2cdf/meta.yaml index 928d636c24950..11a1128c63fc1 100644 --- a/recipes/bioconductor-hgu95av2cdf/meta.yaml +++ b/recipes/bioconductor-hgu95av2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95av2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 026bae2f76433593f75ca6c79bc9a9d0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95av2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95av2probe/meta.yaml b/recipes/bioconductor-hgu95av2probe/meta.yaml index 760925c3269eb..8eb701c5659f3 100644 --- a/recipes/bioconductor-hgu95av2probe/meta.yaml +++ b/recipes/bioconductor-hgu95av2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95av2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d3efb56f7e7a264b633fac787a5a2b95 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95av2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95b.db/meta.yaml b/recipes/bioconductor-hgu95b.db/meta.yaml index 84238ff673fde..ac0f7ed32a448 100644 --- a/recipes/bioconductor-hgu95b.db/meta.yaml +++ b/recipes/bioconductor-hgu95b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu95b.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 12334c263cfd9f7dc835762b4661edc1 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95b.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95bcdf/meta.yaml b/recipes/bioconductor-hgu95bcdf/meta.yaml index 0789a97b2b662..32b337096ddfa 100644 --- a/recipes/bioconductor-hgu95bcdf/meta.yaml +++ b/recipes/bioconductor-hgu95bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95bcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e6e56b7a107bb2df25b3c25a8191385d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95bcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95bprobe/meta.yaml b/recipes/bioconductor-hgu95bprobe/meta.yaml index 75853474446ae..c651f98a9e74e 100644 --- a/recipes/bioconductor-hgu95bprobe/meta.yaml +++ b/recipes/bioconductor-hgu95bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95bprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 60dcb57fd402dc24d53ef9390c893cfc build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95bprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95c.db/meta.yaml b/recipes/bioconductor-hgu95c.db/meta.yaml index 2bf3c22c651f2..5a2400c03379f 100644 --- a/recipes/bioconductor-hgu95c.db/meta.yaml +++ b/recipes/bioconductor-hgu95c.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu95c.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 680cdfc3e63853ace2ec47caa00ded36 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95c.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95ccdf/meta.yaml b/recipes/bioconductor-hgu95ccdf/meta.yaml index 22675144bbd32..1ea680ebb03a3 100644 --- a/recipes/bioconductor-hgu95ccdf/meta.yaml +++ b/recipes/bioconductor-hgu95ccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95ccdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 976151eac05c320aec7a24397a6b5806 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95ccdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95cprobe/meta.yaml b/recipes/bioconductor-hgu95cprobe/meta.yaml index 6d216269dc104..a111dd5f829b2 100644 --- a/recipes/bioconductor-hgu95cprobe/meta.yaml +++ b/recipes/bioconductor-hgu95cprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95cprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3fe935a52c70105dc7a214174c946455 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95cprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95d.db/meta.yaml b/recipes/bioconductor-hgu95d.db/meta.yaml index afceca15d1376..50de9e491ea14 100644 --- a/recipes/bioconductor-hgu95d.db/meta.yaml +++ b/recipes/bioconductor-hgu95d.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu95d.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 90ecf383640f6ab7314fa1babcdd5a0b build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95d.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95dcdf/meta.yaml b/recipes/bioconductor-hgu95dcdf/meta.yaml index 090b3ad17eb89..483baf4b30cfe 100644 --- a/recipes/bioconductor-hgu95dcdf/meta.yaml +++ b/recipes/bioconductor-hgu95dcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95dcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 36e11ff001b1bec3f34ba7c93132ad6f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95dcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95dprobe/meta.yaml b/recipes/bioconductor-hgu95dprobe/meta.yaml index 1846e53e2baa7..030c64728d67d 100644 --- a/recipes/bioconductor-hgu95dprobe/meta.yaml +++ b/recipes/bioconductor-hgu95dprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95dprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 165ce5029f49fc515b9ee0e6a6a29cb5 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95dprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95e.db/meta.yaml b/recipes/bioconductor-hgu95e.db/meta.yaml index 10cbaa486cf3e..2a6007514b8b7 100644 --- a/recipes/bioconductor-hgu95e.db/meta.yaml +++ b/recipes/bioconductor-hgu95e.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu95e.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 116bd146279d19d50a7233bc61c22104 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95e.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95ecdf/meta.yaml b/recipes/bioconductor-hgu95ecdf/meta.yaml index 7ec42cf88cbf1..909814914ac7e 100644 --- a/recipes/bioconductor-hgu95ecdf/meta.yaml +++ b/recipes/bioconductor-hgu95ecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95ecdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fa27cfff62a38fc51640d797bd628105 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95ecdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95eprobe/meta.yaml b/recipes/bioconductor-hgu95eprobe/meta.yaml index 12a28fd1e1e2c..e25fb81f9803c 100644 --- a/recipes/bioconductor-hgu95eprobe/meta.yaml +++ b/recipes/bioconductor-hgu95eprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95eprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9e5407ab80c5bbb4065484be0b9c6191 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95eprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hguatlas13k.db/meta.yaml b/recipes/bioconductor-hguatlas13k.db/meta.yaml index 82cf7b2b762cb..631974fa66149 100644 --- a/recipes/bioconductor-hguatlas13k.db/meta.yaml +++ b/recipes/bioconductor-hguatlas13k.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hguatlas13k.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ab9ffe1a1de44c0f938129f193e7fb63 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hguatlas13k.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgubeta7.db/meta.yaml b/recipes/bioconductor-hgubeta7.db/meta.yaml index 15941b6ed04f7..f952f59819473 100644 --- a/recipes/bioconductor-hgubeta7.db/meta.yaml +++ b/recipes/bioconductor-hgubeta7.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgubeta7.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1b8b065f95d2089985f59f22dcabc824 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgubeta7.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgudkfz31.db/meta.yaml b/recipes/bioconductor-hgudkfz31.db/meta.yaml index 15bad4e0ba983..797b9e34dc787 100644 --- a/recipes/bioconductor-hgudkfz31.db/meta.yaml +++ b/recipes/bioconductor-hgudkfz31.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hguDKFZ31.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fa3ba493cebdac4253dea8fe5d58452b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgudkfz31.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgug4100a.db/meta.yaml b/recipes/bioconductor-hgug4100a.db/meta.yaml index 6e31ffc0fe574..25b4d28578ec5 100644 --- a/recipes/bioconductor-hgug4100a.db/meta.yaml +++ b/recipes/bioconductor-hgug4100a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgug4100a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b7856928278a77d71f963410ea4f2376 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgug4100a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgug4101a.db/meta.yaml b/recipes/bioconductor-hgug4101a.db/meta.yaml index e95648d842503..bbddbf83684d0 100644 --- a/recipes/bioconductor-hgug4101a.db/meta.yaml +++ b/recipes/bioconductor-hgug4101a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgug4101a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e4731217efbffd05d3ee7eec68ce0aa0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgug4101a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgug4110b.db/meta.yaml b/recipes/bioconductor-hgug4110b.db/meta.yaml index a05d1cd3cc88c..288b0336f7a3f 100644 --- a/recipes/bioconductor-hgug4110b.db/meta.yaml +++ b/recipes/bioconductor-hgug4110b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgug4110b.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a9edcdbc121f22d4dec335a64598ff0e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgug4110b.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgug4111a.db/meta.yaml b/recipes/bioconductor-hgug4111a.db/meta.yaml index a693fd1e3985a..23c816d0468e7 100644 --- a/recipes/bioconductor-hgug4111a.db/meta.yaml +++ b/recipes/bioconductor-hgug4111a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgug4111a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a5f2c3b463915fa1ab0ca21e6b0f5840 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgug4111a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgug4112a.db/meta.yaml b/recipes/bioconductor-hgug4112a.db/meta.yaml index 6c34b11fe0f15..1d650ea7689f3 100644 --- a/recipes/bioconductor-hgug4112a.db/meta.yaml +++ b/recipes/bioconductor-hgug4112a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgug4112a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 67ecf8c887e2ebe1941cc51d0f5fb468 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgug4112a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgug4845a.db/meta.yaml b/recipes/bioconductor-hgug4845a.db/meta.yaml index 5417eb330561c..56bdebf753da7 100644 --- a/recipes/bioconductor-hgug4845a.db/meta.yaml +++ b/recipes/bioconductor-hgug4845a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.0.3" %} {% set name = "hgug4845a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 46133d7bcb6d8c24c026304e8ddd150d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgug4845a.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hguqiagenv3.db/meta.yaml b/recipes/bioconductor-hguqiagenv3.db/meta.yaml index 01608bf04fb8f..a89094655e843 100644 --- a/recipes/bioconductor-hguqiagenv3.db/meta.yaml +++ b/recipes/bioconductor-hguqiagenv3.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hguqiagenv3.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 91ebb82e773ff799befdb8921b38e90e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hguqiagenv3.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hi16cod.db/meta.yaml b/recipes/bioconductor-hi16cod.db/meta.yaml index f332984279757..6f2d6f8fea470 100644 --- a/recipes/bioconductor-hi16cod.db/meta.yaml +++ b/recipes/bioconductor-hi16cod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "hi16cod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: abdc77937e8d37fa5468691376ceb6a5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hi16cod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hiannotator/meta.yaml b/recipes/bioconductor-hiannotator/meta.yaml index 9cdebfe36ac76..2e398493417b3 100644 --- a/recipes/bioconductor-hiannotator/meta.yaml +++ b/recipes/bioconductor-hiannotator/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "hiAnnotator" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea7eef5accdcba1b8f0d29b7120bef7e + md5: 67e0fbd27bb6f634ccb9912642a2aeb6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hiannotator", max_pin="x.x") }}' noarch: generic # Suggests: knitr, doParallel, testthat, BiocGenerics, markdown requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-dplyr - r-foreach @@ -31,9 +32,9 @@ requirements: - r-iterators - r-scales run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-dplyr - r-foreach diff --git a/recipes/bioconductor-hibag/meta.yaml b/recipes/bioconductor-hibag/meta.yaml index 179a6f0eff2a6..1c32235779499 100644 --- a/recipes/bioconductor-hibag/meta.yaml +++ b/recipes/bioconductor-hibag/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "HIBAG" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,13 +11,14 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1cef1399370a7c97f74d0c913a1dc390 + md5: 80772de8231b22269fb6ee5401af8292 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ -# Suggests: parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray, knitr, markdown, rmarkdown + run_exports: '{{ pin_subpackage("bioconductor-hibag", max_pin="x.x") }}' +# Suggests: parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray, knitr, markdown, rmarkdown, Rsamtools # SystemRequirements: C++11, GNU make requirements: host: diff --git a/recipes/bioconductor-hibed/meta.yaml b/recipes/bioconductor-hibed/meta.yaml new file mode 100644 index 0000000000000..428afabbff047 --- /dev/null +++ b/recipes/bioconductor-hibed/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.0.0" %} +{% set name = "HiBED" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 282aec6967013cdaa790ff191e4139b4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hibed", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, testthat, IlluminaHumanMethylation450kmanifest +requirements: + host: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-flowsorted.blood.epic >=2.6.0,<2.7.0' + - 'bioconductor-flowsorted.dlpfc.450k >=1.38.0,<1.39.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-dplyr + - r-tibble + run: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-flowsorted.blood.epic >=2.6.0,<2.7.0' + - 'bioconductor-flowsorted.dlpfc.450k >=1.38.0,<1.39.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-dplyr + - r-tibble + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: HiBED + description: 'Hierarchical deconvolution for extensive cell type resolution in the human brain using DNA methylation. The HiBED deconvolution estimates proportions up to 7 cell types (GABAergic neurons, glutamatergic neurons, astrocytes, microglial cells, oligodendrocytes, endothelial cells, and stromal cells) in bulk brain tissues.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-hibed/post-link.sh b/recipes/bioconductor-hibed/post-link.sh new file mode 100644 index 0000000000000..f600caeca45ee --- /dev/null +++ b/recipes/bioconductor-hibed/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "hibed-1.0.0" diff --git a/recipes/bioconductor-hibed/pre-unlink.sh b/recipes/bioconductor-hibed/pre-unlink.sh new file mode 100644 index 0000000000000..6d37acd5139b7 --- /dev/null +++ b/recipes/bioconductor-hibed/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HiBED diff --git a/recipes/bioconductor-hicbricks/meta.yaml b/recipes/bioconductor-hicbricks/meta.yaml index 62562b1137691..929d6db889cb6 100644 --- a/recipes/bioconductor-hicbricks/meta.yaml +++ b/recipes/bioconductor-hicbricks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "HiCBricks" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96079aa0b99e8e59f4131ca070d4b978 + md5: 1c92df374e0660e328cbf53f181afd61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicbricks", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-curl - r-data.table @@ -43,12 +44,12 @@ requirements: - r-tibble - r-viridis run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-curl - r-data.table diff --git a/recipes/bioconductor-hiccompare/meta.yaml b/recipes/bioconductor-hiccompare/meta.yaml index 03eff48770c1c..2ad1ed7f62ae8 100644 --- a/recipes/bioconductor-hiccompare/meta.yaml +++ b/recipes/bioconductor-hiccompare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "HiCcompare" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67b8090713c4a7bb88e2cb00a8de8088 + md5: 081a94597115ed9f99e23930935648dd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hiccompare", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, multiHiCcompare requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr @@ -37,12 +38,12 @@ requirements: - r-mgcv - r-pheatmap run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-hicdatahumanimr90/meta.yaml b/recipes/bioconductor-hicdatahumanimr90/meta.yaml index 8867f1b1be109..f9a4a366087d4 100644 --- a/recipes/bioconductor-hicdatahumanimr90/meta.yaml +++ b/recipes/bioconductor-hicdatahumanimr90/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "HiCDataHumanIMR90" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b6b0a8e4ccf7bd132a94748c2678be4 + md5: 02854f68384130b0bcd3d0f84d94b856 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicdatahumanimr90", max_pin="x.x") }}' noarch: generic # Suggests: HiTC requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hicdatahumanimr90/post-link.sh b/recipes/bioconductor-hicdatahumanimr90/post-link.sh index 2cd37706644ae..5079a3784185d 100644 --- a/recipes/bioconductor-hicdatahumanimr90/post-link.sh +++ b/recipes/bioconductor-hicdatahumanimr90/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hicdatahumanimr90-1.20.0" +installBiocDataPackage.sh "hicdatahumanimr90-1.22.0" diff --git a/recipes/bioconductor-hicdatalymphoblast/meta.yaml b/recipes/bioconductor-hicdatalymphoblast/meta.yaml index afbbac6b1b5bb..36a2e897eb980 100644 --- a/recipes/bioconductor-hicdatalymphoblast/meta.yaml +++ b/recipes/bioconductor-hicdatalymphoblast/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "HiCDataLymphoblast" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f43877109c87896da3954f156798d19f + md5: 4e51d696b30a37414375e6987c7ab59c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicdatalymphoblast", max_pin="x.x") }}' noarch: generic # Suggests: ShortRead requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hicdatalymphoblast/post-link.sh b/recipes/bioconductor-hicdatalymphoblast/post-link.sh index 8012f2140899e..acbb04bef68ba 100644 --- a/recipes/bioconductor-hicdatalymphoblast/post-link.sh +++ b/recipes/bioconductor-hicdatalymphoblast/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hicdatalymphoblast-1.36.0" +installBiocDataPackage.sh "hicdatalymphoblast-1.38.0" diff --git a/recipes/bioconductor-hicdcplus/meta.yaml b/recipes/bioconductor-hicdcplus/meta.yaml index a0cc479209923..e014d6b12ff12 100644 --- a/recipes/bioconductor-hicdcplus/meta.yaml +++ b/recipes/bioconductor-hicdcplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "HiCDCPlus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14987ba2a7f97050a3ec2cc233edc3fd + md5: d129ae6d6c11f6f92e52399c46754b1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicdcplus", max_pin="x.x") }}' # Suggests: BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, RUnit, BiocGenerics, knitr, rmarkdown, HiTC, DESeq2, Matrix, BiocFileCache, rappdirs # SystemRequirements: JRE 8+ requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicinteractions >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bbmle - r-data.table @@ -44,15 +45,15 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicinteractions >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bbmle - r-data.table diff --git a/recipes/bioconductor-hicdoc/meta.yaml b/recipes/bioconductor-hicdoc/meta.yaml index f6b88458d963c..4fc805acafb41 100644 --- a/recipes/bioconductor-hicdoc/meta.yaml +++ b/recipes/bioconductor-hicdoc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "HiCDOC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d250c9afdc0cba742586f5202a6f54c1 + md5: 334df180a7e5e2851bbf6724e8537ffd build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: knitr, rmarkdown, testthat, BiocStyle, BiocManager + run_exports: '{{ pin_subpackage("bioconductor-hicdoc", max_pin="x.x") }}' +# Suggests: knitr, rmarkdown, testthat, BiocStyle, BiocManager, rhdf5 # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-multihiccompare >=1.18.0,<1.19.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-multihiccompare >=1.20.0,<1.21.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base + - r-cowplot - r-data.table - - r-ggextra - r-ggplot2 - - r-ggpubr - r-gridextra - r-gtools - r-pbapply @@ -43,21 +42,19 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-multihiccompare >=1.18.0,<1.19.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-multihiccompare >=1.20.0,<1.21.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base + - r-cowplot - r-data.table - - r-ggextra - r-ggplot2 - - r-ggpubr - r-gridextra - r-gtools - r-pbapply @@ -71,8 +68,8 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 3)' + license: 'file LICENSE' summary: 'A/B compartment detection and differential analysis' description: 'HiCDOC normalizes intrachromosomal Hi-C matrices, uses unsupervised learning to predict A/B compartments from multiple replicates, and detects significant compartment changes between experiment conditions. It provides a collection of functions assembled into a pipeline to filter and normalize the data, predict the compartments and visualize the results. It accepts several type of data: tabular `.tsv` files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + license_file: LICENSE diff --git a/recipes/bioconductor-hicexperiment/meta.yaml b/recipes/bioconductor-hicexperiment/meta.yaml index 564b6ffd902fe..e0267b602fd7d 100644 --- a/recipes/bioconductor-hicexperiment/meta.yaml +++ b/recipes/bioconductor-hicexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "HiCExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9208ad11b1c8c4b78cfd51e1f02c0c6e + md5: 98efc0440886cc84faef975a12f290a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicexperiment", max_pin="x.x") }}' noarch: generic # Suggests: HiContacts, HiContactsData, BiocFileCache, rtracklayer, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-matrix - r-strawr - r-vroom run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-matrix diff --git a/recipes/bioconductor-hicontacts/meta.yaml b/recipes/bioconductor-hicontacts/meta.yaml index 561198fdc347d..29ba194cc6150 100644 --- a/recipes/bioconductor-hicontacts/meta.yaml +++ b/recipes/bioconductor-hicontacts/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "HiContacts" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 023fb0be166964d39ef76d52646605b9 + md5: f7f7341e5b4cbfcd13b04fadd9c472c7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicontacts", max_pin="x.x") }}' noarch: generic # Suggests: HiContactsData, rtracklayer, GenomicFeatures, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra, patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hicexperiment >=1.0.0,<1.1.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -43,16 +44,16 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hicexperiment >=1.0.0,<1.1.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-hicontactsdata/meta.yaml b/recipes/bioconductor-hicontactsdata/meta.yaml index 0cc453c74a918..02887a5d7f1f6 100644 --- a/recipes/bioconductor-hicontactsdata/meta.yaml +++ b/recipes/bioconductor-hicontactsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "HiContactsData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d406482f89b932de475c12470bc8ef2 + md5: bcd518f48342168f7a814a442cf9564c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicontactsdata", max_pin="x.x") }}' noarch: generic # Suggests: testthat, methods, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hicontactsdata/post-link.sh b/recipes/bioconductor-hicontactsdata/post-link.sh index 5d68ca935f0be..7b88fae0e188f 100644 --- a/recipes/bioconductor-hicontactsdata/post-link.sh +++ b/recipes/bioconductor-hicontactsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hicontactsdata-1.2.0" +installBiocDataPackage.sh "hicontactsdata-1.4.0" diff --git a/recipes/bioconductor-hicool/meta.yaml b/recipes/bioconductor-hicool/meta.yaml index 317fa4a355f3a..e83c1ddf394de 100644 --- a/recipes/bioconductor-hicool/meta.yaml +++ b/recipes/bioconductor-hicool/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "HiCool" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 85a6824de7561e4879ae698959606ae3 + md5: 04aa2ef16336d5c43fc0a02291ba7887 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicool", max_pin="x.x") }}' noarch: generic # Suggests: HiContacts, HiContactsData, AnnotationHub, BiocFileCache, BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hicexperiment >=1.0.0,<1.1.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-plotly @@ -38,13 +39,13 @@ requirements: - r-stringr - r-vroom run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hicexperiment >=1.0.0,<1.1.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-plotly diff --git a/recipes/bioconductor-hicvenndiagram/build.sh b/recipes/bioconductor-hicvenndiagram/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hicvenndiagram/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hicvenndiagram/meta.yaml b/recipes/bioconductor-hicvenndiagram/meta.yaml new file mode 100644 index 0000000000000..1af9811467c2e --- /dev/null +++ b/recipes/bioconductor-hicvenndiagram/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.0.0" %} +{% set name = "hicVennDiagram" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 11577b64cc67b69e4b9d712a76cd3310 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicvenndiagram", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat, GenomicRanges, ChIPpeakAnno, grid +requirements: + host: + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-complexupset + - r-eulerr + - r-ggplot2 + - r-htmlwidgets + - r-reshape2 + - r-svglite + run: + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-complexupset + - r-eulerr + - r-ggplot2 + - r-htmlwidgets + - r-reshape2 + - r-svglite +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Venn Diagram for genomic interaction data' + description: 'A package to generate high-resolution Venn and Upset plots for genomic interaction data from HiC, ChIA-PET, HiChIP, PLAC-Seq, Hi-TrAC, HiCAR and etc. The package generates plots specifically crafted to eliminate the deceptive visual representation caused by the counts method.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-hiergwas/meta.yaml b/recipes/bioconductor-hiergwas/meta.yaml index b41f1c2b2abd5..917a0f7876b4a 100644 --- a/recipes/bioconductor-hiergwas/meta.yaml +++ b/recipes/bioconductor-hiergwas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "hierGWAS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45c3d0bd8020ffaecf28ef7286a7a576 + md5: 9f15cfa27c8d57b818fc7913d8a9093b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hiergwas", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, RUnit, MASS requirements: diff --git a/recipes/bioconductor-hierinf/meta.yaml b/recipes/bioconductor-hierinf/meta.yaml index d65f0760094db..b55d1417ca221 100644 --- a/recipes/bioconductor-hierinf/meta.yaml +++ b/recipes/bioconductor-hierinf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "hierinf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8798721587604faf688e4c1b508d672f + md5: 44446a50b3747865eadceabe415ce6f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hierinf", max_pin="x.x") }}' noarch: generic # Suggests: knitr, MASS, testthat requirements: diff --git a/recipes/bioconductor-highlyreplicatedrnaseq/meta.yaml b/recipes/bioconductor-highlyreplicatedrnaseq/meta.yaml index 3567a002b6c79..936d3d703dbea 100644 --- a/recipes/bioconductor-highlyreplicatedrnaseq/meta.yaml +++ b/recipes/bioconductor-highlyreplicatedrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "HighlyReplicatedRNASeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b5773c61f0e87d562b2c18aec8992689 + md5: a397cddffb2dfea70943930b992ea7c0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-highlyreplicatedrnaseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BiocFileCache, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-highlyreplicatedrnaseq/post-link.sh b/recipes/bioconductor-highlyreplicatedrnaseq/post-link.sh index f6a1f5964f310..fdd22acfec305 100644 --- a/recipes/bioconductor-highlyreplicatedrnaseq/post-link.sh +++ b/recipes/bioconductor-highlyreplicatedrnaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "highlyreplicatedrnaseq-1.12.0" +installBiocDataPackage.sh "highlyreplicatedrnaseq-1.14.0" diff --git a/recipes/bioconductor-hiiragi2013/meta.yaml b/recipes/bioconductor-hiiragi2013/meta.yaml index c674fc61ef82e..1db7f4d8b615d 100644 --- a/recipes/bioconductor-hiiragi2013/meta.yaml +++ b/recipes/bioconductor-hiiragi2013/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "Hiiragi2013" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5e1b258226d9b83620113705d7328537 + md5: dde13f333fe218976f71b626ed5eefa4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hiiragi2013", max_pin="x.x") }}' noarch: generic # Suggests: ArrayExpress, BiocStyle requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' - 'bioconductor-mouse4302.db >=3.13.0,<3.14.0' - r-base - r-boot @@ -39,11 +40,11 @@ requirements: - r-rcolorbrewer - r-xtable run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' - 'bioconductor-mouse4302.db >=3.13.0,<3.14.0' - r-base - r-boot @@ -57,7 +58,7 @@ requirements: - r-rcolorbrewer - r-xtable - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hiiragi2013/post-link.sh b/recipes/bioconductor-hiiragi2013/post-link.sh index 54941404046eb..6c78d22253936 100644 --- a/recipes/bioconductor-hiiragi2013/post-link.sh +++ b/recipes/bioconductor-hiiragi2013/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hiiragi2013-1.36.0" +installBiocDataPackage.sh "hiiragi2013-1.38.0" diff --git a/recipes/bioconductor-hilbertcurve/meta.yaml b/recipes/bioconductor-hilbertcurve/meta.yaml index a798fd8a3c838..f707d6bb5a83d 100644 --- a/recipes/bioconductor-hilbertcurve/meta.yaml +++ b/recipes/bioconductor-hilbertcurve/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "HilbertCurve" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ef390a5043853c3354d9e42c80b07c6 + md5: 97eed8a87d8bb062c5d0b900823f6bcc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hilbertcurve", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0), markdown, RColorBrewer, RCurl, GetoptLong, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hilbertvis >=1.58.0,<1.59.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hilbertvis >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-circlize >=0.3.3' - r-png - r-polylabelr run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hilbertvis >=1.58.0,<1.59.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hilbertvis >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-circlize >=0.3.3' - r-png diff --git a/recipes/bioconductor-hilbertvis/meta.yaml b/recipes/bioconductor-hilbertvis/meta.yaml index 451f5b82abc9f..5429956b9e0ec 100644 --- a/recipes/bioconductor-hilbertvis/meta.yaml +++ b/recipes/bioconductor-hilbertvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "HilbertVis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: beb6450c2b3c3d94e39eb524d45afe67 + md5: b30abc9c50034b41daf1399031d657e3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hilbertvis", max_pin="x.x") }}' # Suggests: IRanges, EBImage requirements: host: diff --git a/recipes/bioconductor-hilbertvisgui/meta.yaml b/recipes/bioconductor-hilbertvisgui/meta.yaml index 48b6967bdc1f3..4f51df3df8f16 100644 --- a/recipes/bioconductor-hilbertvisgui/meta.yaml +++ b/recipes/bioconductor-hilbertvisgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "HilbertVisGUI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 136f8bed06155ff4bb34296d1badeeaf + md5: e9e6a2cce82ff0dfcf0828ae7d123537 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hilbertvisgui", max_pin="x.x") }}' # Suggests: lattice, IRanges # SystemRequirements: gtkmm-2.4, GNU make requirements: host: - - 'bioconductor-hilbertvis >=1.58.0,<1.59.0' + - 'bioconductor-hilbertvis >=1.60.0,<1.61.0' - r-base - libblas - liblapack run: - - 'bioconductor-hilbertvis >=1.58.0,<1.59.0' + - 'bioconductor-hilbertvis >=1.60.0,<1.61.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-hilda/meta.yaml b/recipes/bioconductor-hilda/meta.yaml index c033529d0324a..903151efa8394 100644 --- a/recipes/bioconductor-hilda/meta.yaml +++ b/recipes/bioconductor-hilda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "HiLDA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 049c4b0dd5f94cdfe518adce6ea1a06b + md5: e1961cfe72082b160cafb7bed5376673 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hilda", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, BiocStyle # SystemRequirements: JAGS 4.0.0 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-abind - r-base - r-cowplot @@ -41,14 +42,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-abind - r-base - r-cowplot diff --git a/recipes/bioconductor-hipathia/meta.yaml b/recipes/bioconductor-hipathia/meta.yaml index 2b581de926e97..60ebebd0e0391 100644 --- a/recipes/bioconductor-hipathia/meta.yaml +++ b/recipes/bioconductor-hipathia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.0.2" %} +{% set version = "3.2.0" %} {% set name = "hipathia" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c860da6e2d2c33a8d0d95fb98937e84f + md5: 819d2eecca55d3d4708934bbe69e82a7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hipathia", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-coin - r-dplyr @@ -41,13 +42,13 @@ requirements: - r-tibble - r-visnetwork run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-coin - r-dplyr diff --git a/recipes/bioconductor-hippo/meta.yaml b/recipes/bioconductor-hippo/meta.yaml index 80bf3cdc252fc..6daf28263c519 100644 --- a/recipes/bioconductor-hippo/meta.yaml +++ b/recipes/bioconductor-hippo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "HIPPO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9bdc02f89b2c3955b27e6b1f88c56009 + md5: 6c249e5f8b3f2a0622642c945e8d0566 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hippo", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-dplyr - r-ggplot2 @@ -35,7 +36,7 @@ requirements: - r-rtsne - r-umap run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-hireadsprocessor/meta.yaml b/recipes/bioconductor-hireadsprocessor/meta.yaml index a8a127edfc54f..fa5d6a94b7947 100644 --- a/recipes/bioconductor-hireadsprocessor/meta.yaml +++ b/recipes/bioconductor-hireadsprocessor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "hiReadsProcessor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5784280fe7e882437b725ade4fa5be3b + md5: 8a194956515b40e5dc75f90cafdea5c6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hireadsprocessor", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, markdown # SystemRequirements: BLAT, UCSC hg18 in 2bit format for BLAT requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hiannotator >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hiannotator >=1.36.0,<1.37.0' - r-base - r-dplyr - r-readxl - r-soniclength run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hiannotator >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hiannotator >=1.36.0,<1.37.0' - r-base - r-dplyr - r-readxl diff --git a/recipes/bioconductor-hireewas/meta.yaml b/recipes/bioconductor-hireewas/meta.yaml index 87c98011e2791..88bfdf68e2cc3 100644 --- a/recipes/bioconductor-hireewas/meta.yaml +++ b/recipes/bioconductor-hireewas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "HIREewas" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 68ec415918f2959671fd619fb8fbcf90 + md5: fd57bb11c16b2d194d7950ce0d918899 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hireewas", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, BiocGenerics requirements: host: diff --git a/recipes/bioconductor-hitc/meta.yaml b/recipes/bioconductor-hitc/meta.yaml index 98920c992a893..6d1346745d845 100644 --- a/recipes/bioconductor-hitc/meta.yaml +++ b/recipes/bioconductor-hitc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "HiTC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5dceec926506e3c6a416c44671e5cb5f + md5: e530516c0386e2e9bb6ff9afbed5893f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hitc", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, HiCDataHumanIMR90 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-matrix - r-rcolorbrewer run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-matrix - r-rcolorbrewer diff --git a/recipes/bioconductor-hivcdnavantwout03/meta.yaml b/recipes/bioconductor-hivcdnavantwout03/meta.yaml index 6602f1bbdecd6..9f5b6824060b5 100644 --- a/recipes/bioconductor-hivcdnavantwout03/meta.yaml +++ b/recipes/bioconductor-hivcdnavantwout03/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "HIVcDNAvantWout03" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 349ef6469ce73790078ba4b5d5206856 + md5: 4936f53bb66cdf1983a8bcbcd667a188 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hivcdnavantwout03", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hivcdnavantwout03/post-link.sh b/recipes/bioconductor-hivcdnavantwout03/post-link.sh index 4e772af309820..0eb40797b7714 100644 --- a/recipes/bioconductor-hivcdnavantwout03/post-link.sh +++ b/recipes/bioconductor-hivcdnavantwout03/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hivcdnavantwout03-1.40.0" +installBiocDataPackage.sh "hivcdnavantwout03-1.42.0" diff --git a/recipes/bioconductor-hivprtplus2cdf/meta.yaml b/recipes/bioconductor-hivprtplus2cdf/meta.yaml index b28324248c239..31d0377db8de7 100644 --- a/recipes/bioconductor-hivprtplus2cdf/meta.yaml +++ b/recipes/bioconductor-hivprtplus2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hivprtplus2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 143d9c2f5f328786bae7bb8dc4daf261 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hivprtplus2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hmdbquery/meta.yaml b/recipes/bioconductor-hmdbquery/meta.yaml index 47353fc6f4f3d..a34079bd13563 100644 --- a/recipes/bioconductor-hmdbquery/meta.yaml +++ b/recipes/bioconductor-hmdbquery/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "hmdbQuery" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 07cb71866c0245628fece30b4d78c20c + md5: 32b8de26d3b369730bdd7c734da1be06 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hmdbquery", max_pin="x.x") }}' noarch: generic # Suggests: knitr, annotate, gwascat, testthat, rmarkdown requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-xml run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-xml test: diff --git a/recipes/bioconductor-hmmcopy/meta.yaml b/recipes/bioconductor-hmmcopy/meta.yaml index ed6c77c7597a7..a89ef06cc7afb 100644 --- a/recipes/bioconductor-hmmcopy/meta.yaml +++ b/recipes/bioconductor-hmmcopy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "HMMcopy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a987a0438c7464de68cbebfae70d0c21 + md5: 4785371e1642cd191330693396010a6e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hmmcopy", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-hmp16sdata/meta.yaml b/recipes/bioconductor-hmp16sdata/meta.yaml index 71a98fda6e53f..36851b9076422 100644 --- a/recipes/bioconductor-hmp16sdata/meta.yaml +++ b/recipes/bioconductor-hmp16sdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "HMP16SData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a62c1eec817f876e015ee98ab937dfc6 + md5: a137f917000e15acffca9bb0baac8fbb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hmp16sdata", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, circlize, cowplot, dendextend, devtools, ggplot2, gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats, testthat, tidyr requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-dplyr @@ -35,10 +36,10 @@ requirements: - r-stringr - r-tibble run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-dplyr @@ -49,7 +50,7 @@ requirements: - r-stringr - r-tibble - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hmp16sdata/post-link.sh b/recipes/bioconductor-hmp16sdata/post-link.sh index 53146c48205ef..43a01f6fffd29 100644 --- a/recipes/bioconductor-hmp16sdata/post-link.sh +++ b/recipes/bioconductor-hmp16sdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hmp16sdata-1.20.0" +installBiocDataPackage.sh "hmp16sdata-1.22.0" diff --git a/recipes/bioconductor-hmp2data/meta.yaml b/recipes/bioconductor-hmp2data/meta.yaml index 6cb82db03492c..0f1a1a16733fa 100644 --- a/recipes/bioconductor-hmp2data/meta.yaml +++ b/recipes/bioconductor-hmp2data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "HMP2Data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ff1bf8c6b78ebe9c09578c775c35a54a + md5: f334416386d2c1af677494e1fd5743d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hmp2data", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, cowplot, devtools, ggplot2, gridExtra, haven, rmarkdown, roxygen2, stats, testthat, tibble, UpSetR requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-data.table @@ -36,12 +37,12 @@ requirements: - r-magrittr - r-readr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-data.table @@ -51,7 +52,7 @@ requirements: - r-magrittr - r-readr - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hmp2data/post-link.sh b/recipes/bioconductor-hmp2data/post-link.sh index 4529a31a1c7c9..22fac5c1ff254 100644 --- a/recipes/bioconductor-hmp2data/post-link.sh +++ b/recipes/bioconductor-hmp2data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hmp2data-1.14.0" +installBiocDataPackage.sh "hmp2data-1.16.0" diff --git a/recipes/bioconductor-homo.sapiens/meta.yaml b/recipes/bioconductor-homo.sapiens/meta.yaml index e9410c2285835..4f0fdece86a13 100644 --- a/recipes/bioconductor-homo.sapiens/meta.yaml +++ b/recipes/bioconductor-homo.sapiens/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1" %} {% set name = "Homo.sapiens" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 653b60cfcdaefd171729115cd629b585 build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-homo.sapiens", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hoodscanr/build.sh b/recipes/bioconductor-hoodscanr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hoodscanr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hoodscanr/meta.yaml b/recipes/bioconductor-hoodscanr/meta.yaml new file mode 100644 index 0000000000000..61cbf0679547a --- /dev/null +++ b/recipes/bioconductor-hoodscanr/meta.yaml @@ -0,0 +1,64 @@ +{% set version = "1.0.0" %} +{% set name = "hoodscanR" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c5ac598990d1f80bfa526c576abc8d84 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hoodscanr", max_pin="x.x") }}' +# Suggests: testthat (>= 3.0.0), BiocStyle +requirements: + host: + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-circlize + - r-ggplot2 + - r-knitr + - r-rann + - 'r-rcpp >=1.0.9' + - r-rlang + - r-rmarkdown + - r-scico + - libblas + - liblapack + run: + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-circlize + - r-ggplot2 + - r-knitr + - r-rann + - 'r-rcpp >=1.0.9' + - r-rlang + - r-rmarkdown + - r-scico + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'Spatial cellular neighbourhood scanning in R' + description: 'hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. The package can result in cell-level neighborhood annotation output, along with funtions to perform neighborhood colocalization analysis and neighborhood-based cell clustering.' + license_file: LICENSE + diff --git a/recipes/bioconductor-hopach/meta.yaml b/recipes/bioconductor-hopach/meta.yaml index da2f11af0c567..e515605dc2dc5 100644 --- a/recipes/bioconductor-hopach/meta.yaml +++ b/recipes/bioconductor-hopach/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.60.0" %} +{% set version = "2.62.0" %} {% set name = "hopach" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 467cdea6eebc9401118e603250a9bd49 + md5: 0310e9a4e3a34dfe2bb4edf0dbb38b16 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hopach", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-cluster - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-cluster build: diff --git a/recipes/bioconductor-hpaanalyze/meta.yaml b/recipes/bioconductor-hpaanalyze/meta.yaml index 29f4ddb00001f..73545f1379178 100644 --- a/recipes/bioconductor-hpaanalyze/meta.yaml +++ b/recipes/bioconductor-hpaanalyze/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "HPAanalyze" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ebdbe83c9d26b640324bb4274e06c457 + md5: 0916d6c86a23a3c136b3d0f1de2a25f4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hpaanalyze", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, markdown, devtools, BiocStyle requirements: diff --git a/recipes/bioconductor-hpannot/meta.yaml b/recipes/bioconductor-hpannot/meta.yaml index 44551ef27ed75..0f3297ff458a5 100644 --- a/recipes/bioconductor-hpannot/meta.yaml +++ b/recipes/bioconductor-hpannot/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "hpAnnot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fbc94a00b0f33b41bc5ff53fbe060663 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hpannot", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hpar/meta.yaml b/recipes/bioconductor-hpar/meta.yaml index e03e05050d958..a49dd41f591c0 100644 --- a/recipes/bioconductor-hpar/meta.yaml +++ b/recipes/bioconductor-hpar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "hpar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f2a2355b84c7204ab11bec266f8b63c0 + md5: f970b068a2112cd8bf1a8dfb7d29d86a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hpar", max_pin="x.x") }}' noarch: generic # Suggests: org.Hs.eg.db, GO.db, AnnotationDbi, knitr, BiocStyle, testthat, rmarkdown, dplyr, DT requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base test: commands: diff --git a/recipes/bioconductor-hpip/meta.yaml b/recipes/bioconductor-hpip/meta.yaml index 4149d4c6262cf..a97924166d6b7 100644 --- a/recipes/bioconductor-hpip/meta.yaml +++ b/recipes/bioconductor-hpip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "HPiP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90bdbe4811dfb9bad8305ce85a67810f + md5: cbf5bf4735e100b22b184490854f8427 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hpip", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, colorspace, e1071, kernlab, ranger, SummarizedExperiment, Biostrings, randomForest, gprofiler2, gridExtra, ggthemes, BiocStyle, BiocGenerics, RUnit, tools, knitr requirements: diff --git a/recipes/bioconductor-hpo.db/meta.yaml b/recipes/bioconductor-hpo.db/meta.yaml new file mode 100644 index 0000000000000..64e2223e94fa9 --- /dev/null +++ b/recipes/bioconductor-hpo.db/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "0.99.2" %} +{% set name = "HPO.db" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 977cfb31ff344c58fd2dd0a2c6b765ab +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hpo.db", max_pin="x.x") }}' + noarch: generic +# Suggests: rmarkdown, knitr, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - r-base + - r-dbi + run: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - r-base + - r-dbi + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A set of annotation maps describing the entire Human Phenotype Ontology' + description: 'Human Phenotype Ontology (HPO) was developed to create a consistent description of gene products with disease perspectives, and is essential for supporting functional genomics in disease context. Accurate disease descriptions can discover new relationships between genes and disease, and new functions for previous uncharacteried genes and alleles.We have developed the [DOSE](https://bioconductor.org/packages/DOSE/) package for semantic similarity analysis and disease enrichment analysis, and `DOSE` import an Bioconductor package ''DO.db'' to get the relationship(such as parent and child) between MPO terms. But `DO.db` hasn''t been updated for years, and a lot of semantic information is [missing](https://github.com/YuLab-SMU/DOSE/issues/57). So we developed the new package `HPO.db` for Human Human Phenotype Ontology annotation.' + diff --git a/recipes/bioconductor-hpo.db/post-link.sh b/recipes/bioconductor-hpo.db/post-link.sh new file mode 100644 index 0000000000000..4ac86e1be7109 --- /dev/null +++ b/recipes/bioconductor-hpo.db/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "hpo.db-0.99.2" diff --git a/recipes/bioconductor-hpo.db/pre-unlink.sh b/recipes/bioconductor-hpo.db/pre-unlink.sh new file mode 100644 index 0000000000000..9a0102a6c36f3 --- /dev/null +++ b/recipes/bioconductor-hpo.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HPO.db diff --git a/recipes/bioconductor-hs25kresogen.db/meta.yaml b/recipes/bioconductor-hs25kresogen.db/meta.yaml index 8483c7419e451..6c8d7424a4441 100644 --- a/recipes/bioconductor-hs25kresogen.db/meta.yaml +++ b/recipes/bioconductor-hs25kresogen.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.5.0" %} {% set name = "hs25kresogen.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a3800d072ce0e5f6f5d8299538b99cca build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hs25kresogen.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hs6ug171.db/meta.yaml b/recipes/bioconductor-hs6ug171.db/meta.yaml index 1e054aa31431c..17b3f570c6ea2 100644 --- a/recipes/bioconductor-hs6ug171.db/meta.yaml +++ b/recipes/bioconductor-hs6ug171.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "Hs6UG171.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7aaf8a2441941f70247275c93735ed3b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hs6ug171.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml b/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml index 557b34846786b..d5d0b53d117d3 100644 --- a/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml +++ b/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "HsAgilentDesign026652.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: dcd2c748bf9d7c002611cd5cf2ff38c0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hsagilentdesign026652.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hsmmsinglecell/meta.yaml b/recipes/bioconductor-hsmmsinglecell/meta.yaml index 90bf4930e5134..642e145c87cf4 100644 --- a/recipes/bioconductor-hsmmsinglecell/meta.yaml +++ b/recipes/bioconductor-hsmmsinglecell/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "HSMMSingleCell" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 52c7427453286b6ba0f069bdf32457ac + md5: dae440cd20110d25cd699a9a792ac4b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hsmmsinglecell", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hsmmsinglecell/post-link.sh b/recipes/bioconductor-hsmmsinglecell/post-link.sh index 2641c42f34ab9..eac2f6e837b9c 100644 --- a/recipes/bioconductor-hsmmsinglecell/post-link.sh +++ b/recipes/bioconductor-hsmmsinglecell/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hsmmsinglecell-1.20.0" +installBiocDataPackage.sh "hsmmsinglecell-1.22.0" diff --git a/recipes/bioconductor-hspec/meta.yaml b/recipes/bioconductor-hspec/meta.yaml index 02477afe83c34..cdb859d14a07b 100644 --- a/recipes/bioconductor-hspec/meta.yaml +++ b/recipes/bioconductor-hspec/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.1" %} {% set name = "Hspec" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0ade3e3147c8f0086e9be2312cccdfeb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hspec", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hspeccdf/meta.yaml b/recipes/bioconductor-hspeccdf/meta.yaml index 9b21052295be1..9d7ecbfd4107f 100644 --- a/recipes/bioconductor-hspeccdf/meta.yaml +++ b/recipes/bioconductor-hspeccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.1" %} {% set name = "hspeccdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 89f81adf91094710558ce6aec79fc7fd build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hspeccdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hta20probeset.db/meta.yaml b/recipes/bioconductor-hta20probeset.db/meta.yaml index 6f17e022b4c21..8954764a4ca49 100644 --- a/recipes/bioconductor-hta20probeset.db/meta.yaml +++ b/recipes/bioconductor-hta20probeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hta20probeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8cc15bb71f3c2776015e55a2d7df2c2f build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hta20probeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml b/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml index 53b86adaec017..e8c9ccf5eb116 100644 --- a/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hta20transcriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9debbc190cc5f9f0ad97fbc452fe7025 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hta20transcriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133a.db/meta.yaml b/recipes/bioconductor-hthgu133a.db/meta.yaml index 441fc2ed9e54c..726b1974b31d6 100644 --- a/recipes/bioconductor-hthgu133a.db/meta.yaml +++ b/recipes/bioconductor-hthgu133a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hthgu133a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 769ed088760102b61edfb73454d4c642 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133acdf/meta.yaml b/recipes/bioconductor-hthgu133acdf/meta.yaml index b389ed5eb5dc1..beceffbf2be85 100644 --- a/recipes/bioconductor-hthgu133acdf/meta.yaml +++ b/recipes/bioconductor-hthgu133acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hthgu133acdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b92e543867f1f0c08bfa9299e123d608 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133acdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133afrmavecs/meta.yaml b/recipes/bioconductor-hthgu133afrmavecs/meta.yaml index e0c87d4d7752c..c0d9ce5809f99 100644 --- a/recipes/bioconductor-hthgu133afrmavecs/meta.yaml +++ b/recipes/bioconductor-hthgu133afrmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.0" %} {% set name = "hthgu133afrmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: be3f3d67a94dca3b080c184fba5ff6d8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133afrmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133aprobe/meta.yaml b/recipes/bioconductor-hthgu133aprobe/meta.yaml index e5e532ddf982f..e97081613b6ed 100644 --- a/recipes/bioconductor-hthgu133aprobe/meta.yaml +++ b/recipes/bioconductor-hthgu133aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hthgu133aprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: cdc17ea670719f055ee75bea1415c754 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133aprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133b.db/meta.yaml b/recipes/bioconductor-hthgu133b.db/meta.yaml index c3e967bc610b3..3f1e467464b75 100644 --- a/recipes/bioconductor-hthgu133b.db/meta.yaml +++ b/recipes/bioconductor-hthgu133b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hthgu133b.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8501401a7385e28173ea7b60aa3bf3d2 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133b.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133bcdf/meta.yaml b/recipes/bioconductor-hthgu133bcdf/meta.yaml index df1055745d8cc..de3ebaee98b4e 100644 --- a/recipes/bioconductor-hthgu133bcdf/meta.yaml +++ b/recipes/bioconductor-hthgu133bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hthgu133bcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 935ae53fb168d9c7890d71020ef4c366 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133bcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133bprobe/meta.yaml b/recipes/bioconductor-hthgu133bprobe/meta.yaml index 10ebfd0f24b6d..4cb19a19a6c5e 100644 --- a/recipes/bioconductor-hthgu133bprobe/meta.yaml +++ b/recipes/bioconductor-hthgu133bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hthgu133bprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8a2e306638a81fdec3b10a014c04c6b9 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133bprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133plusa.db/meta.yaml b/recipes/bioconductor-hthgu133plusa.db/meta.yaml index cd705a0211333..b6fdded12559a 100644 --- a/recipes/bioconductor-hthgu133plusa.db/meta.yaml +++ b/recipes/bioconductor-hthgu133plusa.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hthgu133plusa.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 477cb32e1d8eb6da894486ad810b4232 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133plusa.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133plusb.db/meta.yaml b/recipes/bioconductor-hthgu133plusb.db/meta.yaml index bbbc178516b64..091a03b1a4e40 100644 --- a/recipes/bioconductor-hthgu133plusb.db/meta.yaml +++ b/recipes/bioconductor-hthgu133plusb.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hthgu133plusb.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f3214792ba174598b0559937f46de937 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133plusb.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133pluspm.db/meta.yaml b/recipes/bioconductor-hthgu133pluspm.db/meta.yaml index 9d1d8b6afe384..b7b803fc73c0b 100644 --- a/recipes/bioconductor-hthgu133pluspm.db/meta.yaml +++ b/recipes/bioconductor-hthgu133pluspm.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hthgu133pluspm.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b0b3cb0174608d5705ae6c80dac02e3c build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133pluspm.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml b/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml index 11cf38a94bffc..a4bcc1b6c3e99 100644 --- a/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml +++ b/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hthgu133pluspmcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 56d15101d59decac7811caa15b349a9c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133pluspmcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml b/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml index aa659bd92d900..4906c52b78aba 100644 --- a/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml +++ b/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hthgu133pluspmprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 74713e822a689007892d0eb92dbd456b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133pluspmprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430a.db/meta.yaml b/recipes/bioconductor-htmg430a.db/meta.yaml index 992f7a3ddbcfd..e8fbd4bfd804b 100644 --- a/recipes/bioconductor-htmg430a.db/meta.yaml +++ b/recipes/bioconductor-htmg430a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "htmg430a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 171e457946a6b485b2ebd928b233abb3 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htmg430a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430acdf/meta.yaml b/recipes/bioconductor-htmg430acdf/meta.yaml index cfe9d18a3c394..4e08e47255617 100644 --- a/recipes/bioconductor-htmg430acdf/meta.yaml +++ b/recipes/bioconductor-htmg430acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htmg430acdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: aef7a3c3af7d2624ee6fc6f2d22472e2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htmg430acdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430aprobe/meta.yaml b/recipes/bioconductor-htmg430aprobe/meta.yaml index 6cbe7e27d40fd..6c1055bf656d9 100644 --- a/recipes/bioconductor-htmg430aprobe/meta.yaml +++ b/recipes/bioconductor-htmg430aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htmg430aprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e50cc49b8887b6ef8ee1152ec12d5010 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htmg430aprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430b.db/meta.yaml b/recipes/bioconductor-htmg430b.db/meta.yaml index f6e1f271c9b60..24cdd2d9eedb8 100644 --- a/recipes/bioconductor-htmg430b.db/meta.yaml +++ b/recipes/bioconductor-htmg430b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "htmg430b.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 70849a636e972a9be604a3320d3bd814 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htmg430b.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430bcdf/meta.yaml b/recipes/bioconductor-htmg430bcdf/meta.yaml index d32357e1f15e4..b404825d00bc8 100644 --- a/recipes/bioconductor-htmg430bcdf/meta.yaml +++ b/recipes/bioconductor-htmg430bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htmg430bcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 53cc1408504a5f07b5655aa46b969157 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htmg430bcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430bprobe/meta.yaml b/recipes/bioconductor-htmg430bprobe/meta.yaml index d40dc72edf64d..bcfd9933555af 100644 --- a/recipes/bioconductor-htmg430bprobe/meta.yaml +++ b/recipes/bioconductor-htmg430bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htmg430bprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f0e3eb56925d786762dee0c2dc82b530 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htmg430bprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430pm.db/meta.yaml b/recipes/bioconductor-htmg430pm.db/meta.yaml index bd147bd809bba..b5ad88deeedc5 100644 --- a/recipes/bioconductor-htmg430pm.db/meta.yaml +++ b/recipes/bioconductor-htmg430pm.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "htmg430pm.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f89738ce2e33d1c626aa2d15cd28a49b build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htmg430pm.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430pmcdf/meta.yaml b/recipes/bioconductor-htmg430pmcdf/meta.yaml index 6598a4053c830..02705c76b099c 100644 --- a/recipes/bioconductor-htmg430pmcdf/meta.yaml +++ b/recipes/bioconductor-htmg430pmcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htmg430pmcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 016a54b47adbbed7db989787646a0084 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htmg430pmcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430pmprobe/meta.yaml b/recipes/bioconductor-htmg430pmprobe/meta.yaml index 7963d5f2b45b5..cd3aa90766fbd 100644 --- a/recipes/bioconductor-htmg430pmprobe/meta.yaml +++ b/recipes/bioconductor-htmg430pmprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htmg430pmprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f0e053fcc0ca4b5f8c539fc0a3fcb076 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htmg430pmprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htqpcr/meta.yaml b/recipes/bioconductor-htqpcr/meta.yaml index 0b89fd93b0257..4edbbedacde98 100644 --- a/recipes/bioconductor-htqpcr/meta.yaml +++ b/recipes/bioconductor-htqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "HTqPCR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0b6c73d30c4d92cb932c68e530ac22d4 + md5: 2deab9ff0c0269549b377a0867482f60 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htqpcr", max_pin="x.x") }}' noarch: generic # Suggests: statmod requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-gplots - r-rcolorbrewer run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-gplots - r-rcolorbrewer diff --git a/recipes/bioconductor-htrat230pm.db/meta.yaml b/recipes/bioconductor-htrat230pm.db/meta.yaml index ce30dfb169040..949dfe5fa1ff5 100644 --- a/recipes/bioconductor-htrat230pm.db/meta.yaml +++ b/recipes/bioconductor-htrat230pm.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "htrat230pm.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 46ed50806c568bf269fe4c51d3df3955 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htrat230pm.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htrat230pmcdf/meta.yaml b/recipes/bioconductor-htrat230pmcdf/meta.yaml index 045ccb437f648..fc6ec741ec909 100644 --- a/recipes/bioconductor-htrat230pmcdf/meta.yaml +++ b/recipes/bioconductor-htrat230pmcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htrat230pmcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c6683d16e8aacccd326f7a7eebb79b98 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htrat230pmcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htrat230pmprobe/meta.yaml b/recipes/bioconductor-htrat230pmprobe/meta.yaml index 720e243a1d53e..b1e1040532964 100644 --- a/recipes/bioconductor-htrat230pmprobe/meta.yaml +++ b/recipes/bioconductor-htrat230pmprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htrat230pmprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e4deeca2dc406367ac4a347e370267cf build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htrat230pmprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htratfocus.db/meta.yaml b/recipes/bioconductor-htratfocus.db/meta.yaml index dc4fbc3c4b3f7..a270b55119363 100644 --- a/recipes/bioconductor-htratfocus.db/meta.yaml +++ b/recipes/bioconductor-htratfocus.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "htratfocus.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 88be90edb1acb31faedde0b66b27a150 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htratfocus.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htratfocuscdf/meta.yaml b/recipes/bioconductor-htratfocuscdf/meta.yaml index 4d6249beb0e25..e0495aa07b0d0 100644 --- a/recipes/bioconductor-htratfocuscdf/meta.yaml +++ b/recipes/bioconductor-htratfocuscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htratfocuscdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 04b4952f7d8b607a7eb0f779c08c57dc build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htratfocuscdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htratfocusprobe/meta.yaml b/recipes/bioconductor-htratfocusprobe/meta.yaml index 89cf2296d49f0..e79a05ee51073 100644 --- a/recipes/bioconductor-htratfocusprobe/meta.yaml +++ b/recipes/bioconductor-htratfocusprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htratfocusprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 26a0963d8aff314a4a1f2c47e9147a8a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htratfocusprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htseqgenie/meta.yaml b/recipes/bioconductor-htseqgenie/meta.yaml index 41cdbbce8ef23..088cb8b6a16d9 100644 --- a/recipes/bioconductor-htseqgenie/meta.yaml +++ b/recipes/bioconductor-htseqgenie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.30.0" %} +{% set version = "4.32.0" %} {% set name = "HTSeqGenie" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,54 +11,55 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ace11ef8422722f14ec1c7fcf7b6164 + md5: 000b728da136ce28e0204ed5b8752792 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htseqgenie", max_pin="x.x") }}' noarch: generic -# Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, LungCancerLines, org.Hs.eg.db +# Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, LungCancerLines, org.Hs.eg.db, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-chipseq >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gmapr >=1.42.0,<1.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-varianttools >=1.42.0,<1.43.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-chipseq >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gmapr >=1.44.0,<1.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-varianttools >=1.44.0,<1.45.0' - r-base - 'r-cairo >=1.5.5' - 'r-hwriter >=1.3.0' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-chipseq >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gmapr >=1.42.0,<1.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-varianttools >=1.42.0,<1.43.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-chipseq >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gmapr >=1.44.0,<1.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-varianttools >=1.44.0,<1.45.0' - r-base - 'r-cairo >=1.5.5' - 'r-hwriter >=1.3.0' diff --git a/recipes/bioconductor-htsfilter/meta.yaml b/recipes/bioconductor-htsfilter/meta.yaml index 5a140bf362057..84f5596a79d3c 100644 --- a/recipes/bioconductor-htsfilter/meta.yaml +++ b/recipes/bioconductor-htsfilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "HTSFilter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e65f6c1f3249d76932b78a1910d0b687 + md5: 6eb5ebe090ac02b5a0099f63f3e6ccc6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htsfilter", max_pin="x.x") }}' noarch: generic # Suggests: EDASeq, testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base test: commands: diff --git a/recipes/bioconductor-hu35ksuba.db/meta.yaml b/recipes/bioconductor-hu35ksuba.db/meta.yaml index 2cb97faadc36e..aa6d56d193767 100644 --- a/recipes/bioconductor-hu35ksuba.db/meta.yaml +++ b/recipes/bioconductor-hu35ksuba.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hu35ksuba.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4c2306a80f26bacb6172e84c896ef911 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksuba.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubacdf/meta.yaml b/recipes/bioconductor-hu35ksubacdf/meta.yaml index b3c4ade0e8d97..6e0051e83251d 100644 --- a/recipes/bioconductor-hu35ksubacdf/meta.yaml +++ b/recipes/bioconductor-hu35ksubacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubacdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c8b82c4755eb62818ca0dbf22de5d25e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubacdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubaprobe/meta.yaml b/recipes/bioconductor-hu35ksubaprobe/meta.yaml index 5f0068482c219..27ff012919986 100644 --- a/recipes/bioconductor-hu35ksubaprobe/meta.yaml +++ b/recipes/bioconductor-hu35ksubaprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubaprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 49bd19ec3b6404211f2e410e473fa644 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubaprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubb.db/meta.yaml b/recipes/bioconductor-hu35ksubb.db/meta.yaml index 906cc80272b08..26b4effc29790 100644 --- a/recipes/bioconductor-hu35ksubb.db/meta.yaml +++ b/recipes/bioconductor-hu35ksubb.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hu35ksubb.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b82ece4860eddff8010faecaae802312 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubb.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubbcdf/meta.yaml b/recipes/bioconductor-hu35ksubbcdf/meta.yaml index 89c4be6fce455..058b2d719b0ab 100644 --- a/recipes/bioconductor-hu35ksubbcdf/meta.yaml +++ b/recipes/bioconductor-hu35ksubbcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubbcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d873b6c521e926b331f799baf10a4e13 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubbcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubbprobe/meta.yaml b/recipes/bioconductor-hu35ksubbprobe/meta.yaml index 94b5b39aa7c4a..f268e43a45ffd 100644 --- a/recipes/bioconductor-hu35ksubbprobe/meta.yaml +++ b/recipes/bioconductor-hu35ksubbprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubbprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0a63051d0faf38a56f17d5865cbed9b1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubbprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubc.db/meta.yaml b/recipes/bioconductor-hu35ksubc.db/meta.yaml index e4b8f21730a8c..12eff013b1335 100644 --- a/recipes/bioconductor-hu35ksubc.db/meta.yaml +++ b/recipes/bioconductor-hu35ksubc.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hu35ksubc.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 57e60b8d025e0e8cf7ac2b355111cf2d build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubc.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubccdf/meta.yaml b/recipes/bioconductor-hu35ksubccdf/meta.yaml index a46bf48696983..e74f1c9802053 100644 --- a/recipes/bioconductor-hu35ksubccdf/meta.yaml +++ b/recipes/bioconductor-hu35ksubccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubccdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: de96e69680c5f8747c99d170272d7c3c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubccdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubcprobe/meta.yaml b/recipes/bioconductor-hu35ksubcprobe/meta.yaml index 4c768cd883634..e34a24730e4a9 100644 --- a/recipes/bioconductor-hu35ksubcprobe/meta.yaml +++ b/recipes/bioconductor-hu35ksubcprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubcprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b10453ea061b09172192bd21baa9083d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubcprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubd.db/meta.yaml b/recipes/bioconductor-hu35ksubd.db/meta.yaml index 8321b024f45f6..1e4d5c25aa532 100644 --- a/recipes/bioconductor-hu35ksubd.db/meta.yaml +++ b/recipes/bioconductor-hu35ksubd.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hu35ksubd.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5ce6b6ede0f9733fd4dc527a28114327 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubd.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubdcdf/meta.yaml b/recipes/bioconductor-hu35ksubdcdf/meta.yaml index 9190d08512c9c..bc47065d4bc5e 100644 --- a/recipes/bioconductor-hu35ksubdcdf/meta.yaml +++ b/recipes/bioconductor-hu35ksubdcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubdcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6f6423426969f306fb0d5171e75b5380 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubdcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubdprobe/meta.yaml b/recipes/bioconductor-hu35ksubdprobe/meta.yaml index 8f374a04f9e97..aecbeb343c4d5 100644 --- a/recipes/bioconductor-hu35ksubdprobe/meta.yaml +++ b/recipes/bioconductor-hu35ksubdprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubdprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 430a9b8ccd646d8cb06e6c1d750eec23 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubdprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800.db/meta.yaml b/recipes/bioconductor-hu6800.db/meta.yaml index f9ea39f7a4194..b0075ffaca4fd 100644 --- a/recipes/bioconductor-hu6800.db/meta.yaml +++ b/recipes/bioconductor-hu6800.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hu6800.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: aa1cb6c107dee6d2ed1929b48aa831e9 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu6800.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800cdf/meta.yaml b/recipes/bioconductor-hu6800cdf/meta.yaml index a3d7f7eb47cc0..e614aa6fa22fa 100644 --- a/recipes/bioconductor-hu6800cdf/meta.yaml +++ b/recipes/bioconductor-hu6800cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu6800cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fa2b2ab8f3aba517c63ad2e65873d2f0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu6800cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800probe/meta.yaml b/recipes/bioconductor-hu6800probe/meta.yaml index 314442af32bc1..f27bcb41f1371 100644 --- a/recipes/bioconductor-hu6800probe/meta.yaml +++ b/recipes/bioconductor-hu6800probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu6800probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7a2383bd870cbc0628c210174e911250 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu6800probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800subacdf/meta.yaml b/recipes/bioconductor-hu6800subacdf/meta.yaml index 269fa0149a80e..14d7f881b2a7e 100644 --- a/recipes/bioconductor-hu6800subacdf/meta.yaml +++ b/recipes/bioconductor-hu6800subacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu6800subacdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9e8ec301e066e400564976cd9750297e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu6800subacdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800subbcdf/meta.yaml b/recipes/bioconductor-hu6800subbcdf/meta.yaml index 38d19b590969e..2d20ea344463a 100644 --- a/recipes/bioconductor-hu6800subbcdf/meta.yaml +++ b/recipes/bioconductor-hu6800subbcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu6800subbcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 529aad5e4e73594c8cb66274d7e4adc5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu6800subbcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800subccdf/meta.yaml b/recipes/bioconductor-hu6800subccdf/meta.yaml index f6e7904c7ab0c..85db4b5ce728c 100644 --- a/recipes/bioconductor-hu6800subccdf/meta.yaml +++ b/recipes/bioconductor-hu6800subccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu6800subccdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 020fe3a6bdf44efbde15432b968433e8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu6800subccdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800subdcdf/meta.yaml b/recipes/bioconductor-hu6800subdcdf/meta.yaml index 8633581ede40a..f3b36b1e7d49c 100644 --- a/recipes/bioconductor-hu6800subdcdf/meta.yaml +++ b/recipes/bioconductor-hu6800subdcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu6800subdcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7966c21babb23e18cca4faafc8720f0a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu6800subdcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hubpub/meta.yaml b/recipes/bioconductor-hubpub/meta.yaml index 3249609e8a7d1..ce98d178e7182 100644 --- a/recipes/bioconductor-hubpub/meta.yaml +++ b/recipes/bioconductor-hubpub/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "HubPub" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 51721091a3789f40a9c60732c92da643 + md5: 9595496f838fced99c75d9604456df25 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hubpub", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationHubData, ExperimentHubData, testthat, knitr, rmarkdown, BiocStyle, requirements: host: - - 'bioconductor-biocthis >=1.10.0,<1.11.0' + - 'bioconductor-biocthis >=1.12.0,<1.13.0' - r-available - r-aws.s3 - r-base @@ -30,7 +31,7 @@ requirements: - r-fs - r-usethis run: - - 'bioconductor-biocthis >=1.10.0,<1.11.0' + - 'bioconductor-biocthis >=1.12.0,<1.13.0' - r-available - r-aws.s3 - r-base diff --git a/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml b/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml index f5e632bc3dcf2..f52623a6d6adc 100644 --- a/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml +++ b/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "huex.1.0.st.v2frmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 982935d07b526ff555790e309fe4147e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-huex.1.0.st.v2frmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-huex10stprobeset.db/meta.yaml b/recipes/bioconductor-huex10stprobeset.db/meta.yaml index 5e94fe7224db8..e46db4b591594 100644 --- a/recipes/bioconductor-huex10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-huex10stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "huex10stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fda9fc7340aeda2564a76756d2b8d4d3 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-huex10stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml index b955652056f57..466ce65126903 100644 --- a/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "huex10sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0789a1e8ee4474bd64c2772eab0db247 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-huex10sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-huexexonprobesetlocation/meta.yaml b/recipes/bioconductor-huexexonprobesetlocation/meta.yaml index 4e27b068904df..5d2372d38e4b0 100644 --- a/recipes/bioconductor-huexexonprobesetlocation/meta.yaml +++ b/recipes/bioconductor-huexexonprobesetlocation/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.15.0" %} {% set name = "HuExExonProbesetLocation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 11bf1b88d9e90711b4064497f611da4f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-huexexonprobesetlocation", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml b/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml index 184e2dcafb9b8..eda440ed446a7 100644 --- a/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml +++ b/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.0.2" %} {% set name = "HuExExonProbesetLocationHg18" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: bb00b7f5e4db2b04dca5951aa6bd073e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-huexexonprobesetlocationhg18", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml b/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml index 05c44b77e47ed..e74f60f8e47af 100644 --- a/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml +++ b/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.0.3" %} {% set name = "HuExExonProbesetLocationHg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1a3843c95c82dc71a043d902961ba33a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-huexexonprobesetlocationhg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml b/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml index 2cda95075af1c..f4e9cd4365fe4 100644 --- a/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml +++ b/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "hugene.1.0.st.v1frmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 711a69e6fa6dd3737a90615222416dfc build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene.1.0.st.v1frmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene10stprobeset.db/meta.yaml b/recipes/bioconductor-hugene10stprobeset.db/meta.yaml index d8d7c54e93ff4..f70af17a40af8 100644 --- a/recipes/bioconductor-hugene10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-hugene10stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hugene10stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0a4a87d64564cbec1e4bb1f9e5a67add build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene10stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml index 9474e61d516a9..b7a09239b1a3a 100644 --- a/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hugene10sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a32fb5729d37e96f157b0a1085dff43e build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene10sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene10stv1cdf/meta.yaml b/recipes/bioconductor-hugene10stv1cdf/meta.yaml index c54c5659638c1..bb829c36e72d1 100644 --- a/recipes/bioconductor-hugene10stv1cdf/meta.yaml +++ b/recipes/bioconductor-hugene10stv1cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hugene10stv1cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f1fb1c7076ac40b9e709f18e645d6181 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene10stv1cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene10stv1probe/meta.yaml b/recipes/bioconductor-hugene10stv1probe/meta.yaml index 288a450e096b6..8f44196d5f02b 100644 --- a/recipes/bioconductor-hugene10stv1probe/meta.yaml +++ b/recipes/bioconductor-hugene10stv1probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hugene10stv1probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6ed3c17dd026acf008658a5994044c62 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene10stv1probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene11stprobeset.db/meta.yaml b/recipes/bioconductor-hugene11stprobeset.db/meta.yaml index f619a84eceed7..a66804c1c2f9b 100644 --- a/recipes/bioconductor-hugene11stprobeset.db/meta.yaml +++ b/recipes/bioconductor-hugene11stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hugene11stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4d22ec32dedd6c8603d5f545faeb4ba4 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene11stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml index 7d8d4ebef3d56..ea292b35aa0c2 100644 --- a/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hugene11sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7fed70c4bd904655459a41b5667f7c23 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene11sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene20stprobeset.db/meta.yaml b/recipes/bioconductor-hugene20stprobeset.db/meta.yaml index 48ebdce03070f..8a24073d3fade 100644 --- a/recipes/bioconductor-hugene20stprobeset.db/meta.yaml +++ b/recipes/bioconductor-hugene20stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hugene20stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bf7909fc41a80da59099327a6d9abb57 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene20stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml index 1208738d62693..761de8398ee20 100644 --- a/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hugene20sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0b929a3a959662e8a7265f58b81b4e35 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene20sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene21stprobeset.db/meta.yaml b/recipes/bioconductor-hugene21stprobeset.db/meta.yaml index 66c1e3cd428e0..e76e57e758538 100644 --- a/recipes/bioconductor-hugene21stprobeset.db/meta.yaml +++ b/recipes/bioconductor-hugene21stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hugene21stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2b816dca48d0b2e1a946469b8d85d257 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene21stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml index d8dee7131293e..e6f8ab5591590 100644 --- a/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hugene21sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ca90de6093bbad760abfcf0cfeada830 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene21sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human.db0/meta.yaml b/recipes/bioconductor-human.db0/meta.yaml index 8421a6640099b..4e65c14b082c3 100644 --- a/recipes/bioconductor-human.db0/meta.yaml +++ b/recipes/bioconductor-human.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "human.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4597ee42fd14b0e83754027205d4ca17 + md5: e3b04d46f0618785b37fb84bb899295e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-human.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human.db0/post-link.sh b/recipes/bioconductor-human.db0/post-link.sh index abdd185f80b1c..ec096e9328845 100644 --- a/recipes/bioconductor-human.db0/post-link.sh +++ b/recipes/bioconductor-human.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "human.db0-3.17.0" +installBiocDataPackage.sh "human.db0-3.18.0" diff --git a/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml b/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml index d0f2dfd66c790..d5179e02efca6 100644 --- a/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml +++ b/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.4" %} {% set name = "human1mduov3bCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0ff9f1e8bcc6348d6777bbb982ae0325 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-human1mduov3bcrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human1mv1ccrlmm/meta.yaml b/recipes/bioconductor-human1mv1ccrlmm/meta.yaml index 6db7fa7d0e95b..31b085def1cd8 100644 --- a/recipes/bioconductor-human1mv1ccrlmm/meta.yaml +++ b/recipes/bioconductor-human1mv1ccrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.3" %} {% set name = "human1mv1cCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b9f638c7b0ede50cb070f1bae85eb4dc build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-human1mv1ccrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml b/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml index 40c13ad7bd002..6d828cffe3c89 100644 --- a/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml +++ b/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.3" %} {% set name = "human370quadv3cCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 33c3ccc3793ed95647418b746a5177f9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-human370quadv3ccrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human370v1ccrlmm/meta.yaml b/recipes/bioconductor-human370v1ccrlmm/meta.yaml index ad69b1464d1fd..36f4345a136f5 100644 --- a/recipes/bioconductor-human370v1ccrlmm/meta.yaml +++ b/recipes/bioconductor-human370v1ccrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.2" %} {% set name = "human370v1cCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9ec4192f533faee2b14484de02548075 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-human370v1ccrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human550v3bcrlmm/meta.yaml b/recipes/bioconductor-human550v3bcrlmm/meta.yaml index 7b775b368e034..7c0d212370923 100644 --- a/recipes/bioconductor-human550v3bcrlmm/meta.yaml +++ b/recipes/bioconductor-human550v3bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.4" %} {% set name = "human550v3bCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 20e6b008fab5e1084354c87ad50d18a8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-human550v3bcrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml b/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml index 800f56624e589..9c38228c1a8c5 100644 --- a/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml +++ b/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.3" %} {% set name = "human610quadv1bCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 609cf09410774e084ee6a3286652bb1a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-human610quadv1bcrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human650v3acrlmm/meta.yaml b/recipes/bioconductor-human650v3acrlmm/meta.yaml index 80118154e125f..9808f0f0abf83 100644 --- a/recipes/bioconductor-human650v3acrlmm/meta.yaml +++ b/recipes/bioconductor-human650v3acrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.3" %} {% set name = "human650v3aCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4b0de367ccc0f7499dcffe21ef1893c2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-human650v3acrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human660quadv1acrlmm/meta.yaml b/recipes/bioconductor-human660quadv1acrlmm/meta.yaml index 6bfc093423ad5..fd3e90ca86186 100644 --- a/recipes/bioconductor-human660quadv1acrlmm/meta.yaml +++ b/recipes/bioconductor-human660quadv1acrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.3" %} {% set name = "human660quadv1aCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5fd2d94a462e150c888f13c5c0975c36 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-human660quadv1acrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanaffydata/meta.yaml b/recipes/bioconductor-humanaffydata/meta.yaml index b54ab8e296b47..c746ebbe83689 100644 --- a/recipes/bioconductor-humanaffydata/meta.yaml +++ b/recipes/bioconductor-humanaffydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "HumanAffyData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bbb55417c9bdc12d387677c47cb8fc19 + md5: 11341e772169b7141b9bd22161e14417 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-humanaffydata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanaffydata/post-link.sh b/recipes/bioconductor-humanaffydata/post-link.sh index dc899f9b002ee..596705396fd7e 100644 --- a/recipes/bioconductor-humanaffydata/post-link.sh +++ b/recipes/bioconductor-humanaffydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "humanaffydata-1.26.0" +installBiocDataPackage.sh "humanaffydata-1.28.0" diff --git a/recipes/bioconductor-humanchrloc/meta.yaml b/recipes/bioconductor-humanchrloc/meta.yaml index 2c1bf4c51a2c8..e535202d4443c 100644 --- a/recipes/bioconductor-humanchrloc/meta.yaml +++ b/recipes/bioconductor-humanchrloc/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.1.6" %} {% set name = "humanCHRLOC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 113450c0822000c9b4e8a0141cf4b819 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-humanchrloc", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml b/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml index 21f2a40ff19ac..00664a6615e8e 100644 --- a/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml +++ b/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "humancytosnp12v2p1hCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: edf80245ddb28afb9fbaa6668187bf3a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-humancytosnp12v2p1hcrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml b/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml index 3ed5297328e11..7b086ab8634cb 100644 --- a/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml +++ b/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.3" %} {% set name = "humanomni1quadv1bCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e81b2603f37d4cda3f28cd69a7296a23 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-humanomni1quadv1bcrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml b/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml index b57f45359f1d6..ea1f4ab912275 100644 --- a/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml +++ b/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.2" %} {% set name = "humanomni25quadv1bCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2ee1fa7bf712d7f81a167079c975d49f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-humanomni25quadv1bcrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml b/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml index a6a531e67d6c3..f90cbd61ccc35 100644 --- a/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml +++ b/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "humanomni5quadv1bCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3ac4d6867c3d5590a6308d6edff0912b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-humanomni5quadv1bcrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml b/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml index f7f3a1ad3d2a4..b15927786e117 100644 --- a/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml +++ b/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "humanomniexpress12v1bCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: abdb730fc230db669e588e024ee7624b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-humanomniexpress12v1bcrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanstemcell/meta.yaml b/recipes/bioconductor-humanstemcell/meta.yaml index 8fe0e1e4e82e5..c0d2b5a0d197e 100644 --- a/recipes/bioconductor-humanstemcell/meta.yaml +++ b/recipes/bioconductor-humanstemcell/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.40.0" %} +{% set version = "0.42.0" %} {% set name = "humanStemCell" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8388d74f0e892de07e04e2e200041e6d + md5: be6367d8fa19187d644247ed8795eb0e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-humanstemcell", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanstemcell/post-link.sh b/recipes/bioconductor-humanstemcell/post-link.sh index 84918843e521c..959dc8dc69bda 100644 --- a/recipes/bioconductor-humanstemcell/post-link.sh +++ b/recipes/bioconductor-humanstemcell/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "humanstemcell-0.40.0" +installBiocDataPackage.sh "humanstemcell-0.42.0" diff --git a/recipes/bioconductor-humantranscriptomecompendium/meta.yaml b/recipes/bioconductor-humantranscriptomecompendium/meta.yaml index 00cb3e294ac9c..104d5c4efe8ea 100644 --- a/recipes/bioconductor-humantranscriptomecompendium/meta.yaml +++ b/recipes/bioconductor-humantranscriptomecompendium/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.17.0" %} {% set name = "HumanTranscriptomeCompendium" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98846960141df3feafef02d8aff9590b + md5: 00689fd704a35eea4e0ba38516603b49 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-humantranscriptomecompendium", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, beeswarm, tximportData, DT, tximport, dplyr, magrittr, BiocFileCache, testthat, rhdf5client, rmarkdown requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-ssrch >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-ssrch >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-shiny run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-ssrch >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-ssrch >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-shiny test: diff --git a/recipes/bioconductor-hummingbird/meta.yaml b/recipes/bioconductor-hummingbird/meta.yaml index 4fb842a74040f..506999c697083 100644 --- a/recipes/bioconductor-hummingbird/meta.yaml +++ b/recipes/bioconductor-hummingbird/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "hummingbird" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 715ef224bb7c7b1b85e2ee22c2b5f52a + md5: 3f2788dadae0f811072b04866fc9e5ed build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hummingbird", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-huo22.db/meta.yaml b/recipes/bioconductor-huo22.db/meta.yaml index ec7936b6b3d7c..b0ae8869cbd58 100644 --- a/recipes/bioconductor-huo22.db/meta.yaml +++ b/recipes/bioconductor-huo22.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "HuO22.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ddabf6c01f94c1dfd6ab35b40852828a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-huo22.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hwgcod.db/meta.yaml b/recipes/bioconductor-hwgcod.db/meta.yaml index 6eb2d50cbb487..dfb997797f058 100644 --- a/recipes/bioconductor-hwgcod.db/meta.yaml +++ b/recipes/bioconductor-hwgcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "hwgcod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a46bf1a242853bbab26351a11b18030a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hwgcod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hybridmtest/meta.yaml b/recipes/bioconductor-hybridmtest/meta.yaml index 28eb5b06abebc..009114237f60b 100644 --- a/recipes/bioconductor-hybridmtest/meta.yaml +++ b/recipes/bioconductor-hybridmtest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "HybridMTest" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dd6c87352381d3c242791b824acc784e + md5: a2b1764b0e458f82e6055a3ebdf90933 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hybridmtest", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-fdrtool - r-mass - r-survival run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-fdrtool - r-mass diff --git a/recipes/bioconductor-hyper/build.sh b/recipes/bioconductor-hyper/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hyper/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hyper/meta.yaml b/recipes/bioconductor-hyper/meta.yaml new file mode 100644 index 0000000000000..99a5d17a40f21 --- /dev/null +++ b/recipes/bioconductor-hyper/meta.yaml @@ -0,0 +1,79 @@ +{% set version = "2.0.0" %} +{% set name = "hypeR" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d2de417437ab81645e7d4702021f349f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hyper", max_pin="x.x") }}' + noarch: generic +# Suggests: tidyverse, devtools, testthat, knitr +requirements: + host: + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - r-base + - r-dplyr + - r-ggforce + - r-ggplot2 + - r-htmltools + - r-httr + - r-igraph + - r-kableextra + - r-magrittr + - r-msigdbr + - r-openxlsx + - r-purrr + - r-r6 + - r-reactable + - r-reshape2 + - r-rlang + - r-rmarkdown + - r-scales + - r-shiny + - r-stringr + - r-visnetwork + run: + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - r-base + - r-dplyr + - r-ggforce + - r-ggplot2 + - r-htmltools + - r-httr + - r-igraph + - r-kableextra + - r-magrittr + - r-msigdbr + - r-openxlsx + - r-purrr + - r-r6 + - r-reactable + - r-reshape2 + - r-rlang + - r-rmarkdown + - r-scales + - r-shiny + - r-stringr + - r-visnetwork +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'An R Package For Geneset Enrichment Workflows' + description: 'An R Package for Geneset Enrichment Workflows.' + license_file: LICENSE + diff --git a/recipes/bioconductor-hyperdraw/meta.yaml b/recipes/bioconductor-hyperdraw/meta.yaml index 21883a6196bb8..10d2f229c833c 100644 --- a/recipes/bioconductor-hyperdraw/meta.yaml +++ b/recipes/bioconductor-hyperdraw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "hyperdraw" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c3cf1dd57ee69e05f8da913acb35477f + md5: 2b1ec2cf9ea920a241f821baa08bb393 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hyperdraw", max_pin="x.x") }}' noarch: generic # SystemRequirements: graphviz requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-hypergraph >=1.72.0,<1.73.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-hypergraph >=1.74.0,<1.75.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - graphviz run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-hypergraph >=1.72.0,<1.73.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-hypergraph >=1.74.0,<1.75.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - graphviz test: diff --git a/recipes/bioconductor-hypergraph/meta.yaml b/recipes/bioconductor-hypergraph/meta.yaml index e51ca8cc87f7d..b46a9d8bbdee9 100644 --- a/recipes/bioconductor-hypergraph/meta.yaml +++ b/recipes/bioconductor-hypergraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "hypergraph" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8bf5823131a132c2be422e4caab4808d + md5: e97653a8503ba0bcb6da1dbdf1a3552b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hypergraph", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, RUnit requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base test: commands: diff --git a/recipes/bioconductor-iaseq/meta.yaml b/recipes/bioconductor-iaseq/meta.yaml index 7772ed35787bd..45a697e239e4e 100644 --- a/recipes/bioconductor-iaseq/meta.yaml +++ b/recipes/bioconductor-iaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "iASeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 74ee0ce567f55f4ff926ec7b03e6d594 + md5: 3086632b16254c5b1f22c4f376bd43a7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iaseq", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-iasva/meta.yaml b/recipes/bioconductor-iasva/meta.yaml index ed0ae3531538c..500fa9d1f76ca 100644 --- a/recipes/bioconductor-iasva/meta.yaml +++ b/recipes/bioconductor-iasva/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "iasva" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 792ad17be82086c6159523192f4c53c6 + md5: a52a31d7564e175a288943ae77b22a93 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iasva", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown, sva, Rtsne, pheatmap, corrplot, DescTools, RColorBrewer requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-irlba run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-irlba diff --git a/recipes/bioconductor-ibbig/meta.yaml b/recipes/bioconductor-ibbig/meta.yaml index 0bd364e0773a1..3ed3cdcd3bd2e 100644 --- a/recipes/bioconductor-ibbig/meta.yaml +++ b/recipes/bioconductor-ibbig/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "iBBiG" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: acb9cdbf601cecd9d30682529bb0db9e + md5: 6114f0b7d488fd60923a6607bf2d59f2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ibbig", max_pin="x.x") }}' # Suggests: methods requirements: host: diff --git a/recipes/bioconductor-ibh/meta.yaml b/recipes/bioconductor-ibh/meta.yaml index d11cb9df8d7cd..9af60c615d1d4 100644 --- a/recipes/bioconductor-ibh/meta.yaml +++ b/recipes/bioconductor-ibh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "ibh" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fbf555dde7ce9991ec258efe6c02c0a1 + md5: 3c87bb1083990548eb09c4e43459ba1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ibh", max_pin="x.x") }}' noarch: generic # Suggests: yeastCC, stats requirements: host: - - 'bioconductor-simpintlists >=1.36.0,<1.37.0' + - 'bioconductor-simpintlists >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-simpintlists >=1.36.0,<1.37.0' + - 'bioconductor-simpintlists >=1.38.0,<1.39.0' - r-base test: commands: diff --git a/recipes/bioconductor-ibmq/meta.yaml b/recipes/bioconductor-ibmq/meta.yaml index e32affd825da3..4633abf58f473 100644 --- a/recipes/bioconductor-ibmq/meta.yaml +++ b/recipes/bioconductor-ibmq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "iBMQ" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8840fcc3cdb49e919fe22cda90a58f3 + md5: 9737c0aee38670491b2f29f73dcb743c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ibmq", max_pin="x.x") }}' # SystemRequirements: GSL and OpenMP requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - 'r-ggplot2 >=0.9.2' - libblas - liblapack - gsl run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - 'r-ggplot2 >=0.9.2' - gsl diff --git a/recipes/bioconductor-icare/meta.yaml b/recipes/bioconductor-icare/meta.yaml index ca7712cc724fd..aded7a26c7465 100644 --- a/recipes/bioconductor-icare/meta.yaml +++ b/recipes/bioconductor-icare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "iCARE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d89ab78df6a178cd7ddeffbba91211a + md5: 9230befcb5d16fdc72a6f87b50397789 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-icare", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics requirements: host: diff --git a/recipes/bioconductor-icens/meta.yaml b/recipes/bioconductor-icens/meta.yaml index 36bc7e42950fe..ee1fb6954e914 100644 --- a/recipes/bioconductor-icens/meta.yaml +++ b/recipes/bioconductor-icens/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "Icens" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 916d3bb72a63cbebfe3890bc15003075 + md5: 07481f23c5b4fdfe9ff465e5a57e33c2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-icens", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-icetea/meta.yaml b/recipes/bioconductor-icetea/meta.yaml index 0ca22f27c1f24..916fb97d57978 100644 --- a/recipes/bioconductor-icetea/meta.yaml +++ b/recipes/bioconductor-icetea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "icetea" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,55 +11,56 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fba08db47284c487627226270b90e5bd + md5: 2e7e3e32b56771089cefcc4295456e49 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-icetea", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, Rsubread (>= 1.29.0), testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene >=3.12.0,<3.13.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggplot2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene >=3.12.0,<3.13.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-icheck/meta.yaml b/recipes/bioconductor-icheck/meta.yaml index 6a71607982e40..51520bfa018ee 100644 --- a/recipes/bioconductor-icheck/meta.yaml +++ b/recipes/bioconductor-icheck/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "iCheck" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b3e3bfe2b8158dd1cc31da69c188f57 + md5: 4404db494985157058a6af6d8c29b0c1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-icheck", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geneselectmmd >=2.44.0,<2.45.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geneselectmmd >=2.46.0,<2.47.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-gplots - r-lmtest @@ -34,12 +35,12 @@ requirements: - r-rgl - r-scatterplot3d run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geneselectmmd >=2.44.0,<2.45.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geneselectmmd >=2.46.0,<2.47.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-gplots - r-lmtest diff --git a/recipes/bioconductor-ichip/meta.yaml b/recipes/bioconductor-ichip/meta.yaml index 3a6c2a4d17a41..6a06380a203bd 100644 --- a/recipes/bioconductor-ichip/meta.yaml +++ b/recipes/bioconductor-ichip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "iChip" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 656d9d28237e68c9e522a9605fee4716 + md5: d50d8db2c1de02e8a1df4de992aa64f4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ichip", max_pin="x.x") }}' requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - libblas - liblapack run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-iclusterplus/build.sh b/recipes/bioconductor-iclusterplus/build.sh index 26b985e8ff4dc..0f7012ed24200 100644 --- a/recipes/bioconductor-iclusterplus/build.sh +++ b/recipes/bioconductor-iclusterplus/build.sh @@ -9,4 +9,4 @@ CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars autoreconf -fi -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iclusterplus/meta.yaml b/recipes/bioconductor-iclusterplus/meta.yaml index 92bc2e5c98015..73b999c654735 100644 --- a/recipes/bioconductor-iclusterplus/meta.yaml +++ b/recipes/bioconductor-iclusterplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.1" %} +{% set version = "1.38.0" %} {% set name = "iClusterPlus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,7 +11,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 951e6b1ec59b05d436130fc3b9b7c6f9 + md5: 133b682823ec6ab41f6f6579413d461d patches: - 0001-Detect-compiler-with-gfortran-suffix.patch build: @@ -19,6 +19,7 @@ build: rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iclusterplus", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics requirements: host: @@ -42,4 +43,3 @@ about: summary: 'Integrative clustering of multi-type genomic data' description: 'Integrative clustering of multiple genomic data using a joint latent variable model.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - diff --git a/recipes/bioconductor-icnv/meta.yaml b/recipes/bioconductor-icnv/meta.yaml index 51defd03f7da6..b1c5eb62c6e2d 100644 --- a/recipes/bioconductor-icnv/meta.yaml +++ b/recipes/bioconductor-icnv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "iCNV" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1064b8c5da8ebf9cd18a1fd0cebb6caf + md5: ff1415b4764c18a3609c4eb3b6d65a30 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-icnv", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, WES.1KG.WUGSC requirements: host: - - 'bioconductor-codex >=1.32.0,<1.33.0' + - 'bioconductor-codex >=1.34.0,<1.35.0' - r-base - r-data.table - r-dplyr @@ -31,7 +32,7 @@ requirements: - r-tidyr - r-truncnorm run: - - 'bioconductor-codex >=1.32.0,<1.33.0' + - 'bioconductor-codex >=1.34.0,<1.35.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-icobra/meta.yaml b/recipes/bioconductor-icobra/meta.yaml index 72fc1539129e6..0a0ef086aa674 100644 --- a/recipes/bioconductor-icobra/meta.yaml +++ b/recipes/bioconductor-icobra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "iCOBRA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 778bba4697e06cbecbb9f0e8e920c4b0 + md5: dc297e102e2b6ee717a494f652a6d6bf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-icobra", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-dplyr - r-dt @@ -35,7 +36,7 @@ requirements: - r-shinydashboard - r-upsetr run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-dplyr - r-dt diff --git a/recipes/bioconductor-ideal/build_failure.linux-64.yaml b/recipes/bioconductor-ideal/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..19d2276079b9f --- /dev/null +++ b/recipes/bioconductor-ideal/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 67de6b5cdabab9789f4141c7b4df882eca324c62877eb622c009398c5cadd390 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + dependency issue +log: |2- + + Leaving build/test directories: + Work: + /opt/conda/conda-bld/work + Test: + /opt/conda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + Build: + source activate /opt/conda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - r-plotly + - r-shinyace + - r-shinybs + - r-upsetr + - bioconductor-limma >=3.58.0,<3.59.0 + - r-rintrojs + - r-base64enc + - bioconductor-iranges >=2.36.0,<2.37.0 + - bioconductor-goseq >=1.54.0,<1.55.0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - r-gplots + - r-rentrez + - bioconductor-topgo >=2.54.0,<2.55.0 + - r-base 4.3.* + - r-shinydashboard + - bioconductor-deseq2 >=1.42.0,<1.43.0 + - bioconductor-go.db >=3.18.0,<3.19.0 + - bioconductor-genomicranges >=1.54.0,<1.55.0 + - r-heatmaply + - r-knitr + - r-shiny >=0.12.0 + - bioconductor-gostats >=2.68.0,<2.69.0 + - r-dplyr + - bioconductor-pcaexplorer >=2.28.0,<2.29.0 + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - r-dt + - r-ggplot2 >=2.0.0 + - r-ggrepel + - bioconductor-annotationdbi >=1.64.0,<1.65.0 + - bioconductor-ihw >=1.30.0,<1.31.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-stringr + - r-pheatmap + - r-rlang + - r-rmarkdown + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-ihw >=1.30.0,<1.31.0 + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-ihw[version='>=1.30.0,<1.31.0']")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ideal/meta.yaml b/recipes/bioconductor-ideal/meta.yaml index 13555fc84538f..3cbe305f544a5 100644 --- a/recipes/bioconductor-ideal/meta.yaml +++ b/recipes/bioconductor-ideal/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.1" %} +{% set version = "1.26.0" %} {% set name = "ideal" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 24f07cba791fbdfe1bdf0539b78de343 + md5: d4714305a9be71a4b4c71da0fb624148 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ideal", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, edgeR requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-goseq >=1.52.0,<1.53.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-ihw >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pcaexplorer >=2.26.0,<2.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-goseq >=1.54.0,<1.55.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-ihw >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pcaexplorer >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-base64enc - r-dplyr @@ -57,20 +58,20 @@ requirements: - r-stringr - r-upsetr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-goseq >=1.52.0,<1.53.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-ihw >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pcaexplorer >=2.26.0,<2.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-goseq >=1.54.0,<1.55.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-ihw >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pcaexplorer >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-base64enc - r-dplyr diff --git a/recipes/bioconductor-ideoviz/meta.yaml b/recipes/bioconductor-ideoviz/meta.yaml index 0495cf2897371..3e85ceeaf3c0f 100644 --- a/recipes/bioconductor-ideoviz/meta.yaml +++ b/recipes/bioconductor-ideoviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.37.0" %} {% set name = "IdeoViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a1eaca9a4537ad7486a764085dde3b6 + md5: 187ebcc3f7a11124ebbe137722672ffc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ideoviz", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-rcolorbrewer test: diff --git a/recipes/bioconductor-idiogram/meta.yaml b/recipes/bioconductor-idiogram/meta.yaml index a94f98655c26c..6fa4e077bdb2d 100644 --- a/recipes/bioconductor-idiogram/meta.yaml +++ b/recipes/bioconductor-idiogram/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "idiogram" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7ce45f1fab62bc32ee380625a7a756f8 + md5: 2ee94ac9719c77f8a2f6b691662a7909 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-idiogram", max_pin="x.x") }}' noarch: generic # Suggests: hu6800.db, hgu95av2.db, golubEsets requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-plotrix run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-plotrix test: diff --git a/recipes/bioconductor-idpr/meta.yaml b/recipes/bioconductor-idpr/meta.yaml index 5392789f5d86e..3450da1b12fbd 100644 --- a/recipes/bioconductor-idpr/meta.yaml +++ b/recipes/bioconductor-idpr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "idpr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b3a120730d6d86dc3a8c8de14a3e5e67 + md5: 16fb786981b0e04b0d094c4867303555 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-idpr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, msa, ape, testthat, seqinr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - 'r-dplyr >=0.8.5' - 'r-ggplot2 >=3.3.0' @@ -30,7 +31,7 @@ requirements: - 'r-plyr >=1.8.6' - 'r-rlang >=0.4.6' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - 'r-dplyr >=0.8.5' - 'r-ggplot2 >=3.3.0' diff --git a/recipes/bioconductor-idr2d/meta.yaml b/recipes/bioconductor-idr2d/meta.yaml index cd5ce13ee1773..f2c297502502b 100644 --- a/recipes/bioconductor-idr2d/meta.yaml +++ b/recipes/bioconductor-idr2d/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "idr2d" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b990982c2b666e7dca09c02ab628b038 + md5: 6662b2b18dc8c6029ad40099c5fcd6a7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-idr2d", max_pin="x.x") }}' noarch: generic # Suggests: DT (>= 0.4), htmltools (>= 0.3.6), knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) # SystemRequirements: Python (>= 3.5.0), hic-straw requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-dplyr >=0.7.6' - 'r-futile.logger >=1.4.3' @@ -35,9 +36,9 @@ requirements: - 'r-scales >=1.0.0' - 'r-stringr >=1.3.1' run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-dplyr >=0.7.6' - 'r-futile.logger >=1.4.3' diff --git a/recipes/bioconductor-ifaa/meta.yaml b/recipes/bioconductor-ifaa/meta.yaml index 2a4a8b2311405..59789aaa6e7d1 100644 --- a/recipes/bioconductor-ifaa/meta.yaml +++ b/recipes/bioconductor-ifaa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "IFAA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2fed85b602afd876a82a6f150f7edcc6 + md5: 393ac86513ddc9adf474c654b5127394 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ifaa", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-desctools - 'r-doparallel >=1.0.11' @@ -36,8 +37,8 @@ requirements: - r-parallelly - r-stringr run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-desctools - 'r-doparallel >=1.0.11' diff --git a/recipes/bioconductor-igc/meta.yaml b/recipes/bioconductor-igc/meta.yaml index 3f15202e91f05..f9eeb7f8b07b8 100644 --- a/recipes/bioconductor-igc/meta.yaml +++ b/recipes/bioconductor-igc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "iGC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b1b2d13eef5b7eb28baba5a0d230f216 + md5: 14007fadd58eaea3e345ba53a279f783 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-igc", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-iggeneusage/meta.yaml b/recipes/bioconductor-iggeneusage/meta.yaml index 09daed914d666..23adf82cfe2f0 100644 --- a/recipes/bioconductor-iggeneusage/meta.yaml +++ b/recipes/bioconductor-iggeneusage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "IgGeneUsage" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d8a81fe690de659ee3671911b6079a9 + md5: 231f1af3465f435ca3bb099a93e51e5b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iggeneusage", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, gridExtra, ggrepel # SystemRequirements: GNU make requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-bh >=1.66.0' - 'r-rcpp >=0.12.0' @@ -31,10 +32,11 @@ requirements: - 'r-rstan >=2.18.1' - 'r-rstantools >=2.2.0' - 'r-stanheaders >=2.18.0' + - r-tidyr - libblas - liblapack run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-bh >=1.66.0' - 'r-rcpp >=0.12.0' @@ -44,6 +46,7 @@ requirements: - 'r-rstan >=2.18.1' - 'r-rstantools >=2.2.0' - 'r-stanheaders >=2.18.0' + - r-tidyr build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-igvr/meta.yaml b/recipes/bioconductor-igvr/meta.yaml index 3e29ec06ef9a8..cb1fe14f9bcc1 100644 --- a/recipes/bioconductor-igvr/meta.yaml +++ b/recipes/bioconductor-igvr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "igvR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4462dcfae2acb5eac59801713beae32b + md5: 318b9d244079439576763028e1731a18 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-igvr", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, knitr, rmarkdown, MotifDb, seqLogo requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-browserviz >=2.22.0,<2.23.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-browserviz >=2.24.0,<2.25.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-httpuv - r-httr - r-rcolorbrewer run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-browserviz >=2.22.0,<2.23.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-browserviz >=2.24.0,<2.25.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-httpuv - r-httr diff --git a/recipes/bioconductor-chipxpress/build_failure.linux-64.yaml b/recipes/bioconductor-ihw/build_failure.linux-64.yaml similarity index 82% rename from recipes/bioconductor-chipxpress/build_failure.linux-64.yaml rename to recipes/bioconductor-ihw/build_failure.linux-64.yaml index 553b01a33d979..49c95de2d51b7 100644 --- a/recipes/bioconductor-chipxpress/build_failure.linux-64.yaml +++ b/recipes/bioconductor-ihw/build_failure.linux-64.yaml @@ -1,33 +1,35 @@ -recipe_sha: a49a4fee0ecc177366a04192b85dfff0fac7cc562b60204a83649bffef6c0934 # The commit at which this recipe failed to build. +recipe_sha: df348495dada1a372be82599b073dacb131efa9c20367ac100389a77a59630c4 # The commit at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- + conda-forge/linux-64 [2K[1A[2K[0G[] 4.9s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.0s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.1s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.2s conda-forge/linux-64 100%[2K[1A[2K[0Gconda-forge/linux-64 [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m [?25l[2K[0G[] 0.0s [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 992.2kB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.2MB/s 0.0s [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m [?25l[2K[0G[] 0.0s [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 2.3MB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.2MB/s 0.0s [?25hMamba failed to solve: - - bioconductor-biobase >=2.60.0,<2.61.0 - - r-bigmemory - - bioconductor-frma >=1.52.0,<1.53.0 + - bioconductor-lpsymphony >=1.30.0,<1.31.0 - r-base 4.3.* - - bioconductor-chipxpressdata >=1.38.0,<1.39.0 - - bioconductor-affy >=1.78.0,<1.79.0 - - bioconductor-geoquery >=2.68.0,<2.69.0 - - r-biganalytics + - r-slam + - r-fdrtool + - bioconductor-biocgenerics >=0.48.0,<0.49.0 with channels: + - file:///opt/host-conda-bld - conda-forge - bioconda - defaults The reported errors are: - Encountered problems while solving: - - - nothing provides requested bioconductor-chipxpressdata >=1.38.0,<1.39.0 + - - nothing provides requested bioconductor-lpsymphony >=1.30.0,<1.31.0 - Leaving build/test directories: @@ -50,23 +52,21 @@ log: |- File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve raise RuntimeError("Solver could not find solution." error_string) RuntimeError: Solver could not find solution.Mamba failed to solve: - - bioconductor-biobase >=2.60.0,<2.61.0 - - r-bigmemory - - bioconductor-frma >=1.52.0,<1.53.0 + - bioconductor-lpsymphony >=1.30.0,<1.31.0 - r-base 4.3.* - - bioconductor-chipxpressdata >=1.38.0,<1.39.0 - - bioconductor-affy >=1.78.0,<1.79.0 - - bioconductor-geoquery >=2.68.0,<2.69.0 - - r-biganalytics + - r-slam + - r-fdrtool + - bioconductor-biocgenerics >=0.48.0,<0.49.0 with channels: + - file:///opt/host-conda-bld - conda-forge - bioconda - defaults The reported errors are: - Encountered problems while solving: - - - nothing provides requested bioconductor-chipxpressdata >=1.38.0,<1.39.0 + - - nothing provides requested bioconductor-lpsymphony >=1.30.0,<1.31.0 - During handling of the above exception, another exception occurred: @@ -100,5 +100,5 @@ log: |- actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-chipxpressdata[version='>=1.38.0,<1.39.0']")} + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-lpsymphony[version='>=1.30.0,<1.31.0']")} # Last 100 lines of the build log. diff --git a/recipes/bioconductor-ihw/meta.yaml b/recipes/bioconductor-ihw/meta.yaml index 18b067cac3df1..74e07fd5f88d8 100644 --- a/recipes/bioconductor-ihw/meta.yaml +++ b/recipes/bioconductor-ihw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "IHW" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 03d60f5df56eb3abb74d8b8c8f7788a2 + md5: aa53165d5f689e8bfdebb02838ae9dab build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ihw", max_pin="x.x") }}' noarch: generic # Suggests: ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat, Matrix, BiocStyle, knitr, rmarkdown, devtools requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-lpsymphony >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-lpsymphony >=1.30.0,<1.31.0' - r-base - r-fdrtool - r-slam run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-lpsymphony >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-lpsymphony >=1.30.0,<1.31.0' - r-base - r-fdrtool - r-slam diff --git a/recipes/bioconductor-ihwpaper/build_failure.linux-64.yaml b/recipes/bioconductor-ihwpaper/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0d1d099182dc8 --- /dev/null +++ b/recipes/bioconductor-ihwpaper/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 366efc448b56ba6b7e86a876417279bedf04156e08c60e0c035fe672c82e0ddc # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - r-ggplot2 + - libgcc-ng >=12 + - r-rcpp + - libstdcxx-ng >=12 + - bioconductor-biobase >=2.62.0,<2.63.0 + - r-fdrtool + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-ihw >=1.30.0,<1.31.0 + - + + Leaving build/test directories: + Work: + /opt/conda/conda-bld/work + Test: + /opt/conda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + Build: + source activate /opt/conda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - liblapack 3.9.* *netlib + - libblas 3.9.* *netlib + - bioconductor-deseq2 >=1.42.0,<1.43.0 + - r-dplyr + - r-base 4.3.* + - bioconductor-genefilter >=1.84.0,<1.85.0 + - bioconductor-ihw >=1.30.0,<1.31.0 + - bioconductor-qvalue >=2.34.0,<2.35.0 + - r-cowplot + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-ggplot2 + - libgcc-ng >=12 + - r-rcpp + - libstdcxx-ng >=12 + - bioconductor-biobase >=2.62.0,<2.63.0 + - r-fdrtool + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-ihw >=1.30.0,<1.31.0 + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-ihw[version='>=1.30.0,<1.31.0']")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ihwpaper/build_failure.osx-64.yaml b/recipes/bioconductor-ihwpaper/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..e81f7f57656d0 --- /dev/null +++ b/recipes/bioconductor-ihwpaper/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 366efc448b56ba6b7e86a876417279bedf04156e08c60e0c035fe672c82e0ddc # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + dependency issue +log: |2- + - r-dplyr + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - libcxx >=14 + - bioconductor-qvalue >=2.34.0,<2.35.0 + - bioconductor-biobase >=2.62.0,<2.63.0 + - bioconductor-genefilter >=1.84.0,<1.85.0 + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-cowplot + + with channels: + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-ihw >=1.30.0,<1.31.0 + - + + Leaving build/test directories: + Work: + /opt/mambaforge/envs/bioconda/conda-bld/work + Test: + /opt/mambaforge/envs/bioconda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/mambaforge/envs/bioconda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + Build: + source activate /opt/mambaforge/envs/bioconda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - r-ggplot2 + - bioconductor-ihw >=1.30.0,<1.31.0 + - liblapack 3.9.* *netlib + - bioconductor-deseq2 >=1.42.0,<1.43.0 + - libblas 3.9.* *netlib + - r-fdrtool + - r-rcpp + - r-base 4.3.* + - r-dplyr + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - libcxx >=14 + - bioconductor-qvalue >=2.34.0,<2.35.0 + - bioconductor-biobase >=2.62.0,<2.63.0 + - bioconductor-genefilter >=1.84.0,<1.85.0 + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-cowplot + + with channels: + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-ihw >=1.30.0,<1.31.0 + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-ihw[version='>=1.30.0,<1.31.0']")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ihwpaper/meta.yaml b/recipes/bioconductor-ihwpaper/meta.yaml index c2f712f88e0a3..4251fc13e6670 100644 --- a/recipes/bioconductor-ihwpaper/meta.yaml +++ b/recipes/bioconductor-ihwpaper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "IHWpaper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 282cb3abcd7ee2a5d1c34c468ce806c2 + md5: 21e65d900bf8e6015fd006fbf01237d5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ihwpaper", max_pin="x.x") }}' # Suggests: testthat, RColorBrewer, wesanderson, scales, gridExtra, BiocStyle, knitr, rmarkdown, airway, locfdr, tidyr, latex2exp requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-ihw >=1.28.0,<1.29.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-ihw >=1.30.0,<1.31.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-dplyr @@ -37,14 +38,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-ihw >=1.28.0,<1.29.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-ihw >=1.30.0,<1.31.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-dplyr @@ -52,7 +53,7 @@ requirements: - r-ggplot2 - r-rcpp - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-ihwpaper/post-link.sh b/recipes/bioconductor-ihwpaper/post-link.sh index 8a0180657a601..cceb85018f40b 100644 --- a/recipes/bioconductor-ihwpaper/post-link.sh +++ b/recipes/bioconductor-ihwpaper/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ihwpaper-1.28.0" +installBiocDataPackage.sh "ihwpaper-1.30.0" diff --git a/recipes/bioconductor-illumina450probevariants.db/meta.yaml b/recipes/bioconductor-illumina450probevariants.db/meta.yaml index 3106b6aca5224..1458b848396e0 100644 --- a/recipes/bioconductor-illumina450probevariants.db/meta.yaml +++ b/recipes/bioconductor-illumina450probevariants.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "Illumina450ProbeVariants.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 362d8731f6c9067d58742be0d772a7ac + md5: ca34eec73a57e5f226b70a20ef706ee3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illumina450probevariants.db", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illumina450probevariants.db/post-link.sh b/recipes/bioconductor-illumina450probevariants.db/post-link.sh index 46896196e904f..1d85e7fc79149 100644 --- a/recipes/bioconductor-illumina450probevariants.db/post-link.sh +++ b/recipes/bioconductor-illumina450probevariants.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "illumina450probevariants.db-1.36.0" +installBiocDataPackage.sh "illumina450probevariants.db-1.38.0" diff --git a/recipes/bioconductor-illuminadatatestfiles/meta.yaml b/recipes/bioconductor-illuminadatatestfiles/meta.yaml index b4c3b0c264549..b9af46bf149a1 100644 --- a/recipes/bioconductor-illuminadatatestfiles/meta.yaml +++ b/recipes/bioconductor-illuminadatatestfiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "IlluminaDataTestFiles" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e11e060ddd803add7efac25b34ab2ff5 + md5: 3afa4b143fbb1dd18b3a7acd8f2984b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminadatatestfiles", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminadatatestfiles/post-link.sh b/recipes/bioconductor-illuminadatatestfiles/post-link.sh index cc992fa91951b..a8b688442f90a 100644 --- a/recipes/bioconductor-illuminadatatestfiles/post-link.sh +++ b/recipes/bioconductor-illuminadatatestfiles/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "illuminadatatestfiles-1.38.0" +installBiocDataPackage.sh "illuminadatatestfiles-1.40.0" diff --git a/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml b/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml index 7ae72f80d8e3d..ae8bb8780986d 100644 --- a/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.8" %} {% set name = "IlluminaHumanMethylation27k.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 70586bda9db01d598723bb439c315367 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylation27k.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml index 13588a0775555..7a1f7e62ecb9c 100644 --- a/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylation27kanno.ilmn12.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 765851336506120467c2e3cc6beef7ed build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml b/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml index 2c8526441bde7..f08b35ab5f4d1 100644 --- a/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.4.0" %} {% set name = "IlluminaHumanMethylation27kmanifest" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c4cdda637dccf85f193342c7262b02a6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylation27kmanifest", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml index fb4c92a4c07bd..263014c5c77c9 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.1" %} {% set name = "IlluminaHumanMethylation450kanno.ilmn12.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: aeafc54d887b128ed265fa704a3efa42 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml b/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml index 86f91eb9c31f9..9c9f591b02e13 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.4.0" %} {% set name = "IlluminaHumanMethylation450kmanifest" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 664d1f5a3892974334faa26757269509 build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylation450kmanifest", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml b/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml index e4b5db62fa0c1..19a1c6a35f21c 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.0.6" %} {% set name = "IlluminaHumanMethylation450kprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 84c31861fcbaddbf2a9c500b8d8d767d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylation450kprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml index c49025c692ee2..54f90a3b90e8d 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylationEPICanno.ilm10b2.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6a8e2398a0f930aa7828a1412fb21e88 build: - number: 14 + number: 15 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml index db9900e6987cf..5f0e19275d213 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylationEPICanno.ilm10b3.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2dac8e889486386eaea1bb7ce1beea2e build: - number: 14 + number: 15 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml index 0b249a0348a72..70a78787f09b0 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylationEPICanno.ilm10b4.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2d0c05917bcbf9ba1e354380d4e17a77 build: - number: 14 + number: 15 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml index 4bd377524a966..2f570b1de65ff 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.3.0" %} {% set name = "IlluminaHumanMethylationEPICmanifest" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c6b0268de177badfe0b8184002da7e16 build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylationepicmanifest", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanv1.db/meta.yaml b/recipes/bioconductor-illuminahumanv1.db/meta.yaml index 8d558abb79012..cc147efd5d97d 100644 --- a/recipes/bioconductor-illuminahumanv1.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanv1.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2c362256b7be2861b8bf6e0d1fe46786 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanv1.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanv2.db/meta.yaml b/recipes/bioconductor-illuminahumanv2.db/meta.yaml index 9161dd42903b4..e86b530f95ba8 100644 --- a/recipes/bioconductor-illuminahumanv2.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanv2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 006de5f671a9a68fb27a6b6bce39c555 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanv2.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml b/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml index 2894b87d91690..b94e962adf513 100644 --- a/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.8.0" %} {% set name = "illuminaHumanv2BeadID.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b5a2b2deaa9a9b245a141043e7bc5270 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanv2beadid.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanv3.db/meta.yaml b/recipes/bioconductor-illuminahumanv3.db/meta.yaml index b0ca58eadc49d..004dc46800cdb 100644 --- a/recipes/bioconductor-illuminahumanv3.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv3.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanv3.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7d9e7534f0b60f0e3e7473e545ef373d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanv3.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanv4.db/meta.yaml b/recipes/bioconductor-illuminahumanv4.db/meta.yaml index 0c26073b8d705..e40ca66f6cf27 100644 --- a/recipes/bioconductor-illuminahumanv4.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv4.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanv4.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 42d554559ac0106dc71317ffaf466421 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanv4.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml b/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml index e5dd2c30187ae..dcb880875fc8c 100644 --- a/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanWGDASLv3.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 32e8e24555c16f6d0148438d4a841ab8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanwgdaslv3.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml b/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml index 5f61508cc064d..da9c7a5e9aa5d 100644 --- a/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanWGDASLv4.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4cc1f192de838f2b6c1b148706d354ca build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanwgdaslv4.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminaio/meta.yaml b/recipes/bioconductor-illuminaio/meta.yaml index 1f45cdc02f008..54acd4f3c77da 100644 --- a/recipes/bioconductor-illuminaio/meta.yaml +++ b/recipes/bioconductor-illuminaio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.42.0" %} +{% set version = "0.44.0" %} {% set name = "illuminaio" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b049b6f3cf366b151994de20502d7df4 + md5: 5bf0b60249c92ef8408564391a69a97d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminaio", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2), BiocStyle requirements: host: diff --git a/recipes/bioconductor-illuminamousev1.db/meta.yaml b/recipes/bioconductor-illuminamousev1.db/meta.yaml index 9a4c1ebb7aab7..f0095683a0190 100644 --- a/recipes/bioconductor-illuminamousev1.db/meta.yaml +++ b/recipes/bioconductor-illuminamousev1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaMousev1.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 13818c3b9acabe75550492bbe638fc05 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminamousev1.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminamousev1p1.db/meta.yaml b/recipes/bioconductor-illuminamousev1p1.db/meta.yaml index 4403ddfb1b720..e2dbd5a55ed59 100644 --- a/recipes/bioconductor-illuminamousev1p1.db/meta.yaml +++ b/recipes/bioconductor-illuminamousev1p1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaMousev1p1.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f6a4af01480a6f8d1d2d9b9b64a2b073 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminamousev1p1.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminamousev2.db/meta.yaml b/recipes/bioconductor-illuminamousev2.db/meta.yaml index 4c6f1570a86b9..405b1d50f2aa1 100644 --- a/recipes/bioconductor-illuminamousev2.db/meta.yaml +++ b/recipes/bioconductor-illuminamousev2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaMousev2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fba228a71f264f976d8cdb035861974d build: - number: 16 + number: 17 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminamousev2.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminaratv1.db/meta.yaml b/recipes/bioconductor-illuminaratv1.db/meta.yaml index 0337c5cbcc114..68fc32da96338 100644 --- a/recipes/bioconductor-illuminaratv1.db/meta.yaml +++ b/recipes/bioconductor-illuminaratv1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaRatv1.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5de2324d7b96c0cdb3301ef269341aa8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminaratv1.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-imas/meta.yaml b/recipes/bioconductor-imas/meta.yaml index f68bfd0d5c84f..9000f1e30f504 100644 --- a/recipes/bioconductor-imas/meta.yaml +++ b/recipes/bioconductor-imas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "IMAS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dc40485d764674bc1b01b1b5dccc80fc + md5: c86deaedf1d19981dbfcea7a3b53d331 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-imas", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-ivas >=2.20.0,<2.21.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-ivas >=2.22.0,<2.23.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-foreach @@ -43,17 +44,17 @@ requirements: - r-matrix - r-survival run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-ivas >=2.20.0,<2.21.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-ivas >=2.22.0,<2.23.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-imcdatasets/meta.yaml b/recipes/bioconductor-imcdatasets/meta.yaml index 2208795414271..50be0d4514827 100644 --- a/recipes/bioconductor-imcdatasets/meta.yaml +++ b/recipes/bioconductor-imcdatasets/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "imcdatasets" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1e0e9d5ecc4a826887de1abc773d86b3 + md5: 6e687f10502d7d9d369c384e99977953 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-imcdatasets", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat requirements: host: - - 'bioconductor-cytomapper >=1.12.0,<1.13.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-cytomapper >=1.14.0,<1.15.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-cytomapper >=1.12.0,<1.13.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-cytomapper >=1.14.0,<1.15.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-imcdatasets/post-link.sh b/recipes/bioconductor-imcdatasets/post-link.sh index f353b2a1ae091..12db5126d417b 100644 --- a/recipes/bioconductor-imcdatasets/post-link.sh +++ b/recipes/bioconductor-imcdatasets/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "imcdatasets-1.8.0" +installBiocDataPackage.sh "imcdatasets-1.10.0" diff --git a/recipes/bioconductor-imcrtools/meta.yaml b/recipes/bioconductor-imcrtools/meta.yaml index b56409bd2fdbe..50de270226360 100644 --- a/recipes/bioconductor-imcrtools/meta.yaml +++ b/recipes/bioconductor-imcrtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.3" %} +{% set version = "1.8.0" %} {% set name = "imcRtools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94eb20c85197b1461d9d5ab126b31c9d + md5: 483b782cf0adc433cf956e4ca52c393c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-imcrtools", max_pin="x.x") }}' noarch: generic # Suggests: CATALYST, grid, BiocStyle, knitr, rmarkdown, markdown, testthat requirements: host: - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-cytomapper >=1.12.0,<1.13.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-cytomapper >=1.14.0,<1.15.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-concaveman @@ -52,16 +53,16 @@ requirements: - r-viridis - r-vroom run: - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-cytomapper >=1.12.0,<1.13.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-cytomapper >=1.14.0,<1.15.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-concaveman diff --git a/recipes/bioconductor-imman/meta.yaml b/recipes/bioconductor-imman/meta.yaml index a70a804e1068e..4a0b5412457fe 100644 --- a/recipes/bioconductor-imman/meta.yaml +++ b/recipes/bioconductor-imman/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "IMMAN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3588d8794020fb9d369910d822b5b1e4 + md5: 6e3ac40584a93ea233ba0b082a4d79aa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-imman", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' - r-base - r-igraph - r-seqinr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' - r-base - r-igraph - r-seqinr diff --git a/recipes/bioconductor-immunespacer/meta.yaml b/recipes/bioconductor-immunespacer/meta.yaml index e195e9f0a49c0..20db0e898252b 100644 --- a/recipes/bioconductor-immunespacer/meta.yaml +++ b/recipes/bioconductor-immunespacer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "ImmuneSpaceR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7365d830f8a7ec436b6737932cb6c1b + md5: 3d19d0b03625db9bd86ce96b98dbe438 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-immunespacer", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, covr, withr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-curl - r-data.table @@ -41,10 +42,10 @@ requirements: - r-rmarkdown - r-scales run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-curl - r-data.table diff --git a/recipes/bioconductor-immunoclust/meta.yaml b/recipes/bioconductor-immunoclust/meta.yaml index de5de744faf41..32861095ef561 100644 --- a/recipes/bioconductor-immunoclust/meta.yaml +++ b/recipes/bioconductor-immunoclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "immunoClust" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c5d377e5265f45ceb2a4da80d355fc47 + md5: b83f47eaa19d45984b19f4071b455873 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-immunoclust", max_pin="x.x") }}' # Suggests: BiocStyle, utils, testthat +# SystemRequirements: gsl requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-lattice - libblas - liblapack + - gsl run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-lattice + - gsl build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-immunotation/meta.yaml b/recipes/bioconductor-immunotation/meta.yaml index 232bdbeb588c2..eb969b28a159d 100644 --- a/recipes/bioconductor-immunotation/meta.yaml +++ b/recipes/bioconductor-immunotation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "immunotation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4dff1d35e677b860b005364788695243 + md5: b05bb33e3987de27d181d8e44e468f62 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-immunotation", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT requirements: diff --git a/recipes/bioconductor-impcdata/meta.yaml b/recipes/bioconductor-impcdata/meta.yaml index f99c7b47fac93..6d8b9e6c09f7b 100644 --- a/recipes/bioconductor-impcdata/meta.yaml +++ b/recipes/bioconductor-impcdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "IMPCdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3db8a9ef20ab4890eb5dede2f53fc44 + md5: c4a243d4a15f680abfb5d61a951c620d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-impcdata", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-impute/meta.yaml b/recipes/bioconductor-impute/meta.yaml index ffa18e5707df0..0f5d1d5aed6cc 100644 --- a/recipes/bioconductor-impute/meta.yaml +++ b/recipes/bioconductor-impute/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.1" %} +{% set version = "1.76.0" %} {% set name = "impute" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cf3ffdc0f5d6caac43d3e3e7d73a8096 + md5: 8e974dcc31c3507ebcc8984b2d7943f9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-impute", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-indac.db/meta.yaml b/recipes/bioconductor-indac.db/meta.yaml index be1f05bca5b39..280f0ef419b4f 100644 --- a/recipes/bioconductor-indac.db/meta.yaml +++ b/recipes/bioconductor-indac.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "indac.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: cba72edcf7278033151e0eac077d8ff8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-indac.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-indeed/meta.yaml b/recipes/bioconductor-indeed/meta.yaml index e8089c504c58d..1e3e32686ddea 100644 --- a/recipes/bioconductor-indeed/meta.yaml +++ b/recipes/bioconductor-indeed/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "INDEED" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7441181a9c207fbd3288dd9b8ee500b7 + md5: 457badfae1608eb2c198b89526abe740 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-indeed", max_pin="x.x") }}' noarch: generic # Suggests: knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0) requirements: diff --git a/recipes/bioconductor-inetgrate/build.sh b/recipes/bioconductor-inetgrate/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-inetgrate/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-inetgrate/meta.yaml b/recipes/bioconductor-inetgrate/meta.yaml new file mode 100644 index 0000000000000..2e2f82d637edc --- /dev/null +++ b/recipes/bioconductor-inetgrate/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.0.0" %} +{% set name = "iNETgrate" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fb3e503060d4294162e8690a6bb41059 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-inetgrate", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, IlluminaHumanMethylation450kanno.ilmn12.hg19, AnnotationDbi, sesameData, TCGAbiolinks (>= 2.29.4) +requirements: + host: + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-pigengene >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-caret + - r-glmnet + - r-gplots + - r-igraph + - r-matrixstats + - r-rfast + - r-survival + - r-tidyr + - r-tidyselect + - r-wgcna + run: + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-pigengene >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-caret + - r-glmnet + - r-gplots + - r-igraph + - r-matrixstats + - r-rfast + - r-survival + - r-tidyr + - r-tidyselect + - r-wgcna +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Integrates DNA methylation data with gene expression in a single gene network' + description: 'The iNETgrate package provides functions to build a correlation network in which nodes are genes. DNA methylation and gene expression data are integrated to define the connections between genes. This network is used to identify modules (clusters) of genes. The biological information in each of the resulting modules is represented by an eigengene. These biological signatures can be used as features e.g., for classification of patients into risk categories. The resulting biological signatures are very robust and give a holistic view of the underlying molecular changes.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-infercnv/meta.yaml b/recipes/bioconductor-infercnv/meta.yaml index 015d148d0fac9..846a226731767 100644 --- a/recipes/bioconductor-infercnv/meta.yaml +++ b/recipes/bioconductor-infercnv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.1" %} {% set name = "infercnv" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9e09bfc20a01a9aebdf76bd5bb15eb0e + md5: d5bce5518c27e86b3fb26b6fedad5d7b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-infercnv", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat # SystemRequirements: JAGS 4.x.y requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-argparse - r-base @@ -56,10 +57,10 @@ requirements: - r-tidyr - 'jags 4.*.*' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-argparse - r-base diff --git a/recipes/bioconductor-infinityflow/meta.yaml b/recipes/bioconductor-infinityflow/meta.yaml index d4b597682299b..f1047378cf0e6 100644 --- a/recipes/bioconductor-infinityflow/meta.yaml +++ b/recipes/bioconductor-infinityflow/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "infinityFlow" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54c32c8b8be6ae8dd92483ea3fe25f2b + md5: e65e5163632d9351a8a1f1bb30d74d8f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-infinityflow", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-generics - r-gtools @@ -33,8 +34,8 @@ requirements: - r-uwot - r-xgboost run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-generics - r-gtools diff --git a/recipes/bioconductor-inpas/meta.yaml b/recipes/bioconductor-inpas/meta.yaml index 0c6fd56ba7c4d..9d51c47ac6612 100644 --- a/recipes/bioconductor-inpas/meta.yaml +++ b/recipes/bioconductor-inpas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "InPAS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d43e5034da4ada85c372c1f7f415a95a + md5: d11dbf3351e3fec486c3da1a61bf6050 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-inpas", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics,BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, knitr, markdown, rmarkdown, rtracklayer, RUnit, grDevices, TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-cleanupdtseq >=1.38.0,<1.39.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-cleanupdtseq >=1.40.0,<1.41.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-batchtools - r-depmixs4 @@ -48,19 +49,19 @@ requirements: - r-reshape2 - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-cleanupdtseq >=1.38.0,<1.39.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-cleanupdtseq >=1.40.0,<1.41.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-batchtools - r-depmixs4 diff --git a/recipes/bioconductor-inpower/meta.yaml b/recipes/bioconductor-inpower/meta.yaml index 991b764e5def3..352b849653f39 100644 --- a/recipes/bioconductor-inpower/meta.yaml +++ b/recipes/bioconductor-inpower/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "INPower" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af7a75d26eefaadd42eb6b31e5d4aae0 + md5: 3b769c08ded506c713da036c30fe4da9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-inpower", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: diff --git a/recipes/bioconductor-inspect/build_failure.linux-64.yaml b/recipes/bioconductor-inspect/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..95ece71c08362 --- /dev/null +++ b/recipes/bioconductor-inspect/build_failure.linux-64.yaml @@ -0,0 +1,33 @@ +recipe_sha: b6bbddaaff8dbbb23dad96d68412111023807b708179b0d3fa28588e58a8759a # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + Error: object ‘read.xls’ is not exported by 'namespace:gdata' +category: |- + compiler error +log: |- + 14:32:11 BIOCONDA INFO (OUT) ERROR: lazy loading failed for package ‘INSPEcT’ + 14:32:11 BIOCONDA INFO (OUT) During startup - Warning message: + 14:32:11 BIOCONDA INFO (OUT) Setting LC_TIME failed, using "C" + 14:32:11 BIOCONDA INFO (OUT) Error: object ‘read.xls’ is not exported by 'namespace:gdata' + 14:32:11 BIOCONDA INFO (OUT) Execution halted + 14:32:11 BIOCONDA INFO (OUT) * removing ‘/opt/conda/conda-bld/bioconductor-inspect_1702304851717/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/INSPEcT’ + 14:32:12 BIOCONDA INFO (OUT) Traceback (most recent call last): + 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/bin/conda-mambabuild", line 10, in + 14:32:12 BIOCONDA INFO (OUT) sys.exit(main()) + 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + 14:32:12 BIOCONDA INFO (OUT) call_conda_build(action, config) + 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + 14:32:12 BIOCONDA INFO (OUT) result = api.build( + 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + 14:32:12 BIOCONDA INFO (OUT) return build_tree( + 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + 14:32:12 BIOCONDA INFO (OUT) packages_from_this = build(metadata, stats, + 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build + 14:32:12 BIOCONDA INFO (OUT) utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, + 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + 14:32:12 BIOCONDA INFO (OUT) return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + 14:32:12 BIOCONDA INFO (OUT) raise subprocess.CalledProcessError(proc.returncode, _args) + 14:32:12 BIOCONDA INFO (OUT) subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-inspect_1702304851717/work/conda_build.sh']' returned non-zero exit status 1. + 14:32:21 BIOCONDA ERROR COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /tmp/tmp24i5m63r/build_script.bash:/opt/build_script.bash -v /opt/mambaforge/envs/bioconda/conda-bld/:/opt/host-conda-bld -v /home/runner/work/bioconda-recipes/bioconda-recipes/recipes/bioconductor-inspect:/opt/recipe -e LANG=C.UTF-8 -e HOST_USER_ID=1001 quay.io/bioconda/bioconda-utils-build-env-cos7:2.11.0 /bin/bash /opt/build_script.bash + diff --git a/recipes/bioconductor-inspect/meta.yaml b/recipes/bioconductor-inspect/meta.yaml index c1d37877c12d5..8036e06f7ea1b 100644 --- a/recipes/bioconductor-inspect/meta.yaml +++ b/recipes/bioconductor-inspect/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.31.0" %} {% set name = "INSPEcT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 731b56f9ee71c545653a62ba8bada39c + md5: e48ba19e529a7072f52817ecd08d2b9c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-inspect", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plgem >=1.72.0,<1.73.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plgem >=1.74.0,<1.75.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base - r-desolve @@ -44,20 +45,20 @@ requirements: - r-rootsolve - r-shiny run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plgem >=1.72.0,<1.73.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plgem >=1.74.0,<1.75.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base - r-desolve diff --git a/recipes/bioconductor-intact/meta.yaml b/recipes/bioconductor-intact/meta.yaml index 60af61e8dc338..a273c8c9b8cd1 100644 --- a/recipes/bioconductor-intact/meta.yaml +++ b/recipes/bioconductor-intact/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "INTACT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ceaf5b083b46ba3d8dd3948502fef80 + md5: d8646f4acb0cbb31ccf53a672818be40 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-intact", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-intad/meta.yaml b/recipes/bioconductor-intad/meta.yaml index d8c2c7e930a40..754ba4a2adcb7 100644 --- a/recipes/bioconductor-intad/meta.yaml +++ b/recipes/bioconductor-intad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "InTAD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 21d458b9b5a25c878f821311e1fd1cdf + md5: 2502f954bc06e364560216eb972c18f7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-intad", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggpubr - r-mclust run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggpubr diff --git a/recipes/bioconductor-intansv/meta.yaml b/recipes/bioconductor-intansv/meta.yaml index e37045506cf7c..7b67061f38d88 100644 --- a/recipes/bioconductor-intansv/meta.yaml +++ b/recipes/bioconductor-intansv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "intansv" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5af1bb5f5651006c1f7eaa0e439d4bcf + md5: d23f9f69f23ab113ea9ac7100cafb3f1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-intansv", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-plyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-plyr test: diff --git a/recipes/bioconductor-interaccircos/meta.yaml b/recipes/bioconductor-interaccircos/meta.yaml index 0889e8f21d8f0..df5cf27ff94e8 100644 --- a/recipes/bioconductor-interaccircos/meta.yaml +++ b/recipes/bioconductor-interaccircos/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "interacCircos" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec5b4dc1bd80300f335376278c1b37fc + md5: d97429da8da823bf80547b4ac8ca2505 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-interaccircos", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-interactionset/meta.yaml b/recipes/bioconductor-interactionset/meta.yaml index 4177427dc658b..246555c250fde 100644 --- a/recipes/bioconductor-interactionset/meta.yaml +++ b/recipes/bioconductor-interactionset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "InteractionSet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a37d06db719d31ff11c614171d612d0 + md5: 273175864f47083ba4b983c72ba0c1dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-interactionset", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, BiocStyle # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-interactivecomplexheatmap/meta.yaml b/recipes/bioconductor-interactivecomplexheatmap/meta.yaml index 8453899d820fb..1fc9f6c2b98ff 100644 --- a/recipes/bioconductor-interactivecomplexheatmap/meta.yaml +++ b/recipes/bioconductor-interactivecomplexheatmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "InteractiveComplexHeatmap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d0c5ce2f87cb18bd8dd6523db4abc358 + md5: 87fef3e4c9035cbfab5dc4a2242223dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-interactivecomplexheatmap", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, EnrichedHeatmap, GenomicRanges, data.table, circlize, GenomicFeatures, tidyverse, tidyHeatmap, cluster, org.Hs.eg.db, simplifyEnrichment, GO.db, SC3, GOexpress, SingleCellExperiment, scater, gplots, pheatmap, airway, DESeq2, DT, cola, BiocManager, gridtext, HilbertCurve (>= 1.21.1), shinydashboard, SummarizedExperiment, pkgndep, ks requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-clisymbols - r-digest @@ -36,9 +37,9 @@ requirements: - r-shiny - r-svglite run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-clisymbols - r-digest diff --git a/recipes/bioconductor-interactivedisplay/build_failure.linux-64.yaml b/recipes/bioconductor-interactivedisplay/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..9eba9918043d4 --- /dev/null +++ b/recipes/bioconductor-interactivedisplay/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 9c517fc772ed28be827019592f5023b076b81fbe7358c247a963d5f1d48acc90 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + sysroot_linux-64: 2.12-he073ed8_16 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h0c5db8f_5 conda-forge + toml: 0.10.2-pyhd8ed1ab_0 conda-forge + tomlkit: 0.12.3-pyha770c72_0 conda-forge + tzdata: 2023c-h71feb2d_0 conda-forge + wheel: 0.42.0-pyhd8ed1ab_0 conda-forge + xmltodict: 0.13.0-pyhd8ed1ab_0 conda-forge + xorg-kbproto: 1.0.7-h7f98852_1002 conda-forge + xorg-libice: 1.1.1-hd590300_0 conda-forge + xorg-libsm: 1.2.4-h7391055_0 conda-forge + xorg-libx11: 1.8.7-h8ee46fc_0 conda-forge + xorg-libxau: 1.0.11-hd590300_0 conda-forge + xorg-libxdmcp: 1.1.3-h7f98852_0 conda-forge + xorg-libxext: 1.3.4-h0b41bf4_2 conda-forge + xorg-libxrender: 0.9.11-hd590300_0 conda-forge + xorg-libxt: 1.3.0-hd590300_1 conda-forge + xorg-renderproto: 0.11.1-h7f98852_1002 conda-forge + xorg-xextproto: 7.3.0-h0b41bf4_1003 conda-forge + xorg-xproto: 7.0.31-h7f98852_1007 conda-forge + xz: 5.2.6-h166bdaf_0 conda-forge + yaml: 0.2.5-h7f98852_2 conda-forge + yq: 3.2.3-pyhd8ed1ab_0 conda-forge + zlib: 1.2.13-hd590300_5 conda-forge + zstd: 1.5.5-hfc55251_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... + To install TinyTeX with tinytex::install_tinytex() the system must have a functional Perl + installation with a File::Find module. Most end-user systems will already satisfy this + requirement; however, some minimal contexts (e.g., containers) may not. Perl is available + via Conda Forge as the package perl. See https://github.com/rstudio/tinytex/issues/419 + + + done + [34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.0MB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.5MB/s 0.0s + [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.0MB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.5MB/s 0.0s + [?25h + ## Package Plan ## + + environment location: /opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/_build_env + + + Source cache directory is: /opt/conda/conda-bld/src_cache + INFO:conda_build.source:Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: interactiveDisplay_1.40.0_4adec73e76.tar.gz + INFO:conda_build.source:Downloading source to cache: interactiveDisplay_1.40.0_4adec73e76.tar.gz + Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/interactiveDisplay_1.40.0.tar.gz + INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/interactiveDisplay_1.40.0.tar.gz + Success + INFO:conda_build.source:Success + Extracting download + source tree in: /opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/work + export PREFIX=/opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/work + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library + * installing *source* package interactiveDisplay ... + ** using staged installation + ** R + ** data + ** inst + ** byte-compile and prepare package for lazy loading + During startup - Warning message: + Setting LC_TIME failed, using "C" + Installing package into $PREFIX/lib/R/library/00LOCK-work/00new + (as lib is unspecified) + Error in contrib.url(repos, type) : + trying to use CRAN without setting a mirror + Error: unable to load R code in package interactiveDisplay + Execution halted + ERROR: lazy loading failed for package interactiveDisplay + * removing /opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/interactiveDisplay + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build + utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, + File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-interactivedisplay/meta.yaml b/recipes/bioconductor-interactivedisplay/meta.yaml index bf5cbb9038509..d76299068acbc 100644 --- a/recipes/bioconductor-interactivedisplay/meta.yaml +++ b/recipes/bioconductor-interactivedisplay/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "interactiveDisplay" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 32075538ec509a9743bb5e6baf5b0655 + md5: 4adec73e763df3dc2e697e41bff3ead8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-interactivedisplay", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, hgu95av2.db, knitr, GenomicRanges, SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer, metagenomeSeq, gplots, vegan, Biobase requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-interactivedisplaybase >=1.38.0,<1.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-interactivedisplaybase >=1.40.0,<1.41.0' - r-base - r-ggplot2 - r-gridsvg @@ -33,12 +34,11 @@ requirements: - r-reshape2 - r-shiny - r-xml - - r-biocmanager run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-interactivedisplaybase >=1.38.0,<1.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-interactivedisplaybase >=1.40.0,<1.41.0' - r-base - r-ggplot2 - r-gridsvg @@ -47,10 +47,8 @@ requirements: - r-reshape2 - r-shiny - r-xml - - r-biocmanager test: commands: - - ls $PREFIX/bin - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' diff --git a/recipes/bioconductor-interactivedisplaybase/meta.yaml b/recipes/bioconductor-interactivedisplaybase/meta.yaml index 7e4aac617b04d..6457aaceb53ef 100644 --- a/recipes/bioconductor-interactivedisplaybase/meta.yaml +++ b/recipes/bioconductor-interactivedisplaybase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "interactiveDisplayBase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b348c5193f2b96439ef86cb82c03247f + md5: 9ae8be7104ab2debe258b504bcd24e38 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-interactivedisplaybase", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dt - r-shiny run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dt - r-shiny diff --git a/recipes/bioconductor-intercellar/meta.yaml b/recipes/bioconductor-intercellar/meta.yaml index 950572f1a13c1..81dde8f9efb34 100644 --- a/recipes/bioconductor-intercellar/meta.yaml +++ b/recipes/bioconductor-intercellar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "InterCellar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aebf615461677efa93c2c73cbcdfa318 + md5: a331a8a5f0161dd1e5afa2430660b785 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-intercellar", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite, processx, attempt, BiocStyle, httr requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - r-base - r-circlize - r-colorspace @@ -58,8 +59,8 @@ requirements: - r-visnetwork - r-wordcloud2 run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - r-base - r-circlize - r-colorspace diff --git a/recipes/bioconductor-interest/meta.yaml b/recipes/bioconductor-interest/meta.yaml index 66e3569a8415b..80b57c6986664 100644 --- a/recipes/bioconductor-interest/meta.yaml +++ b/recipes/bioconductor-interest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "IntEREst" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,51 +11,52 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a96a9adbc5e4a9299cdbeed5f7061ced + md5: b9b473ea53b89a32487163ef6a664905 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-interest", max_pin="x.x") }}' noarch: generic # Suggests: clinfun, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dexseq >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dbi - r-rmysql - r-seqinr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dexseq >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dbi - r-rmysql diff --git a/recipes/bioconductor-interminer/meta.yaml b/recipes/bioconductor-interminer/meta.yaml index 2269b69153c9a..bd1ae0276f056 100644 --- a/recipes/bioconductor-interminer/meta.yaml +++ b/recipes/bioconductor-interminer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "InterMineR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09d5528d9f3bdfcfddfa5a54ebf99f98 + md5: a401e91084a8393592ceb3305b6cbfa2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-interminer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, Gviz, knitr, rmarkdown, GO.db, org.Hs.eg.db requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-httr - r-igraph @@ -35,11 +36,11 @@ requirements: - r-xml - r-xml2 run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-httr - r-igraph diff --git a/recipes/bioconductor-intomics/meta.yaml b/recipes/bioconductor-intomics/meta.yaml index 599f5b5e98d63..7eb05b0cf719f 100644 --- a/recipes/bioconductor-intomics/meta.yaml +++ b/recipes/bioconductor-intomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "IntOMICS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eec7530ce0fd9941c0cfe06c864e7511 + md5: 61628ea37535123f71455b77b194b08c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-intomics", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, curatedTCGAData, TCGAutils, testthat requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bestnormalize - r-bnlearn @@ -36,7 +37,7 @@ requirements: - r-rcolorbrewer - r-rlang run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bestnormalize - r-bnlearn diff --git a/recipes/bioconductor-intramirexplorer/meta.yaml b/recipes/bioconductor-intramirexplorer/meta.yaml index dc6432a215aac..8e70e8e286ee9 100644 --- a/recipes/bioconductor-intramirexplorer/meta.yaml +++ b/recipes/bioconductor-intramirexplorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "IntramiRExploreR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9f037f313236ed7acb47a038d70b7593 + md5: e319d73695e5e1f12d9fc79896c49674 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-intramirexplorer", max_pin="x.x") }}' noarch: generic # Suggests: gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat requirements: host: - - 'bioconductor-fgnet >=3.34.0,<3.35.0' + - 'bioconductor-fgnet >=3.36.0,<3.37.0' - r-base - 'r-igraph >=1.0.1' - 'r-knitr >=1.12.3' run: - - 'bioconductor-fgnet >=3.34.0,<3.35.0' + - 'bioconductor-fgnet >=3.36.0,<3.37.0' - r-base - 'r-igraph >=1.0.1' - 'r-knitr >=1.12.3' diff --git a/recipes/bioconductor-ioniser/meta.yaml b/recipes/bioconductor-ioniser/meta.yaml index 400b9e5ff444b..d6dce6d5af852 100644 --- a/recipes/bioconductor-ioniser/meta.yaml +++ b/recipes/bioconductor-ioniser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "IONiseR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1247c90a347c1886045bdca153fe5196 + md5: 10a3ed3f75ba8be8989b90d197096b40 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ioniser", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-bit64 - r-dplyr @@ -36,12 +37,12 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-bit64 - r-dplyr diff --git a/recipes/bioconductor-ipac/meta.yaml b/recipes/bioconductor-ipac/meta.yaml index 51dc95556d71c..c8ac07446c2ae 100644 --- a/recipes/bioconductor-ipac/meta.yaml +++ b/recipes/bioconductor-ipac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "iPAC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f48c2f8e363a774893839a48379a8d87 + md5: 2ea1fca8a80c62d82be0ef8d6313e52b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ipac", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-gdata - r-scatterplot3d run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-gdata - r-scatterplot3d diff --git a/recipes/bioconductor-ipath/meta.yaml b/recipes/bioconductor-ipath/meta.yaml index 6f73e3afe26e8..c942c0964afed 100644 --- a/recipes/bioconductor-ipath/meta.yaml +++ b/recipes/bioconductor-ipath/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "iPath" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 186f06f5b67f1987457d4b8a8b999d9b + md5: 71bdeccc2d0192cd080c4c190831d792 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ipath", max_pin="x.x") }}' # Suggests: rmarkdown, BiocStyle, knitr # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-ggplot2 - r-ggpubr @@ -34,7 +35,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-ggplot2 - r-ggpubr diff --git a/recipes/bioconductor-ipddb/meta.yaml b/recipes/bioconductor-ipddb/meta.yaml index 90e5b808a3a52..685bfe5c5e978 100644 --- a/recipes/bioconductor-ipddb/meta.yaml +++ b/recipes/bioconductor-ipddb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "ipdDb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0afd5495c9ebce5bb6ad475f9d44236e + md5: 0346f5dcca05a1bfb117214c54f36524 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ipddb", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-assertthat - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-assertthat - r-base - r-dbi diff --git a/recipes/bioconductor-ipo/meta.yaml b/recipes/bioconductor-ipo/meta.yaml index b488d197c0948..85a6e762813ff 100644 --- a/recipes/bioconductor-ipo/meta.yaml +++ b/recipes/bioconductor-ipo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "IPO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d99c69c85047b339955ff0a6bc2365d0 + md5: a1275d6f177754744bcceb9a8aed44a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ipo", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-rsm run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-rsm test: diff --git a/recipes/bioconductor-iranges/meta.yaml b/recipes/bioconductor-iranges/meta.yaml index 04fb73abd9293..9f429ff8f8074 100644 --- a/recipes/bioconductor-iranges/meta.yaml +++ b/recipes/bioconductor-iranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.1" %} +{% set version = "2.36.0" %} {% set name = "IRanges" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c9b9645aee1db4455dea509cedd7e157 + md5: 87618d2e5ee94d7ab81d2e1c4d847120 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iranges", max_pin="x.x") }}' # Suggests: XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-isanalytics/meta.yaml b/recipes/bioconductor-isanalytics/meta.yaml index ae6d0b78dc25b..bb03455bd7935 100644 --- a/recipes/bioconductor-isanalytics/meta.yaml +++ b/recipes/bioconductor-isanalytics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "ISAnalytics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ceb361c936fc5adc1ae9eb2b5122839c + md5: d1962980b18dd3ff8fdcc1bb0c855eaf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-isanalytics", max_pin="x.x") }}' noarch: generic # Suggests: testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown, roxygen2, vegan, withr, extraDistr, ggalluvial, scales, gridExtra, R.utils, RefManageR, flexdashboard, circlize, plotly, gtools, eulerr, openxlsx, jsonlite, pheatmap, BiocParallel, progressr, future, doFuture, foreach, psych, data.table, Rcapture requirements: diff --git a/recipes/bioconductor-isee/meta.yaml b/recipes/bioconductor-isee/meta.yaml index 09bb9622763bd..1cb011c60e377 100644 --- a/recipes/bioconductor-isee/meta.yaml +++ b/recipes/bioconductor-isee/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "iSEE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a933b7c4b34541ff8e3f477b24c354c2 + md5: e6d2be3afb9bc484d594cbd21887ec53 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-isee", max_pin="x.x") }}' noarch: generic # Suggests: testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-colourpicker @@ -43,11 +44,11 @@ requirements: - r-vipor - r-viridislite run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-colourpicker diff --git a/recipes/bioconductor-iseede/build.sh b/recipes/bioconductor-iseede/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-iseede/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iseede/meta.yaml b/recipes/bioconductor-iseede/meta.yaml new file mode 100644 index 0000000000000..68f2097a44e14 --- /dev/null +++ b/recipes/bioconductor-iseede/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.0.0" %} +{% set name = "iSEEde" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4d6215b9243635ed9dd3b6fcf5cbf166 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iseede", max_pin="x.x") }}' + noarch: generic +# Suggests: airway, BiocStyle, covr, knitr, limma, org.Hs.eg.db, RefManageR, rmarkdown, scuttle, sessioninfo, statmod, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-shiny + run: + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'iSEE extension for panels related to differential expression analysis' + description: 'This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of differential expression results. This package does not perform differential expression. Instead, it provides methods to embed precomputed differential expression results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.' + diff --git a/recipes/bioconductor-iseehex/meta.yaml b/recipes/bioconductor-iseehex/meta.yaml index 721af6f3acd45..45547ab3c80ac 100644 --- a/recipes/bioconductor-iseehex/meta.yaml +++ b/recipes/bioconductor-iseehex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "iSEEhex" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 49e7fb29541fb2ac12ad0ac21926d277 + md5: 9bc98dc14114c756f97c130adf061a4b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iseehex", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), scRNAseq, scater requirements: host: - - 'bioconductor-isee >=2.12.0,<2.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-hexbin - r-shiny run: - - 'bioconductor-isee >=2.12.0,<2.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-hexbin diff --git a/recipes/bioconductor-iseehub/meta.yaml b/recipes/bioconductor-iseehub/meta.yaml index 3cc96f0d3f3f5..0a193959471a0 100644 --- a/recipes/bioconductor-iseehub/meta.yaml +++ b/recipes/bioconductor-iseehub/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.1.1" %} +{% set version = "1.4.0" %} {% set name = "iSEEhub" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98bd83d25a30d3029b20350423b76e6e + md5: 6ebb32da66242f608b83522fca1d9a62 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iseehub", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), nullrangesData requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-isee >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biocmanager - r-dt @@ -35,12 +36,12 @@ requirements: - r-shinydashboard - r-shinyjs run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-isee >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biocmanager - r-dt diff --git a/recipes/bioconductor-iseeindex/build.sh b/recipes/bioconductor-iseeindex/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-iseeindex/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iseeindex/meta.yaml b/recipes/bioconductor-iseeindex/meta.yaml new file mode 100644 index 0000000000000..e795471cb94d1 --- /dev/null +++ b/recipes/bioconductor-iseeindex/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "1.0.0" %} +{% set name = "iSEEindex" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 98a9141431a3206fd242b5b0b4056c41 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iseeindex", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), yaml +requirements: + host: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-dt + - r-paws.storage + - r-rintrojs + - r-shiny + - r-shinydashboard + - r-shinyjs + - r-stringr + - r-urltools + run: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-dt + - r-paws.storage + - r-rintrojs + - r-shiny + - r-shinydashboard + - r-shinyjs + - r-stringr + - r-urltools +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'iSEE extension for a landing page to a custom collection of data sets' + description: 'This package provides an interface to any collection of data sets within a single iSEE web-application. The main functionality of this package is to define a custom landing page allowing app maintainers to list a custom collection of data sets that users can selected from and directly load objects into an iSEE web-application.' + diff --git a/recipes/bioconductor-iseepathways/build.sh b/recipes/bioconductor-iseepathways/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-iseepathways/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iseepathways/meta.yaml b/recipes/bioconductor-iseepathways/meta.yaml new file mode 100644 index 0000000000000..b1ecb82d75020 --- /dev/null +++ b/recipes/bioconductor-iseepathways/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.0.0" %} +{% set name = "iSEEpathways" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 52b84dcbd5e5ab0a6bbdc27120d7e86a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iseepathways", max_pin="x.x") }}' + noarch: generic +# Suggests: airway, BiocStyle, covr, edgeR, fgsea, GO.db, iSEEde, knitr, org.Hs.eg.db, RefManageR, rmarkdown, scater, scuttle, sessioninfo, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-ggplot2 + - r-shiny + - r-shinywidgets + run: + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-ggplot2 + - r-shiny + - r-shinywidgets +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'iSEE extension for panels related to pathway analysis' + description: 'This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of pathway analysis results. This package does not perform pathway analysis. Instead, it provides methods to embed precomputed pathway analysis results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.' + diff --git a/recipes/bioconductor-iseeu/meta.yaml b/recipes/bioconductor-iseeu/meta.yaml index 5ad45b2cbf5f2..b0845ec64ecd3 100644 --- a/recipes/bioconductor-iseeu/meta.yaml +++ b/recipes/bioconductor-iseeu/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "iSEEu" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 320331a5b0bf6929e03ba9003d0d8aad + md5: d9349d85759c37c8a971b4ffcebcecea build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iseeu", max_pin="x.x") }}' noarch: generic # Suggests: scRNAseq, scater, scran, airway, edgeR, AnnotationDbi, org.Hs.eg.db, GO.db, KEGGREST, knitr, igraph, rmarkdown, BiocStyle, htmltools, Rtsne, uwot, testthat (>= 2.1.0), covr requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-isee >=2.12.0,<2.13.0' - - 'bioconductor-iseehex >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-iseehex >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-colourpicker - r-dt @@ -34,12 +35,12 @@ requirements: - r-shiny - r-shinyace run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-isee >=2.12.0,<2.13.0' - - 'bioconductor-iseehex >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-iseehex >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-colourpicker - r-dt diff --git a/recipes/bioconductor-iseq/meta.yaml b/recipes/bioconductor-iseq/meta.yaml index c55d6f5819474..326c46a55f5f7 100644 --- a/recipes/bioconductor-iseq/meta.yaml +++ b/recipes/bioconductor-iseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "iSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f68d848b58ee7cc917534a00c27d69c + md5: 1798c4c248175516afc66ee7f45d5051 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iseq", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-islet/meta.yaml b/recipes/bioconductor-islet/meta.yaml index 19564678e2d71..78b454e10d2aa 100644 --- a/recipes/bioconductor-islet/meta.yaml +++ b/recipes/bioconductor-islet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ISLET" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a76f8e90e5662a93b09be8f1f06b863 + md5: 5cf5ae7df60062c1822ca64c3989a4e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-islet", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, htmltools, RUnit +# Suggests: BiocStyle, knitr, rmarkdown, htmltools, RUnit, dplyr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-abind - r-base + - r-lme4 - r-matrix + - r-nnls + - r-purrr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-abind - r-base + - r-lme4 - r-matrix + - r-nnls + - r-purrr test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,6 +48,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Individual-Specific ceLl typE referencing Tool' - description: 'ISLET is a method to conduct signal deconvolution for general -omics data. It can estimate the individual-specific and cell-type-specific reference panels, when there are multiple samples observed from each subject. It takes the input of the observed mixture data (feature by sample matrix), and the cell type mixture proportions (sample by cell type matrix), and the sample-to-subject information. It can solve for the reference panel on the individual-basis. It can also conduct test to identify cell-type-specific differential expression (csDE) genes.' + description: 'ISLET is a method to conduct signal deconvolution for general -omics data. It can estimate the individual-specific and cell-type-specific reference panels, when there are multiple samples observed from each subject. It takes the input of the observed mixture data (feature by sample matrix), and the cell type mixture proportions (sample by cell type matrix), and the sample-to-subject information. It can solve for the reference panel on the individual-basis and conduct test to identify cell-type-specific differential expression (csDE) genes. It also improves estimated cell type mixture proportions by integrating personalized reference panels.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' diff --git a/recipes/bioconductor-isobar/meta.yaml b/recipes/bioconductor-isobar/meta.yaml index dd3209fcd717f..b900b92c86f60 100644 --- a/recipes/bioconductor-isobar/meta.yaml +++ b/recipes/bioconductor-isobar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "isobar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1795587748211afa4d437207a552d936 + md5: bf7b66ee10cfc2f8b24f22642bbc395a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-isobar", max_pin="x.x") }}' noarch: generic # Suggests: MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, DBI, MASS requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base - r-distr - r-ggplot2 - r-plyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base - r-distr - r-ggplot2 diff --git a/recipes/bioconductor-isobayes/build.sh b/recipes/bioconductor-isobayes/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-isobayes/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-isobayes/meta.yaml b/recipes/bioconductor-isobayes/meta.yaml new file mode 100644 index 0000000000000..39f49ed83d0d2 --- /dev/null +++ b/recipes/bioconductor-isobayes/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "1.0.1" %} +{% set name = "IsoBayes" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d9e1de9f5a1f8279117fde4cc997725d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-isobayes", max_pin="x.x") }}' +# Suggests: knitr, rmarkdown, testthat, BiocStyle +# SystemRequirements: C++17 +requirements: + host: + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-data.table + - r-doparallel + - r-dorng + - r-foreach + - r-ggplot2 + - r-glue + - r-hdinterval + - r-iterators + - r-rcpp + - r-rcpparmadillo + - libblas + - liblapack + run: + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-data.table + - r-doparallel + - r-dorng + - r-foreach + - r-ggplot2 + - r-glue + - r-hdinterval + - r-iterators + - r-rcpp + - r-rcpparmadillo + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'IsoBayes: Single Isoform protein inference Method via Bayesian Analyses' + description: 'IsoBayes is a Bayesian method to perform inference on single protein isoforms. Our approach infers the presence/absence of protein isoforms, and also estimates their abundance; additionally, it provides a measure of the uncertainty of these estimates, via: i) the posterior probability that a protein isoform is present in the sample; ii) a posterior credible interval of its abundance. IsoBayes inputs liquid cromatography mass spectrometry (MS) data, and can work with both PSM counts, and intensities. When available, trascript isoform abundances (i.e., TPMs) are also incorporated: TPMs are used to formulate an informative prior for the respective protein isoform relative abundance. We further identify isoforms where the relative abundance of proteins and transcripts significantly differ. We use a two-layer latent variable approach to model two sources of uncertainty typical of MS data: i) peptides may be erroneously detected (even when absent); ii) many peptides are compatible with multiple protein isoforms. In the first layer, we sample the presence/absence of each peptide based on its estimated probability of being mistakenly detected, also known as PEP (i.e., posterior error probability). In the second layer, for peptides that were estimated as being present, we allocate their abundance across the protein isoforms they map to. These two steps allow us to recover the presence and abundance of each protein isoform.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-isocorrector/meta.yaml b/recipes/bioconductor-isocorrector/meta.yaml index 9bf3067bb9cbd..f21aefe95aded 100644 --- a/recipes/bioconductor-isocorrector/meta.yaml +++ b/recipes/bioconductor-isocorrector/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "IsoCorrectoR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90680864d0b6b71e3da4ae275894e35f + md5: ba3b19c2ad9ed8f9b7f6929c49828bb5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-isocorrector", max_pin="x.x") }}' noarch: generic # Suggests: IsoCorrectoRGUI, knitr, rmarkdown, testthat, BiocStyle requirements: diff --git a/recipes/bioconductor-isocorrectorgui/meta.yaml b/recipes/bioconductor-isocorrectorgui/meta.yaml index cbf371b5fd158..93ca3c9414cfc 100644 --- a/recipes/bioconductor-isocorrectorgui/meta.yaml +++ b/recipes/bioconductor-isocorrectorgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "IsoCorrectoRGUI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e197b90dc85263bbc0ef320e2a3b08c + md5: 2f46ff7c7647616cced839067b9e1b39 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-isocorrectorgui", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-isocorrector >=1.18.0,<1.19.0' + - 'bioconductor-isocorrector >=1.20.0,<1.21.0' - r-base - r-readxl - r-tcltk2 run: - - 'bioconductor-isocorrector >=1.18.0,<1.19.0' + - 'bioconductor-isocorrector >=1.20.0,<1.21.0' - r-base - r-readxl - r-tcltk2 diff --git a/recipes/bioconductor-isoformswitchanalyzer/meta.yaml b/recipes/bioconductor-isoformswitchanalyzer/meta.yaml index 73d0d270ba44e..83124db0611eb 100644 --- a/recipes/bioconductor-isoformswitchanalyzer/meta.yaml +++ b/recipes/bioconductor-isoformswitchanalyzer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.1" %} +{% set version = "2.2.0" %} {% set name = "IsoformSwitchAnalyzeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 764485e548e3d6cea542d472e5da6b32 + md5: 6aad6b0133da9e103b4385ff31b7028c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-isoformswitchanalyzer", max_pin="x.x") }}' # Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-dexseq >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pfamanalyzer >=1.0.0,<1.1.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-saturn >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' - - 'bioconductor-tximeta >=1.18.0,<1.19.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pfamanalyzer >=1.2.0,<1.3.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-saturn >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' + - 'bioconductor-tximeta >=1.20.0,<1.21.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-dbi - r-dplyr @@ -59,26 +60,26 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-dexseq >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pfamanalyzer >=1.0.0,<1.1.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-saturn >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' - - 'bioconductor-tximeta >=1.18.0,<1.19.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pfamanalyzer >=1.2.0,<1.3.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-saturn >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' + - 'bioconductor-tximeta >=1.20.0,<1.21.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-dbi - r-dplyr diff --git a/recipes/bioconductor-isolde/meta.yaml b/recipes/bioconductor-isolde/meta.yaml index 64ca75be07f2e..4999dfce68598 100644 --- a/recipes/bioconductor-isolde/meta.yaml +++ b/recipes/bioconductor-isolde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "ISoLDE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,13 +11,14 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dc7e409a60d1773ea7b12e413f20ef82 + md5: 448414b250ff7c903395638de3688411 build: - skip: true # [osx] - number: 0 + skip: True # [osx] + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-isolde", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-isomirs/meta.yaml b/recipes/bioconductor-isomirs/meta.yaml index 1dea0e508a153..f101815c26500 100644 --- a/recipes/bioconductor-isomirs/meta.yaml +++ b/recipes/bioconductor-isomirs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "isomiRs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b48363905238cb50facd569971942f72 + md5: 95b301f966153c00b98359bb6a0986cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-isomirs", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, org.Mm.eg.db, targetscan.Hs.eg.db, pheatmap, BiocStyle, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-degreport >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-degreport >=1.38.0,<1.39.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertive.sets - r-base - r-broom @@ -50,16 +51,16 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-degreport >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-degreport >=1.38.0,<1.39.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertive.sets - r-base - r-broom diff --git a/recipes/bioconductor-italics/meta.yaml b/recipes/bioconductor-italics/meta.yaml index c549517d8af3a..a6482e448f84b 100644 --- a/recipes/bioconductor-italics/meta.yaml +++ b/recipes/bioconductor-italics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.60.0" %} +{% set version = "2.62.0" %} {% set name = "ITALICS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 144200839aef6c79c6f6d7ea1a90d0d0 + md5: 05a5c23fcec3a45b6ff9b36b66b89752 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-italics", max_pin="x.x") }}' noarch: generic # Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp requirements: host: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-glad >=2.64.0,<2.65.0' - - 'bioconductor-italicsdata >=2.38.0,<2.39.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' + - 'bioconductor-italicsdata >=2.40.0,<2.41.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - 'bioconductor-pd.mapping50k.xba240 >=3.12.0,<3.13.0' - r-base - r-dbi run: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-glad >=2.64.0,<2.65.0' - - 'bioconductor-italicsdata >=2.38.0,<2.39.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' + - 'bioconductor-italicsdata >=2.40.0,<2.41.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - 'bioconductor-pd.mapping50k.xba240 >=3.12.0,<3.13.0' - r-base - r-dbi diff --git a/recipes/bioconductor-italicsdata/meta.yaml b/recipes/bioconductor-italicsdata/meta.yaml index 4c530d3cbb61a..9a246291d9dd4 100644 --- a/recipes/bioconductor-italicsdata/meta.yaml +++ b/recipes/bioconductor-italicsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.38.0" %} +{% set version = "2.40.0" %} {% set name = "ITALICSData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 390829582a6ace43fc47218d8f11e3c0 + md5: e154526c43e11840acfd4c92ff1cee8f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-italicsdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-italicsdata/post-link.sh b/recipes/bioconductor-italicsdata/post-link.sh index 3492e076baef6..606e7a5f75eef 100644 --- a/recipes/bioconductor-italicsdata/post-link.sh +++ b/recipes/bioconductor-italicsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "italicsdata-2.38.0" +installBiocDataPackage.sh "italicsdata-2.40.0" diff --git a/recipes/bioconductor-iterativebma/meta.yaml b/recipes/bioconductor-iterativebma/meta.yaml index 34e78b6da95c9..60232f6f7d1a5 100644 --- a/recipes/bioconductor-iterativebma/meta.yaml +++ b/recipes/bioconductor-iterativebma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "iterativeBMA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4e4143bab9e90dfd557a054ce813f67b + md5: be5e8911f1a2493bdf001fbe0a7cecfa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iterativebma", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-bma - r-leaps run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-bma - r-leaps diff --git a/recipes/bioconductor-iterativebmasurv/meta.yaml b/recipes/bioconductor-iterativebmasurv/meta.yaml index 3692bf30ef168..3d92067ce1446 100644 --- a/recipes/bioconductor-iterativebmasurv/meta.yaml +++ b/recipes/bioconductor-iterativebmasurv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "iterativeBMAsurv" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e7cc92900486c78f40ed28fbc4f5058e + md5: d2ced120a3665f0ebb69a462a072ad63 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iterativebmasurv", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-iterclust/meta.yaml b/recipes/bioconductor-iterclust/meta.yaml index f4fdf6993584d..e6ec04af4f7eb 100644 --- a/recipes/bioconductor-iterclust/meta.yaml +++ b/recipes/bioconductor-iterclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "iterClust" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5cad04ff9c73325942d2e3409f70149 + md5: af72d13d4200d5883ae63a99f0a49a69 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iterclust", max_pin="x.x") }}' noarch: generic # Suggests: tsne, bcellViper requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-cluster run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-cluster test: diff --git a/recipes/bioconductor-ivas/meta.yaml b/recipes/bioconductor-ivas/meta.yaml index 366afca6ebbe3..2759fdf777900 100644 --- a/recipes/bioconductor-ivas/meta.yaml +++ b/recipes/bioconductor-ivas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "IVAS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0cf4fb64fd7d23e080c55936659e5259 + md5: bf3c824233bc6ad5feffc4463554f57f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ivas", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-foreach @@ -38,15 +39,15 @@ requirements: - r-lme4 - r-matrix run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-ivygapse/meta.yaml b/recipes/bioconductor-ivygapse/meta.yaml index bbdb49d43cfe0..cd26902f032a0 100644 --- a/recipes/bioconductor-ivygapse/meta.yaml +++ b/recipes/bioconductor-ivygapse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "ivygapSE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 21c568e4f1ff5b0da5e6bac07de65eb4 + md5: d58fa85c46a9447719fa06aa57cc217d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ivygapse", max_pin="x.x") }}' noarch: generic # Suggests: knitr, png, limma, grid, DT, randomForest, digest, testthat, rmarkdown, BiocStyle, magick, statmod, codetools requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-hwriter @@ -32,8 +33,8 @@ requirements: - r-survminer - r-upsetr run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-hwriter diff --git a/recipes/bioconductor-iwtomics/meta.yaml b/recipes/bioconductor-iwtomics/meta.yaml index 7a8494052df91..4149664fdced6 100644 --- a/recipes/bioconductor-iwtomics/meta.yaml +++ b/recipes/bioconductor-iwtomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "IWTomics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6226d4962dd65dd0089c609e940bedf7 + md5: f571644700ff672c2ac90aa49b611158 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iwtomics", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fda - r-gtable - r-kernsmooth run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fda - r-gtable diff --git a/recipes/bioconductor-iyer517/meta.yaml b/recipes/bioconductor-iyer517/meta.yaml index 1c593ed51557a..0f3cf9d1d1a9d 100644 --- a/recipes/bioconductor-iyer517/meta.yaml +++ b/recipes/bioconductor-iyer517/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "Iyer517" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 962d1b3895541924544fd080008a5bc9 + md5: 81226f1ad5acd16cff4c7371f37d1881 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iyer517", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-iyer517/post-link.sh b/recipes/bioconductor-iyer517/post-link.sh index 9103dc3771e2b..6eb9d2b69a88b 100644 --- a/recipes/bioconductor-iyer517/post-link.sh +++ b/recipes/bioconductor-iyer517/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "iyer517-1.42.0" +installBiocDataPackage.sh "iyer517-1.44.0" diff --git a/recipes/bioconductor-jaspar2014/meta.yaml b/recipes/bioconductor-jaspar2014/meta.yaml index 4fba103ceb0d6..a7de5670f7d7f 100644 --- a/recipes/bioconductor-jaspar2014/meta.yaml +++ b/recipes/bioconductor-jaspar2014/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "JASPAR2014" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 63249cf2e663d3823da3359b8e584ede + md5: 6ef536411db46944f6d5b9a23ee13be6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-jaspar2014", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-jaspar2014/post-link.sh b/recipes/bioconductor-jaspar2014/post-link.sh index fa7b37c9d1561..0e2548b04d68b 100644 --- a/recipes/bioconductor-jaspar2014/post-link.sh +++ b/recipes/bioconductor-jaspar2014/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "jaspar2014-1.36.0" +installBiocDataPackage.sh "jaspar2014-1.38.0" diff --git a/recipes/bioconductor-jaspar2016/meta.yaml b/recipes/bioconductor-jaspar2016/meta.yaml index a4fb2145e9b1a..9085e136ba423 100644 --- a/recipes/bioconductor-jaspar2016/meta.yaml +++ b/recipes/bioconductor-jaspar2016/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "JASPAR2016" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9022c6f9720312b9da10800535edec62 + md5: 2976e4678291944f664396385049180b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-jaspar2016", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-jaspar2016/post-link.sh b/recipes/bioconductor-jaspar2016/post-link.sh index 628e268562d10..692043bcfa04f 100644 --- a/recipes/bioconductor-jaspar2016/post-link.sh +++ b/recipes/bioconductor-jaspar2016/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "jaspar2016-1.28.0" +installBiocDataPackage.sh "jaspar2016-1.30.0" diff --git a/recipes/bioconductor-jaspar2018/meta.yaml b/recipes/bioconductor-jaspar2018/meta.yaml index 4e513a835be7d..d6ddb786027d8 100644 --- a/recipes/bioconductor-jaspar2018/meta.yaml +++ b/recipes/bioconductor-jaspar2018/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.1" %} {% set name = "JASPAR2018" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: d91fce6ea0dc9fa6a3be6ebc05c1af5d build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-jaspar2018", max_pin="x.x") }}' noarch: generic # Suggests: TFBSTools (>= 1.15.6) requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-jaspar2020/meta.yaml b/recipes/bioconductor-jaspar2020/meta.yaml index a7be771640b73..4fb9b4b049b1e 100644 --- a/recipes/bioconductor-jaspar2020/meta.yaml +++ b/recipes/bioconductor-jaspar2020/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.10" %} {% set name = "JASPAR2020" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: bfcaf41ebf0935b8d146afd37719de2d build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-jaspar2020", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, TFBSTools (>= 1.23.1) requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-jaspar2022/build_failure.linux-64.yaml b/recipes/bioconductor-jaspar2022/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..12aa18bc75ecd --- /dev/null +++ b/recipes/bioconductor-jaspar2022/build_failure.linux-64.yaml @@ -0,0 +1,43 @@ +recipe_sha: 686f49bcd245205318d59d6a520044055090f8bfdb5ed23f0ddd8ceb5b88b41e # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + ValueError: unsupported format character 'T' (0x54) at index 5523 +category: |- + compiler error +log: |- + 09:04:38 BIOCONDA INFO (OUT) ERROR: loading failed + 09:04:38 BIOCONDA INFO (OUT) * removing ‘/opt/conda/conda-bld/bioconductor-jaspar2022_1702026057787/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/R/library/JASPAR2022’ + 09:04:38 BIOCONDA INFO (OUT) + 09:04:38 BIOCONDA INFO (OUT) return code: 1 + 09:04:38 BIOCONDA INFO (OUT) + 09:04:38 BIOCONDA INFO (OUT) kwargs: + 09:04:38 BIOCONDA INFO (OUT) {} + 09:04:38 BIOCONDA INFO (OUT) + 09:04:38 BIOCONDA INFO (OUT) : + 09:04:38 BIOCONDA INFO (OUT) + 09:04:38 BIOCONDA INFO (OUT) During handling of the above exception, another exception occurred: + 09:04:38 BIOCONDA INFO (OUT) + 09:04:38 BIOCONDA INFO (OUT) Traceback (most recent call last): + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/bin/conda-mambabuild", line 10, in + 09:04:38 BIOCONDA INFO (OUT) sys.exit(main()) + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + 09:04:38 BIOCONDA INFO (OUT) call_conda_build(action, config) + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + 09:04:38 BIOCONDA INFO (OUT) result = api.build( + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + 09:04:38 BIOCONDA INFO (OUT) return build_tree( + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3089, in build_tree + 09:04:38 BIOCONDA INFO (OUT) test(pkg, config=metadata.config.copy(), stats=stats) + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2879, in test + 09:04:38 BIOCONDA INFO (OUT) environ.create_env(metadata.config.test_prefix, actions, config=metadata.config, + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/environ.py", line 1068, in create_env + 09:04:38 BIOCONDA INFO (OUT) "too short in" in str(exc) + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda/__init__.py", line 104, in __str__ + 09:04:38 BIOCONDA INFO (OUT) return "\n".join(str(e) for e in self.errors) + "\n" + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda/__init__.py", line 104, in + 09:04:38 BIOCONDA INFO (OUT) return "\n".join(str(e) for e in self.errors) + "\n" + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda/__init__.py", line 58, in __str__ + 09:04:38 BIOCONDA INFO (OUT) return str(self.message % self._kwargs) + 09:04:38 BIOCONDA INFO (OUT) ValueError: unsupported format character 'T' (0x54) at index 5523 + 09:04:47 BIOCONDA ERROR COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /tmp/tmptio6n346/build_script.bash:/opt/build_script.bash -v /opt/mambaforge/envs/bioconda/conda-bld/:/opt/host-conda-bld -v /home/runner/work/bioconda-recipes/bioconda-recipes/recipes/bioconductor-jaspar2022:/opt/recipe -e LANG=C.UTF-8 -e HOST_USER_ID=1001 quay.io/bioconda/bioconda-utils-build-env-cos7:2.11.0 /bin/bash /opt/build_script.bash + diff --git a/recipes/bioconductor-jaspar2022/meta.yaml b/recipes/bioconductor-jaspar2022/meta.yaml index a3cb58956eea5..f9be32b043fea 100644 --- a/recipes/bioconductor-jaspar2022/meta.yaml +++ b/recipes/bioconductor-jaspar2022/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.7" %} {% set name = "JASPAR2022" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 282af23228198a377fa9bd76c94dd5eb build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-jaspar2022", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, TFBSTools (>= 1.31.2) requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-jaspar2024/meta.yaml b/recipes/bioconductor-jaspar2024/meta.yaml new file mode 100644 index 0000000000000..76fe59cb071b2 --- /dev/null +++ b/recipes/bioconductor-jaspar2024/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "0.99.6" %} +{% set name = "JASPAR2024" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9c8144547873a36473a5f9cad793f578 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-jaspar2024", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, RSQLite +requirements: + host: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - r-base + run: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: GPL-2 + summary: 'Data package for JASPAR database (version 2024)' + description: 'JASPAR (https://testjaspar.uio.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20 percent increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF-binding sites in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + diff --git a/recipes/bioconductor-jaspar2024/post-link.sh b/recipes/bioconductor-jaspar2024/post-link.sh new file mode 100644 index 0000000000000..699e53fdaf711 --- /dev/null +++ b/recipes/bioconductor-jaspar2024/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "jaspar2024-0.99.6" diff --git a/recipes/bioconductor-jaspar2024/pre-unlink.sh b/recipes/bioconductor-jaspar2024/pre-unlink.sh new file mode 100644 index 0000000000000..fb38fe4c01a48 --- /dev/null +++ b/recipes/bioconductor-jaspar2024/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ JASPAR2024 diff --git a/recipes/bioconductor-jazaerimetadata.db/meta.yaml b/recipes/bioconductor-jazaerimetadata.db/meta.yaml index ba4e64d4fc9d4..102a58956d8c4 100644 --- a/recipes/bioconductor-jazaerimetadata.db/meta.yaml +++ b/recipes/bioconductor-jazaerimetadata.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "JazaeriMetaData.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3a154a74ac2acebe3471b039c9d9a4dc build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-jazaerimetadata.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-karyoploter/meta.yaml b/recipes/bioconductor-karyoploter/meta.yaml index 87701bc6b9367..f19c5440e562c 100644 --- a/recipes/bioconductor-karyoploter/meta.yaml +++ b/recipes/bioconductor-karyoploter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "karyoploteR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a91ddbf95305d1b2d7537e0648b69597 + md5: b9fcbfd3b5d7f3349cce595751b31a41 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-karyoploter", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat, magrittr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Hs.eg.db, org.Mm.eg.db, pasillaBamSubset requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-bezier - r-digest - r-memoise run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-bezier - r-digest diff --git a/recipes/bioconductor-katdetectr/meta.yaml b/recipes/bioconductor-katdetectr/meta.yaml index cebbe6099fde9..3ee2e89e53520 100644 --- a/recipes/bioconductor-katdetectr/meta.yaml +++ b/recipes/bioconductor-katdetectr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "katdetectr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aef9b68945ff582541a046cc4ca01557 + md5: 7ae9895a26f752a9e8502913ef8ce410 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-katdetectr", max_pin="x.x") }}' noarch: generic # Suggests: scales (>= 1.2.0), knitr (>= 1.37), rmarkdown (>= 2.13), testthat (>= 3.0.0), BiocStyle (>= 2.26.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-maftools >=2.16.0,<2.17.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-maftools >=2.18.0,<2.19.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-changepoint >=2.2.3' - 'r-changepoint.np >=1.0.3' @@ -45,18 +46,18 @@ requirements: - 'r-tibble >=3.1.6' - 'r-tidyr >=1.2.0' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-maftools >=2.16.0,<2.17.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-maftools >=2.18.0,<2.19.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-changepoint >=2.2.3' - 'r-changepoint.np >=1.0.3' diff --git a/recipes/bioconductor-kboost/meta.yaml b/recipes/bioconductor-kboost/meta.yaml index 01b41adc99a96..8c45d97eb7d3f 100644 --- a/recipes/bioconductor-kboost/meta.yaml +++ b/recipes/bioconductor-kboost/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "KBoost" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1931b8d58cb833db15f7a321acbf5608 + md5: 853c93af3367a8af56b60aea8495f44b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-kboost", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-kcsmart/meta.yaml b/recipes/bioconductor-kcsmart/meta.yaml index 94f10d9fc9b55..e23a15eee3b25 100644 --- a/recipes/bioconductor-kcsmart/meta.yaml +++ b/recipes/bioconductor-kcsmart/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.58.0" %} +{% set version = "2.60.0" %} {% set name = "KCsmart" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9fa9942f40a2363507b71aefaea90658 + md5: e50f547d912df8deb29537d5e27fc5d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-kcsmart", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-siggenes >=1.74.0,<1.75.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' - r-base - r-kernsmooth run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-siggenes >=1.74.0,<1.75.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' - r-base - r-kernsmooth test: diff --git a/recipes/bioconductor-kebabs/meta.yaml b/recipes/bioconductor-kebabs/meta.yaml index ee341cf72deee..d3fae5cd61e11 100644 --- a/recipes/bioconductor-kebabs/meta.yaml +++ b/recipes/bioconductor-kebabs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "kebabs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f175288f436debe8eb7617836263df01 + md5: d6c4a16d9fd157b1e68acc8d4816017e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-kebabs", max_pin="x.x") }}' # Suggests: SparseM, Biobase, BiocGenerics, knitr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-apcluster - r-base - r-e1071 @@ -34,10 +35,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-apcluster - r-base - r-e1071 diff --git a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml index 863b25df9b046..184fb7d2a89ea 100644 --- a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml +++ b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "KEGGandMetacoreDzPathwaysGEO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a4483556f83ea2f860efe15052eebe9 + md5: 3a5180de47f1c28949b77db9f79b44ed build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-keggandmetacoredzpathwaysgeo", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh index b922daf4b0474..30e63a47b1f7d 100644 --- a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh +++ b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "keggandmetacoredzpathwaysgeo-1.20.0" +installBiocDataPackage.sh "keggandmetacoredzpathwaysgeo-1.22.0" diff --git a/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml b/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml index 17e283c691bfa..1cbbda4787238 100644 --- a/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml +++ b/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "KEGGdzPathwaysGEO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfdb271eede41d51e01844f8c7b06b70 + md5: 2f30f9ac05c04214d25a9d49fb4ce8bd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-keggdzpathwaysgeo", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh b/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh index ea3d52b80514f..872a58fcfdea7 100644 --- a/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh +++ b/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "keggdzpathwaysgeo-1.38.0" +installBiocDataPackage.sh "keggdzpathwaysgeo-1.40.0" diff --git a/recipes/bioconductor-kegggraph/meta.yaml b/recipes/bioconductor-kegggraph/meta.yaml index de4bc9cdf6fd2..d5e9a057135c4 100644 --- a/recipes/bioconductor-kegggraph/meta.yaml +++ b/recipes/bioconductor-kegggraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "KEGGgraph" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5aaf23d2bbd58de35e6d03aa1d61de6b + md5: 9a4fb63b5bab3eeb0af51af22fa2dc16 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-kegggraph", max_pin="x.x") }}' noarch: generic # Suggests: RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db, SPIA requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-rcurl - 'r-xml >=2.3-0' run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-rcurl - 'r-xml >=2.3-0' diff --git a/recipes/bioconductor-kegglincs/meta.yaml b/recipes/bioconductor-kegglincs/meta.yaml index 3afae5ed786f9..f94dbdc65d52e 100644 --- a/recipes/bioconductor-kegglincs/meta.yaml +++ b/recipes/bioconductor-kegglincs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "KEGGlincs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f4e8a9944dc0cf5c69cf22425054b71 + md5: 9ef4b8d4652560f3e9fddb3209adb0dd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-kegglincs", max_pin="x.x") }}' noarch: generic # Suggests: BiocManager (>= 1.20.3), knitr, graph # SystemRequirements: Cytoscape (>= 3.3.0), Java (>= 8) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-kodata >=1.26.0,<1.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-kodata >=1.28.0,<1.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-gtools - r-httr @@ -37,12 +38,12 @@ requirements: - r-xml - 'cytoscape >=3.3.0' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-kodata >=1.26.0,<1.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-kodata >=1.28.0,<1.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-gtools - r-httr diff --git a/recipes/bioconductor-keggorthology/meta.yaml b/recipes/bioconductor-keggorthology/meta.yaml index dc3a795c2a023..9d57eb0840070 100644 --- a/recipes/bioconductor-keggorthology/meta.yaml +++ b/recipes/bioconductor-keggorthology/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.52.0" %} +{% set version = "2.54.0" %} {% set name = "keggorthology" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bc7b0a7f975976918bc42630a5063139 + md5: 56d510a339dd4fb984bad81624d83142 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-keggorthology", max_pin="x.x") }}' noarch: generic # Suggests: RBGL,ALL requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - 'bioconductor-hgu95av2.db >=3.13.0,<3.14.0' - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - 'bioconductor-hgu95av2.db >=3.13.0,<3.14.0' - r-base - r-dbi diff --git a/recipes/bioconductor-keggrest/meta.yaml b/recipes/bioconductor-keggrest/meta.yaml index 440747d88b20b..3da5fe6a36e58 100644 --- a/recipes/bioconductor-keggrest/meta.yaml +++ b/recipes/bioconductor-keggrest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "KEGGREST" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 884dbd36ae576a2c3c62ceec855cf077 + md5: 805cb8808b0ffa6f57999b880337b504 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-keggrest", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, markdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-httr - r-png run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-httr - r-png diff --git a/recipes/bioconductor-kidpack/meta.yaml b/recipes/bioconductor-kidpack/meta.yaml index 613abaca81982..c56508e1335ec 100644 --- a/recipes/bioconductor-kidpack/meta.yaml +++ b/recipes/bioconductor-kidpack/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "kidpack" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4b8ee4f61037cd1b55cee61efe7101e9 + md5: 26f5ad5fba1c63156e282d8eac7ac385 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-kidpack", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-kidpack/post-link.sh b/recipes/bioconductor-kidpack/post-link.sh index 55b9d6d1a1d2d..ac98a263cffef 100644 --- a/recipes/bioconductor-kidpack/post-link.sh +++ b/recipes/bioconductor-kidpack/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "kidpack-1.42.0" +installBiocDataPackage.sh "kidpack-1.44.0" diff --git a/recipes/bioconductor-kinswingr/meta.yaml b/recipes/bioconductor-kinswingr/meta.yaml index ad5f4f07ab129..8f1012a7708bc 100644 --- a/recipes/bioconductor-kinswingr/meta.yaml +++ b/recipes/bioconductor-kinswingr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "KinSwingR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7872f2ffd62b269f62e8a9dd5b64adba + md5: fae1cbd6c179b4fdd5ac12a32ce50eb7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-kinswingr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-data.table - r-sqldf run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-data.table - r-sqldf diff --git a/recipes/bioconductor-knowseq/meta.yaml b/recipes/bioconductor-knowseq/meta.yaml index df2607b654937..b000d31472de7 100644 --- a/recipes/bioconductor-knowseq/meta.yaml +++ b/recipes/bioconductor-knowseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "KnowSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73da4e117a703251b6ea5e3a5e74ff41 + md5: b57c9661e3de8e27e79e3809a609acda build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-knowseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-cqn >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-cqn >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-caret - r-e1071 @@ -43,10 +44,10 @@ requirements: - r-stringr - r-xml run: - - 'bioconductor-cqn >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-cqn >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-caret - r-e1071 diff --git a/recipes/bioconductor-kodata/meta.yaml b/recipes/bioconductor-kodata/meta.yaml index f398239257119..c6d97424dd478 100644 --- a/recipes/bioconductor-kodata/meta.yaml +++ b/recipes/bioconductor-kodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "KOdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11d0727f1c7e40be104b3d24168f2ae7 + md5: 40e099053eae889ad66256a94427ac54 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-kodata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-kodata/post-link.sh b/recipes/bioconductor-kodata/post-link.sh index 1040e3628131f..d0c7715575049 100644 --- a/recipes/bioconductor-kodata/post-link.sh +++ b/recipes/bioconductor-kodata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "kodata-1.26.0" +installBiocDataPackage.sh "kodata-1.28.0" diff --git a/recipes/bioconductor-lace/meta.yaml b/recipes/bioconductor-lace/meta.yaml index 6ba5c9df85469..40a6921d22e8c 100644 --- a/recipes/bioconductor-lace/meta.yaml +++ b/recipes/bioconductor-lace/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "LACE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b13337a86c2b8b322531939e79e94166 + md5: d11f64211d10d293c2931b49765b5d61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lace", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bsplus - r-callr @@ -60,8 +61,8 @@ requirements: - r-svglite - r-tidyr run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bsplus - r-callr diff --git a/recipes/bioconductor-lapmix/meta.yaml b/recipes/bioconductor-lapmix/meta.yaml index 4b5789801fb82..76e3e6dc36bb5 100644 --- a/recipes/bioconductor-lapmix/meta.yaml +++ b/recipes/bioconductor-lapmix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "lapmix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 088e76c4d42b5f1c432cffebd1bb0188 + md5: 5d2611d1b39b06b05ed64ffab459a5a9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lapmix", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-lapointe.db/meta.yaml b/recipes/bioconductor-lapointe.db/meta.yaml index e1e73ef07267e..2e19eca313c84 100644 --- a/recipes/bioconductor-lapointe.db/meta.yaml +++ b/recipes/bioconductor-lapointe.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "LAPOINTE.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 434b25ad7411201d8be6bb1a0463b387 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lapointe.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lbe/meta.yaml b/recipes/bioconductor-lbe/meta.yaml index d1dd76272ef40..5c71cafda8ca6 100644 --- a/recipes/bioconductor-lbe/meta.yaml +++ b/recipes/bioconductor-lbe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.0" %} {% set name = "LBE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0f317f8253df3b83ef48202063e0417f + md5: 36559f365f1dbd53056e6b43bc1e06e9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lbe", max_pin="x.x") }}' noarch: generic # Suggests: qvalue requirements: diff --git a/recipes/bioconductor-ldblock/meta.yaml b/recipes/bioconductor-ldblock/meta.yaml index eea6863caf204..9863043358259 100644 --- a/recipes/bioconductor-ldblock/meta.yaml +++ b/recipes/bioconductor-ldblock/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "ldblock" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6a63dbccca085d4b33bcf2b19215c22f + md5: 579c380a003913fde7767f15b47a6692 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ldblock", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, knitr, BiocStyle, gwascat, rmarkdown, snpStats, VariantAnnotation, GenomeInfoDb, ensembldb, EnsDb.Hsapiens.v75, Rsamtools, GenomicFiles (>= 1.13.6) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-httr - r-matrix - r-rlang run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-httr - r-matrix diff --git a/recipes/bioconductor-lea/meta.yaml b/recipes/bioconductor-lea/meta.yaml index aa0936c3594b2..51dd613a14f2e 100644 --- a/recipes/bioconductor-lea/meta.yaml +++ b/recipes/bioconductor-lea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.12.2" %} +{% set version = "3.14.0" %} {% set name = "LEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 66645aa4efbb19674772b485df256216 + md5: e32cbc2a97921f9b911eef1a5d1ef3d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lea", max_pin="x.x") }}' # Suggests: knitr requirements: host: diff --git a/recipes/bioconductor-ledpred/meta.yaml b/recipes/bioconductor-ledpred/meta.yaml index ef41921f97eb4..add26d8b55ec8 100644 --- a/recipes/bioconductor-ledpred/meta.yaml +++ b/recipes/bioconductor-ledpred/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "LedPred" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0a868e369e350943980eaa621d63503c + md5: 4a083c0408938618b62557ece5682e61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ledpred", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-leebamviews/meta.yaml b/recipes/bioconductor-leebamviews/meta.yaml index 09d78a9570174..23ddd91fec827 100644 --- a/recipes/bioconductor-leebamviews/meta.yaml +++ b/recipes/bioconductor-leebamviews/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "leeBamViews" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8364b9ac80fcc1cbdd4eca1501d6651b + md5: 58f7c7fdbb1f949f48924ac79d31b580 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-leebamviews", max_pin="x.x") }}' noarch: generic # Suggests: biomaRt, org.Sc.sgd.db, edgeR requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-leebamviews/post-link.sh b/recipes/bioconductor-leebamviews/post-link.sh index 0440089dce09f..f1275b766d7ad 100644 --- a/recipes/bioconductor-leebamviews/post-link.sh +++ b/recipes/bioconductor-leebamviews/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "leebamviews-1.36.0" +installBiocDataPackage.sh "leebamviews-1.38.0" diff --git a/recipes/bioconductor-lefser/meta.yaml b/recipes/bioconductor-lefser/meta.yaml index 875f2cf293425..e6ee9347ff280 100644 --- a/recipes/bioconductor-lefser/meta.yaml +++ b/recipes/bioconductor-lefser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.1" %} {% set name = "lefser" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 02d16723642d25f2432b098f6fa4f04c + md5: c3b2deaf4b58de1bb930164df11a388f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lefser", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, curatedMetagenomicData, BiocStyle, testthat, pkgdown, covr, withr +# Suggests: knitr, rmarkdown, curatedMetagenomicData, BiocStyle, phyloseq, testthat, pkgdown, covr, withr requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-coin - r-ggplot2 - r-mass run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-coin - r-ggplot2 diff --git a/recipes/bioconductor-lemur/build.sh b/recipes/bioconductor-lemur/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-lemur/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lemur/build_failure.osx-64.yaml b/recipes/bioconductor-lemur/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..9beef668bed41 --- /dev/null +++ b/recipes/bioconductor-lemur/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 9ec1f5c47eca7b1c8d8b7db53ce0866846a9c61f157f39bec7526f0c5cbe3856 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + dependency issue +log: |2- + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - r-base 4.3.* + - bioconductor-matrixgenerics >=1.14.0,<1.15.0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 + + with channels: + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - package bioconductor-summarizedexperiment-1.32.0-r43hdfd78af_0 requires r-base >=4.3,<4.4.0a0, but none of the providers can be installed + - + + Leaving build/test directories: + Work: + /opt/mambaforge/envs/bioconda/conda-bld/work + Test: + /opt/mambaforge/envs/bioconda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/mambaforge/envs/bioconda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + Build: + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + source activate /opt/mambaforge/envs/bioconda/conda-bld/_build_env + + + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - bioconductor-hdf5array >=1.30.0,<1.31.0 + - r-rcpparmadillo + - r-rcpp + - r-harmony + - r-matrixstats + - r-vctrs + - liblapack 3.9.* *netlib + - bioconductor-delayedmatrixstats >=1.24.0,<1.25.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - libblas 3.9.* *netlib + - bioconductor-biocneighbors >=1.20.0,<1.21.0 + - libcxx >=14 + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - r-irlba + - r-matrix + - r-rlang + - bioconductor-limma >=3.58.0,<3.59.0 + - bioconductor-glmgampoi >=1.14.0,<1.15.0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - r-base 4.3.* + - bioconductor-matrixgenerics >=1.14.0,<1.15.0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 + + with channels: + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - package bioconductor-summarizedexperiment-1.32.0-r43hdfd78af_0 requires r-base >=4.3,<4.4.0a0, but none of the providers can be installed + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("r-base[version='>=4.3,<4.4.0a0']"), MatchSpec("bioconductor-summarizedexperiment==1.32.0=r43hdfd78af_0")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-lemur/meta.yaml b/recipes/bioconductor-lemur/meta.yaml new file mode 100644 index 0000000000000..71c676e618440 --- /dev/null +++ b/recipes/bioconductor-lemur/meta.yaml @@ -0,0 +1,78 @@ +{% set version = "1.0.4" %} +{% set name = "lemur" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 76ef0d01a8f6f23e0f125274af96522d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lemur", max_pin="x.x") }}' +# Suggests: testthat (>= 3.0.0), tidyverse, uwot, dplyr, edgeR, knitr, rmarkdown, BiocStyle +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-glmgampoi >=1.14.0,<1.15.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-harmony + - r-irlba + - r-matrix + - r-matrixstats + - r-rcpp + - r-rcpparmadillo + - r-rlang + - r-vctrs + - libblas + - liblapack + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-glmgampoi >=1.14.0,<1.15.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-harmony + - r-irlba + - r-matrix + - r-matrixstats + - r-rcpp + - r-rcpparmadillo + - r-rlang + - r-vctrs + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Latent Embedding Multivariate Regression' + description: 'Fit a latent embedding multivariate regression (LEMUR) model to multi-condition single-cell data. The model provides a parametric description of single-cell data measured with complex experimental designs. The parametric model is used to (1) align conditions, (2) predict log fold changes between conditions for all cells, and (3) identify cell neighborhoods with consistent log fold changes. For those neighborhoods, a pseudobulked differential expression test is conducted to assess which genes are significantly changed.' + license_file: LICENSE + diff --git a/recipes/bioconductor-les/meta.yaml b/recipes/bioconductor-les/meta.yaml index 6a17dc15d9a18..2c610c014b1e5 100644 --- a/recipes/bioconductor-les/meta.yaml +++ b/recipes/bioconductor-les/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "les" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5484dca35e8f46307aa2d8729a1ba1fa + md5: b0418480f87e364b451a3f940bcdcb8c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-les", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, limma requirements: diff --git a/recipes/bioconductor-leukemiaseset/meta.yaml b/recipes/bioconductor-leukemiaseset/meta.yaml index 5e567639f1d1d..d3bfaf2adc95a 100644 --- a/recipes/bioconductor-leukemiaseset/meta.yaml +++ b/recipes/bioconductor-leukemiaseset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "leukemiasEset" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f2498f78d93dc35ed04c9e2e8abfad7 + md5: f9e8274856b0d78de6da7ec0bce171f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-leukemiaseset", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-leukemiaseset/post-link.sh b/recipes/bioconductor-leukemiaseset/post-link.sh index d2bae20eed808..f03618f99ae1e 100644 --- a/recipes/bioconductor-leukemiaseset/post-link.sh +++ b/recipes/bioconductor-leukemiaseset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "leukemiaseset-1.36.0" +installBiocDataPackage.sh "leukemiaseset-1.38.0" diff --git a/recipes/bioconductor-levi/meta.yaml b/recipes/bioconductor-levi/meta.yaml index a1f8a6f2379e3..863283e9eb2fd 100644 --- a/recipes/bioconductor-levi/meta.yaml +++ b/recipes/bioconductor-levi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "levi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dd7ccfc06d8acb7def3c3f53cfc7680b + md5: fff39f74d44cb186d14ebb591b3fa3a1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-levi", max_pin="x.x") }}' # Suggests: rmarkdown, BiocStyle requirements: host: diff --git a/recipes/bioconductor-lfa/meta.yaml b/recipes/bioconductor-lfa/meta.yaml index e3d2e660065c6..ef404bf4b9e2b 100644 --- a/recipes/bioconductor-lfa/meta.yaml +++ b/recipes/bioconductor-lfa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.11" %} +{% set version = "2.2.0" %} {% set name = "lfa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 58264321db9388649768e3fc74e9a4ab + md5: 83d3c5671422b432d992834ae675e020 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lfa", max_pin="x.x") }}' # Suggests: knitr, ggplot2, testthat, BEDMatrix, genio requirements: host: diff --git a/recipes/bioconductor-liebermanaidenhic2009/meta.yaml b/recipes/bioconductor-liebermanaidenhic2009/meta.yaml index 53f1731a0f859..d71d5f911cfaf 100644 --- a/recipes/bioconductor-liebermanaidenhic2009/meta.yaml +++ b/recipes/bioconductor-liebermanaidenhic2009/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "LiebermanAidenHiC2009" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43f7f158c73c12d62e6cf471cd690667 + md5: 34818101f902d251b339864716cd2d1a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-liebermanaidenhic2009", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-kernsmooth run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-kernsmooth - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-liebermanaidenhic2009/post-link.sh b/recipes/bioconductor-liebermanaidenhic2009/post-link.sh index 44699d13bf699..e899cf7938d0f 100644 --- a/recipes/bioconductor-liebermanaidenhic2009/post-link.sh +++ b/recipes/bioconductor-liebermanaidenhic2009/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "liebermanaidenhic2009-0.38.0" +installBiocDataPackage.sh "liebermanaidenhic2009-0.40.0" diff --git a/recipes/bioconductor-limma/meta.yaml b/recipes/bioconductor-limma/meta.yaml index 6ac8b334140e0..0441416406623 100644 --- a/recipes/bioconductor-limma/meta.yaml +++ b/recipes/bioconductor-limma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.56.2" %} +{% set version = "3.58.1" %} {% set name = "limma" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4b1df28cbb7c38b621db2ee3c42e6cc8 + md5: f52a816d0d34b01f721654f90a1fb5f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db, gplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn + run_exports: '{{ pin_subpackage("bioconductor-limma", max_pin="x.x") }}' +# Suggests: BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines, affy, AnnotationDbi, Biobase, BiocStyle, GO.db, illuminaio, org.Hs.eg.db, vsn requirements: host: - r-base + - r-statmod - libblas - liblapack run: - r-base + - r-statmod build: - {{ compiler('c') }} - make diff --git a/recipes/bioconductor-limmagui/meta.yaml b/recipes/bioconductor-limmagui/meta.yaml index 80cbd76d1e52e..f6bc9994f2951 100644 --- a/recipes/bioconductor-limmagui/meta.yaml +++ b/recipes/bioconductor-limmagui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "limmaGUI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfdbc7483e30730dd2fc9072e8f96bb7 + md5: b0c7c34dfac5955d26908f730a73b880 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-limmagui", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-r2html - r-tkrplot - r-xtable run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-r2html - r-tkrplot diff --git a/recipes/bioconductor-lineagepulse/meta.yaml b/recipes/bioconductor-lineagepulse/meta.yaml index ae7329e00d703..a99b5c3e27db3 100644 --- a/recipes/bioconductor-lineagepulse/meta.yaml +++ b/recipes/bioconductor-lineagepulse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.21.0" %} {% set name = "LineagePulse" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b8c7c63f4301507c384fe65eee3990d + md5: c17825342234d6f0e327853b8fc52944 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lineagepulse", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-ggplot2 @@ -32,10 +33,10 @@ requirements: - r-matrix - r-rcolorbrewer run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-ggplot2 diff --git a/recipes/bioconductor-lineagespot/meta.yaml b/recipes/bioconductor-lineagespot/meta.yaml index 229810771245a..a0a3a46e80bc1 100644 --- a/recipes/bioconductor-lineagespot/meta.yaml +++ b/recipes/bioconductor-lineagespot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "lineagespot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b44c5d4601a486a1047c3c5bc1f0e274 + md5: 7a06bfea8fdf81ea88ebe7f4478607f6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lineagespot", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, RefManageR, rmarkdown, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-httr - r-stringr run: - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-httr diff --git a/recipes/bioconductor-linkhd/meta.yaml b/recipes/bioconductor-linkhd/meta.yaml index ef08fe0904124..c4ba0e55eb6ef 100644 --- a/recipes/bioconductor-linkhd/meta.yaml +++ b/recipes/bioconductor-linkhd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "LinkHD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d22be0c6560788254aff6967d0b953c + md5: 64515bedacee602d8f8c92785e075039 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-linkhd", max_pin="x.x") }}' noarch: generic # Suggests: MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - r-base - r-cluster - r-data.table @@ -34,7 +35,7 @@ requirements: - r-scales - r-vegan run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - r-base - r-cluster - r-data.table diff --git a/recipes/bioconductor-linnorm/meta.yaml b/recipes/bioconductor-linnorm/meta.yaml index fb21be3973482..5c346153764e9 100644 --- a/recipes/bioconductor-linnorm/meta.yaml +++ b/recipes/bioconductor-linnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.1" %} +{% set version = "2.26.0" %} {% set name = "Linnorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aecbf8861def918c6f11fa1b10714a28 + md5: 8fc0ff0d6e9c2d274137b0e99ce0f4a2 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer, moments, testthat + run_exports: '{{ pin_subpackage("bioconductor-linnorm", max_pin="x.x") }}' +# Suggests: BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer, moments, testthat, matrixStats requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-amap - r-apcluster - r-base @@ -42,7 +43,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-amap - r-apcluster - r-base diff --git a/recipes/bioconductor-lintind/meta.yaml b/recipes/bioconductor-lintind/meta.yaml index d401f17371fcc..954eb5cb07f07 100644 --- a/recipes/bioconductor-lintind/meta.yaml +++ b/recipes/bioconductor-lintind/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "LinTInd" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 229a83bd7db103d7e92cbf8378c0dcb5 + md5: 3dd8f8601ee8df3a0a53a02dc0c4d272 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lintind", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-ape - r-base - r-cowplot @@ -41,11 +42,11 @@ requirements: - r-stringdist - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-ape - r-base - r-cowplot diff --git a/recipes/bioconductor-lionessr/meta.yaml b/recipes/bioconductor-lionessr/meta.yaml index 7c51b62f289ac..6af7c447fb9c4 100644 --- a/recipes/bioconductor-lionessr/meta.yaml +++ b/recipes/bioconductor-lionessr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "lionessR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3b3552c919620f8bf987753d882d5802 + md5: 4301a7fed98cbe717433fa80791ad9a6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lionessr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, igraph, reshape2, limma, requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-lipidr/meta.yaml b/recipes/bioconductor-lipidr/meta.yaml index 757575e6e210e..046cb235bf30f 100644 --- a/recipes/bioconductor-lipidr/meta.yaml +++ b/recipes/bioconductor-lipidr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.1" %} +{% set version = "2.16.0" %} {% set name = "lipidr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f8d642d778bcb314c248231f46ddad43 + md5: 27b17acc2b4de0439304799e0a7cba2a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lipidr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, ggrepel, plotly, spelling, testthat requirements: host: - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr @@ -36,11 +37,11 @@ requirements: - r-rlang - r-tidyr run: - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-liquidassociation/meta.yaml b/recipes/bioconductor-liquidassociation/meta.yaml index 7a4f3a1785241..456d16ad1c383 100644 --- a/recipes/bioconductor-liquidassociation/meta.yaml +++ b/recipes/bioconductor-liquidassociation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "LiquidAssociation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea14603091d58ee44de956e48a0911bb + md5: b484ed119d8ef9ebb19bfd7497eb33af build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-liquidassociation", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-org.sc.sgd.db >=3.17.0,<3.18.0' - - 'bioconductor-yeastcc >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' + - 'bioconductor-yeastcc >=1.42.0,<1.43.0' - r-base - r-geepack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-org.sc.sgd.db >=3.17.0,<3.18.0' - - 'bioconductor-yeastcc >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' + - 'bioconductor-yeastcc >=1.42.0,<1.43.0' - r-base - r-geepack test: diff --git a/recipes/bioconductor-lisaclust/meta.yaml b/recipes/bioconductor-lisaclust/meta.yaml index fe1b83d19530e..0658217e488ff 100644 --- a/recipes/bioconductor-lisaclust/meta.yaml +++ b/recipes/bioconductor-lisaclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.1" %} {% set name = "lisaClust" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91925b5c9bbe5d0f3afb6e81b1496003 + md5: fa6fe90f1866b21dce3d34bb8471c9e1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lisaclust", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-spicyr >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-spicyr >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-class - r-concaveman @@ -38,15 +39,16 @@ requirements: - r-purrr - r-spatstat.explore - r-spatstat.geom + - r-spatstat.random - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-spicyr >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-spicyr >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-class - r-concaveman @@ -57,6 +59,7 @@ requirements: - r-purrr - r-spatstat.explore - r-spatstat.geom + - r-spatstat.random - r-tidyr test: commands: diff --git a/recipes/bioconductor-listeretalbsseq/meta.yaml b/recipes/bioconductor-listeretalbsseq/meta.yaml index 5a665140c3d5e..dee27377bbb58 100644 --- a/recipes/bioconductor-listeretalbsseq/meta.yaml +++ b/recipes/bioconductor-listeretalbsseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.1" %} +{% set version = "1.34.0" %} {% set name = "ListerEtAlBSseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b0138cce25976d0d9180442505679d2 + md5: 302e026ae021a5f26c149b5086569db1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-listeretalbsseq", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg18 requirements: host: - - 'bioconductor-methylpipe >=1.34.0,<1.35.0' + - 'bioconductor-methylpipe >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-methylpipe >=1.34.0,<1.35.0' + - 'bioconductor-methylpipe >=1.36.0,<1.37.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-listeretalbsseq/post-link.sh b/recipes/bioconductor-listeretalbsseq/post-link.sh index b6aae194fcd09..683046c9aced0 100644 --- a/recipes/bioconductor-listeretalbsseq/post-link.sh +++ b/recipes/bioconductor-listeretalbsseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "listeretalbsseq-1.32.1" +installBiocDataPackage.sh "listeretalbsseq-1.34.0" diff --git a/recipes/bioconductor-lmdme/meta.yaml b/recipes/bioconductor-lmdme/meta.yaml index 946b71daa6bf8..3a621770cd470 100644 --- a/recipes/bioconductor-lmdme/meta.yaml +++ b/recipes/bioconductor-lmdme/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "lmdme" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 66a2da7ce067e15aab8fccdb7f124eed + md5: 9a1b98d738df482adb30496ac028b924 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lmdme", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-stemhypoxia >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-stemhypoxia >=1.38.0,<1.39.0' - r-base - r-pls run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-stemhypoxia >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-stemhypoxia >=1.38.0,<1.39.0' - r-base - r-pls test: diff --git a/recipes/bioconductor-lobstahs/meta.yaml b/recipes/bioconductor-lobstahs/meta.yaml index dada12f2bd5f3..eea31dbdaeae0 100644 --- a/recipes/bioconductor-lobstahs/meta.yaml +++ b/recipes/bioconductor-lobstahs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "LOBSTAHS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f66c6f04dd23801992184f8b1f6515ec + md5: 45092babf761359e504ae5ad71d21ab8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lobstahs", max_pin="x.x") }}' noarch: generic # Suggests: PtH2O2lipids, knitr, rmarkdown requirements: host: - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base run: - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base test: commands: diff --git a/recipes/bioconductor-loci2path/meta.yaml b/recipes/bioconductor-loci2path/meta.yaml index fc0b0ebc53368..a8e5177b97e07 100644 --- a/recipes/bioconductor-loci2path/meta.yaml +++ b/recipes/bioconductor-loci2path/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "loci2path" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b0dfe9a1ddd6aa3d993d369c452786ea + md5: 3527f58dccf385bbc6f71a4c659a37c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-loci2path", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-pheatmap - r-rcolorbrewer - r-wordcloud run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-pheatmap diff --git a/recipes/bioconductor-logicfs/meta.yaml b/recipes/bioconductor-logicfs/meta.yaml index d8e679ffb6237..6824cb2b44a4e 100644 --- a/recipes/bioconductor-logicfs/meta.yaml +++ b/recipes/bioconductor-logicfs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "logicFS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4840a9d851ffe6dbbb08fa539ddbb5b + md5: af46ee02e89efc5057af01be3f530a4f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-logicfs", max_pin="x.x") }}' noarch: generic # Suggests: genefilter, siggenes requirements: diff --git a/recipes/bioconductor-lola/meta.yaml b/recipes/bioconductor-lola/meta.yaml index 88217cfeea8ac..58d33f706a825 100644 --- a/recipes/bioconductor-lola/meta.yaml +++ b/recipes/bioconductor-lola/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "LOLA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f85cca2393dba22ce00574478e065c11 + md5: e3ff8271b0433c6098fd7380af165742 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lola", max_pin="x.x") }}' noarch: generic # Suggests: parallel, testthat, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-reshape2 diff --git a/recipes/bioconductor-loomexperiment/meta.yaml b/recipes/bioconductor-loomexperiment/meta.yaml index 514eb89c78660..a46c9fe2eeebc 100644 --- a/recipes/bioconductor-loomexperiment/meta.yaml +++ b/recipes/bioconductor-loomexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "LoomExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 48fb26e59c5d77ce931e53d1dd251334 + md5: f69aaf53b56cebfe748b8c0c029af481 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-loomexperiment", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, reticulate requirements: host: - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-stringr run: - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-stringr diff --git a/recipes/bioconductor-lowmacaannotation/meta.yaml b/recipes/bioconductor-lowmacaannotation/meta.yaml index e9be52191301f..5ad4a74a0e5db 100644 --- a/recipes/bioconductor-lowmacaannotation/meta.yaml +++ b/recipes/bioconductor-lowmacaannotation/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.3" %} {% set name = "LowMACAAnnotation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9e0d3fe7f30fe48aef9c4387eb5bacfa build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lowmacaannotation", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lpe/meta.yaml b/recipes/bioconductor-lpe/meta.yaml index ff237d9fe0b82..d286d7876465c 100644 --- a/recipes/bioconductor-lpe/meta.yaml +++ b/recipes/bioconductor-lpe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "LPE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 583b56963ed12c046a559fe3db8e3a4c + md5: 9001fbe949f64e59e79de1f81bd4aa01 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lpe", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-lpeadj/meta.yaml b/recipes/bioconductor-lpeadj/meta.yaml index 5d8587e24b716..c56a4a44fc24f 100644 --- a/recipes/bioconductor-lpeadj/meta.yaml +++ b/recipes/bioconductor-lpeadj/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "LPEadj" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54870f0c718c22c66d51a3831463415b + md5: ebb9c5bc6d113688787fadb2739bc75a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lpeadj", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-lpe >=1.74.0,<1.75.0' + - 'bioconductor-lpe >=1.76.0,<1.77.0' - r-base run: - - 'bioconductor-lpe >=1.74.0,<1.75.0' + - 'bioconductor-lpe >=1.76.0,<1.77.0' - r-base test: commands: diff --git a/recipes/bioconductor-lpnet/meta.yaml b/recipes/bioconductor-lpnet/meta.yaml index ef802e2badfa7..b0d2a9dd75db3 100644 --- a/recipes/bioconductor-lpnet/meta.yaml +++ b/recipes/bioconductor-lpnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "lpNet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bdabe53b6db49978cb400e44c75651f7 + md5: b2aa2f27ba2f75f595f718f9c9f6e737 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lpnet", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-lpsymphony/build.sh b/recipes/bioconductor-lpsymphony/build.sh index daad3abb543cb..b12d3b6a8730e 100644 --- a/recipes/bioconductor-lpsymphony/build.sh +++ b/recipes/bioconductor-lpsymphony/build.sh @@ -10,4 +10,4 @@ CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars sed -i.bak "s/-TP//" src/SYMPHONY/SYMPHONY/configure.ac sed -i.bak "s/-TP//" src/SYMPHONY/SYMPHONY/configure -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lpsymphony/build_failure.linux-64.yaml b/recipes/bioconductor-lpsymphony/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..7895e96771c2c --- /dev/null +++ b/recipes/bioconductor-lpsymphony/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: fc3c0b78a302a196c67dd12bb2d7378a8e0cfce2422bd52ac55af76b95b1b9c6 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + checking if $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c supports -c -o file.o... yes + checking whether the $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c linker ($BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld) supports shared libraries... yes + cat: ld.so.conf.d/*.conf: No such file or directory + checking dynamic linker characteristics... GNU/Linux ld.so + checking how to hardcode library paths into programs... immediate + appending configuration tag "F77" to libtool + checking if libtool supports shared libraries... yes + checking whether to build shared libraries... no + checking whether to build static libraries... yes + checking for x86_64-conda-linux-gnu-gfortran option to produce PIC... -fPIC + checking if x86_64-conda-linux-gnu-gfortran PIC flag -fPIC works... yes + checking if x86_64-conda-linux-gnu-gfortran static flag -static works... no + checking if x86_64-conda-linux-gnu-gfortran supports -c -o file.o... yes + checking whether the x86_64-conda-linux-gnu-gfortran linker ($BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld) supports shared libraries... yes + cat: ld.so.conf.d/*.conf: No such file or directory + checking dynamic linker characteristics... GNU/Linux ld.so + checking how to hardcode library paths into programs... immediate + configure: Build is "x86_64-conda-linux-gnu". + checking if library version is set... no + checking whether source of project Blas is available and should be compiled... no, source file ./ThirdParty/Blas/daxpy.f not available + checking whether source of project Lapack is available and should be compiled... no, source file ./ThirdParty/Lapack/LAPACK/SRC/dlarf.f not available + checking whether source of project Glpk is available and should be compiled... no, source file ./ThirdParty/Glpk/glpk/src/glplpx01.c not available + checking whether source of project Sample is available and should be compiled... no + checking whether source of project miblib3 is available and should be compiled... no + checking whether source of project CoinUtils is available and should be compiled... yes, source in CoinUtils + checking whether source of project Osi is available and should be compiled... yes, source in Osi + checking whether source of project Clp is available and should be compiled... yes, source in Clp + checking whether source of project Cgl is available and should be compiled... yes, source in Cgl + checking whether source of project DyLP is available and should be compiled... no + checking whether source of project Vol is available and should be compiled... no + checking whether source of project SYMPHONY is available and should be compiled... yes, source in SYMPHONY + checking whether Clp is required... yes + checking which command should be used to link input files... ln -s + configure: creating ./config.status + config.status: creating Makefile + config.status: executing depfiles commands + configure: configuring in CoinUtils + configure: running /bin/sh './configure' --prefix=$SRC_DIR/src/SYMPHONY '--enable-static' '--disable-shared' '--with-pic' '--with-application=no' '--disable-dependency-tracking' '--disable-zlib' '--disable-bzlib' '--disable-cplex-libcheck' '--disable-glpk-libcheck' '--disable-osl-libcheck' '--disable-soplex-libcheck' '--disable-xpress-libcheck' 'CFLAGS=-w -g -O2' 'CXXFLAGS=-w -g -O2' 'CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc' 'CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include' 'CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp' 'CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c' 'LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib' 'build_alias=x86_64-conda-linux-gnu' 'host_alias=x86_64-conda-linux-gnu' --cache-file=/dev/null --srcdir=. + configure: loading site script $SRC_DIR/src/SYMPHONY/share/config.site + checking build system type... x86_64-conda-linux-gnu + checking for svnversion... no + checking whether we want to compile in debug mode... no + checking for x86_64-conda-linux-gnu-gcc... $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + checking for C compiler default output file name... a.out + checking whether the C compiler works... yes + checking whether we are cross compiling... no + checking for suffix of executables... + checking for suffix of object files... o + checking whether we are using the GNU C compiler... yes + checking whether $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc accepts -g... yes + checking for $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc option to accept ANSI C... none needed + configure: C compiler options are: -w -g -O2 -DCOINUTILS_BUILD + checking for x86_64-conda-linux-gnu-g... $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + checking whether we are using the GNU C compiler... yes + checking whether $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c accepts -g... yes + checking whether C compiler $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c works... yes + configure: C compiler options are: -w -g -O2 -DCOINUTILS_BUILD + configure: Trying to determine Fortran compiler name + checking for x86_64-conda-linux-gnu-gfortran... x86_64-conda-linux-gnu-gfortran + checking for x86_64-conda-linux-gnu-gfortran... (cached) x86_64-conda-linux-gnu-gfortran + checking whether we are using the GNU Fortran 77 compiler... yes + checking whether x86_64-conda-linux-gnu-gfortran accepts -g... yes + configure: Fortran compiler options are: -O3 -pipe + checking how to get verbose linking output from x86_64-conda-linux-gnu-gfortran... -v + checking for Fortran libraries of x86_64-conda-linux-gnu-gfortran... -L$PREFIX/lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0 -L$PREFIX/bin/../lib/gcc -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/lib/../lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../lib -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../.. -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/lib -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib -lgfortran -lm -lgcc_s -lquadmath + configure: Corrected Fortran libraries: -L$PREFIX/lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0 -L$PREFIX/bin/../lib/gcc -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/lib/../lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../lib -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../.. -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/lib -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib -lgfortran -lm -lquadmath + configure: error: linking to Fortran libraries from C fails + See config.log' for more details. + checking for dummy main to link with Fortran libraries... unknown + configure: error: /bin/sh './configure' failed for CoinUtils + ** libs + using C compiler: x86_64-conda-linux-gnu-c (conda-forge gcc 12.3.0-3) 12.3.0 + make[1]: Entering directory '$SRC_DIR/src/SYMPHONY' + Making all in CoinUtils + make[2]: *** No rule to make target 'all'. Stop. + make[2]: Entering directory '$SRC_DIR/src/SYMPHONY/CoinUtils' + make[2]: Leaving directory '$SRC_DIR/src/SYMPHONY/CoinUtils' + make[1]: *** [Makefile:324: all-recursive] Error 1 + make[1]: Leaving directory '$SRC_DIR/src/SYMPHONY' + make: *** [Makevars:14: SYMPHONY.ts] Error 2 + ERROR: compilation failed for package lpsymphony + * removing /opt/conda/conda-bld/bioconductor-lpsymphony_1703079915102/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/R/library/lpsymphony + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build + utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, + File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-lpsymphony_1703079915102/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-lpsymphony/meta.yaml b/recipes/bioconductor-lpsymphony/meta.yaml index 59fe830c990dd..141bac727f2ab 100644 --- a/recipes/bioconductor-lpsymphony/meta.yaml +++ b/recipes/bioconductor-lpsymphony/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "lpsymphony" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a04276f8329ae09e82e3e16bc3a7b78e + md5: 106ec54272f27574ea1eea2d5721d7e4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lpsymphony", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, testthat # SystemRequirements: GNU make requirements: diff --git a/recipes/bioconductor-lrbasedbi/meta.yaml b/recipes/bioconductor-lrbasedbi/meta.yaml index 49e21f44674dc..ea0d85aceaab3 100644 --- a/recipes/bioconductor-lrbasedbi/meta.yaml +++ b/recipes/bioconductor-lrbasedbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "LRBaseDbi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 557f533713533ea65e003805bed36368 + md5: 4ed780d2b26059691bd1a1e859ca5003 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lrbasedbi", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-dbi - r-rsqlite diff --git a/recipes/bioconductor-lrcell/meta.yaml b/recipes/bioconductor-lrcell/meta.yaml index 4478c83b35c15..e7c109ef9e482 100644 --- a/recipes/bioconductor-lrcell/meta.yaml +++ b/recipes/bioconductor-lrcell/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "LRcell" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 38340be2b5eefde6251d6dc2fb14aff7 + md5: 845d68fab279d4a81933621a81085179 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lrcell", max_pin="x.x") }}' noarch: generic # Suggests: LRcellTypeMarkers, BiocStyle, knitr, rmarkdown, roxygen2, testthat requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - r-dplyr - r-ggplot2 - r-ggrepel - r-magrittr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-lrcelltypemarkers/meta.yaml b/recipes/bioconductor-lrcelltypemarkers/meta.yaml index d4d5a86cb8c07..ab499894e1e20 100644 --- a/recipes/bioconductor-lrcelltypemarkers/meta.yaml +++ b/recipes/bioconductor-lrcelltypemarkers/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "LRcellTypeMarkers" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 342747afa842b8009a5e2a6183c1bd83 + md5: f5731667b56b631291d22a830d212f04 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lrcelltypemarkers", max_pin="x.x") }}' noarch: generic # Suggests: LRcell, BiocStyle, knitr, rmarkdown, roxygen2, testthat requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lrcelltypemarkers/post-link.sh b/recipes/bioconductor-lrcelltypemarkers/post-link.sh index a402099179b36..5ea30236a697f 100644 --- a/recipes/bioconductor-lrcelltypemarkers/post-link.sh +++ b/recipes/bioconductor-lrcelltypemarkers/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "lrcelltypemarkers-1.8.0" +installBiocDataPackage.sh "lrcelltypemarkers-1.10.0" diff --git a/recipes/bioconductor-lumi/meta.yaml b/recipes/bioconductor-lumi/meta.yaml index 6ebb4746e410d..1511bffa3477a 100644 --- a/recipes/bioconductor-lumi/meta.yaml +++ b/recipes/bioconductor-lumi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.52.0" %} +{% set version = "2.54.0" %} {% set name = "lumi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e8abe917a62ecdf21d85b510773a0bed + md5: 59fdd5b0a2e145d7a8772635121bb2ec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lumi", max_pin="x.x") }}' noarch: generic # Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dbi - r-kernsmooth @@ -38,14 +39,14 @@ requirements: - r-nleqslv - r-rsqlite run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dbi - r-kernsmooth diff --git a/recipes/bioconductor-lumibarnes/meta.yaml b/recipes/bioconductor-lumibarnes/meta.yaml index 7833a1d0b2a49..a83dcd4119b6d 100644 --- a/recipes/bioconductor-lumibarnes/meta.yaml +++ b/recipes/bioconductor-lumibarnes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "lumiBarnes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 971e2cf62606ab98813418f8032b20dc + md5: 2be75f5470fd60f9919045fc8147b613 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lumibarnes", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumibarnes/post-link.sh b/recipes/bioconductor-lumibarnes/post-link.sh index 4ea7acd69238d..96d26854e3ad0 100644 --- a/recipes/bioconductor-lumibarnes/post-link.sh +++ b/recipes/bioconductor-lumibarnes/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "lumibarnes-1.40.0" +installBiocDataPackage.sh "lumibarnes-1.42.0" diff --git a/recipes/bioconductor-lumihumanall.db/meta.yaml b/recipes/bioconductor-lumihumanall.db/meta.yaml index 22fcb67087468..e61a5dd476ab5 100644 --- a/recipes/bioconductor-lumihumanall.db/meta.yaml +++ b/recipes/bioconductor-lumihumanall.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.22.0" %} {% set name = "lumiHumanAll.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ce7e219b50833ceab203f0bbfb11d917 build: - number: 14 + number: 15 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lumihumanall.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumihumanidmapping/meta.yaml b/recipes/bioconductor-lumihumanidmapping/meta.yaml index ee31fe63c1247..6a28062e422f4 100644 --- a/recipes/bioconductor-lumihumanidmapping/meta.yaml +++ b/recipes/bioconductor-lumihumanidmapping/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.10.1" %} {% set name = "lumiHumanIDMapping" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,24 +13,25 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 007e5aa2f1596cc08d888ba6dce7148a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lumihumanidmapping", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base - r-dbi - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumimouseall.db/meta.yaml b/recipes/bioconductor-lumimouseall.db/meta.yaml index 1c8ed90955b5d..7046c1ded1218 100644 --- a/recipes/bioconductor-lumimouseall.db/meta.yaml +++ b/recipes/bioconductor-lumimouseall.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.22.0" %} {% set name = "lumiMouseAll.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6f12330377aaddc83bfa9c37477b999e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lumimouseall.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumimouseidmapping/meta.yaml b/recipes/bioconductor-lumimouseidmapping/meta.yaml index 944b71d3a338c..4d70e4fb54cf8 100644 --- a/recipes/bioconductor-lumimouseidmapping/meta.yaml +++ b/recipes/bioconductor-lumimouseidmapping/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.10.0" %} {% set name = "lumiMouseIDMapping" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 305aba80ebf6ef4c26899302ea9e50e8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lumimouseidmapping", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumiratall.db/meta.yaml b/recipes/bioconductor-lumiratall.db/meta.yaml index 4b230f3339cde..2bec6ec9618a5 100644 --- a/recipes/bioconductor-lumiratall.db/meta.yaml +++ b/recipes/bioconductor-lumiratall.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.22.0" %} {% set name = "lumiRatAll.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 65027624574d5e33f18b0a54a54f4be9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lumiratall.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumiratidmapping/meta.yaml b/recipes/bioconductor-lumiratidmapping/meta.yaml index 373ae2eee954b..fa2629353e6c9 100644 --- a/recipes/bioconductor-lumiratidmapping/meta.yaml +++ b/recipes/bioconductor-lumiratidmapping/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.10.0" %} {% set name = "lumiRatIDMapping" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1122fc25e3fff62678bed36f9d7b5709 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lumiratidmapping", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml b/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml index 5a52744c9da9d..5af4751df9291 100644 --- a/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml +++ b/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "LungCancerACvsSCCGEO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4313ab0bff32de6945d2b4e159979b4f + md5: f353aa0cc36dc25e67cdf1ba0738985e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lungcanceracvssccgeo", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh b/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh index 6145d97cbb5fb..b44b1fa903eb7 100644 --- a/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh +++ b/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "lungcanceracvssccgeo-1.36.0" +installBiocDataPackage.sh "lungcanceracvssccgeo-1.38.0" diff --git a/recipes/bioconductor-lungcancerlines/meta.yaml b/recipes/bioconductor-lungcancerlines/meta.yaml index 085d28a4fdb82..a54b8590d329e 100644 --- a/recipes/bioconductor-lungcancerlines/meta.yaml +++ b/recipes/bioconductor-lungcancerlines/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "LungCancerLines" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: be24350e8e8312e9421f0f4dd1ffbf85 + md5: 17b67ca0eac14ef832832b949972b277 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lungcancerlines", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base run: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lungcancerlines/post-link.sh b/recipes/bioconductor-lungcancerlines/post-link.sh index 0e6a6de527781..3191b811f3162 100644 --- a/recipes/bioconductor-lungcancerlines/post-link.sh +++ b/recipes/bioconductor-lungcancerlines/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "lungcancerlines-0.38.0" +installBiocDataPackage.sh "lungcancerlines-0.40.0" diff --git a/recipes/bioconductor-lungexpression/meta.yaml b/recipes/bioconductor-lungexpression/meta.yaml index b89c507fd4577..13240159ee3d6 100644 --- a/recipes/bioconductor-lungexpression/meta.yaml +++ b/recipes/bioconductor-lungexpression/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "lungExpression" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 56e3a841d35e5167328f7a3cc3f04349 + md5: 35eab717cb2e24c92faf417ad7fb9cb8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lungexpression", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lungexpression/post-link.sh b/recipes/bioconductor-lungexpression/post-link.sh index 68c94b5c0228b..a98eb220db162 100644 --- a/recipes/bioconductor-lungexpression/post-link.sh +++ b/recipes/bioconductor-lungexpression/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "lungexpression-0.38.0" +installBiocDataPackage.sh "lungexpression-0.40.0" diff --git a/recipes/bioconductor-lydata/meta.yaml b/recipes/bioconductor-lydata/meta.yaml index ea78d701bde18..5bd099c210424 100644 --- a/recipes/bioconductor-lydata/meta.yaml +++ b/recipes/bioconductor-lydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "lydata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: caffcda965c0d055e69f6f0eb2fe9d67 + md5: 4541ec0aad2bbee135b19b0bed4ea0af build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lydata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lydata/post-link.sh b/recipes/bioconductor-lydata/post-link.sh index b3fde371b303b..1e814b39963f5 100644 --- a/recipes/bioconductor-lydata/post-link.sh +++ b/recipes/bioconductor-lydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "lydata-1.26.0" +installBiocDataPackage.sh "lydata-1.28.0" diff --git a/recipes/bioconductor-lymphoseq/meta.yaml b/recipes/bioconductor-lymphoseq/meta.yaml index 5b8ca6d01685f..444c73883de46 100644 --- a/recipes/bioconductor-lymphoseq/meta.yaml +++ b/recipes/bioconductor-lymphoseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "LymphoSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 88d2862cfcae6c156660190a4dcf631c + md5: c7a311767150648a29d45e5cd5ee5c30 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lymphoseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, pheatmap, wordcloud, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - 'bioconductor-lymphoseqdb >=0.99.0,<0.100.0' - - 'bioconductor-msa >=1.32.0,<1.33.0' + - 'bioconductor-msa >=1.34.0,<1.35.0' - r-base - r-circlize - r-data.table @@ -39,10 +40,10 @@ requirements: - r-upsetr - r-venndiagram run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - 'bioconductor-lymphoseqdb >=0.99.0,<0.100.0' - - 'bioconductor-msa >=1.32.0,<1.33.0' + - 'bioconductor-msa >=1.34.0,<1.35.0' - r-base - r-circlize - r-data.table diff --git a/recipes/bioconductor-lymphoseqdb/meta.yaml b/recipes/bioconductor-lymphoseqdb/meta.yaml index e6bf9ca1dd2c0..9ae31ac173cd1 100644 --- a/recipes/bioconductor-lymphoseqdb/meta.yaml +++ b/recipes/bioconductor-lymphoseqdb/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.2" %} {% set name = "LymphoSeqDB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 22fc0dc2439ef497982a5ffddda1e418 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lymphoseqdb", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-m10kcod.db/meta.yaml b/recipes/bioconductor-m10kcod.db/meta.yaml index cd3a43bcb94bf..82e91d08de883 100644 --- a/recipes/bioconductor-m10kcod.db/meta.yaml +++ b/recipes/bioconductor-m10kcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "m10kcod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 04811628e4b37cd6d24e0b2a17d79ab8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-m10kcod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-m20kcod.db/meta.yaml b/recipes/bioconductor-m20kcod.db/meta.yaml index 8e44660a56326..6f7477b00a514 100644 --- a/recipes/bioconductor-m20kcod.db/meta.yaml +++ b/recipes/bioconductor-m20kcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "m20kcod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f2f734fb41e1ae4e949abf09687733bf build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-m20kcod.db", max_pin="x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20231202 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-m3c/meta.yaml b/recipes/bioconductor-m3c/meta.yaml index 582342cbed4ad..d5ae69bc55ced 100644 --- a/recipes/bioconductor-m3c/meta.yaml +++ b/recipes/bioconductor-m3c/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "M3C" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a15f91d6f63abdcffa1131c797fd619c + md5: e04534528d39712026e9b1de15a12c3d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-m3c", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-m3dexampledata/meta.yaml b/recipes/bioconductor-m3dexampledata/meta.yaml index 211786630fde3..f1420a70bec4e 100644 --- a/recipes/bioconductor-m3dexampledata/meta.yaml +++ b/recipes/bioconductor-m3dexampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "M3DExampleData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1181ab509a8a85961ef586709f3eaba3 + md5: 6988767aab7572ae3e701fd6854c061f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-m3dexampledata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-m3dexampledata/post-link.sh b/recipes/bioconductor-m3dexampledata/post-link.sh index 77c73e1387515..72da968afa952 100644 --- a/recipes/bioconductor-m3dexampledata/post-link.sh +++ b/recipes/bioconductor-m3dexampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "m3dexampledata-1.26.0" +installBiocDataPackage.sh "m3dexampledata-1.28.0" diff --git a/recipes/bioconductor-m3drop/meta.yaml b/recipes/bioconductor-m3drop/meta.yaml index c72f822e24787..29a92577f3e60 100644 --- a/recipes/bioconductor-m3drop/meta.yaml +++ b/recipes/bioconductor-m3drop/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "M3Drop" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d8dec066ec2a494fd8e2b9c2771ab37 + md5: ad347f93f1a297543e7ab0e74437dd4d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-m3drop", max_pin="x.x") }}' noarch: generic # Suggests: ROCR, knitr, M3DExampleData, scater, SingleCellExperiment, monocle, Seurat, Biobase requirements: diff --git a/recipes/bioconductor-m6aboost/meta.yaml b/recipes/bioconductor-m6aboost/meta.yaml index d93a008c5c87b..929ee2436e646 100644 --- a/recipes/bioconductor-m6aboost/meta.yaml +++ b/recipes/bioconductor-m6aboost/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "m6Aboost" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e39557c678ff999ad58cdaa49b01746b + md5: 17bd39bcc17e45a0bb22be3e2e15c533 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-m6aboost", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-adabag - r-base - r-dplyr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-adabag - r-base - r-dplyr diff --git a/recipes/bioconductor-maaslin2/meta.yaml b/recipes/bioconductor-maaslin2/meta.yaml index 8842f8735025c..344540a1fbdb1 100644 --- a/recipes/bioconductor-maaslin2/meta.yaml +++ b/recipes/bioconductor-maaslin2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "Maaslin2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7f70167c230537ebff1f132b2a2d46bf + md5: 0f92778b2d59935191e2ac58621da8f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-maaslin2", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat (>= 2.1.0), rmarkdown, markdown requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base - r-biglm - r-car @@ -46,8 +47,8 @@ requirements: - r-tibble - r-vegan run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base - r-biglm - r-car diff --git a/recipes/bioconductor-macarron/meta.yaml b/recipes/bioconductor-macarron/meta.yaml index 83b29fe0c4d5f..ff3a24d53a9d3 100644 --- a/recipes/bioconductor-macarron/meta.yaml +++ b/recipes/bioconductor-macarron/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "Macarron" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e2f02b7a780b42d3e9a805aa266ef831 + md5: 525669e56fccd2be5524315ee6a0eafb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-macarron", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, optparse, testthat (>= 2.1.0), rmarkdown, markdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-maaslin2 >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-maaslin2 >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dynamictreecut @@ -37,10 +38,10 @@ requirements: - r-wgcna - r-xml2 run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-maaslin2 >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-maaslin2 >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dynamictreecut diff --git a/recipes/bioconductor-macat/meta.yaml b/recipes/bioconductor-macat/meta.yaml index 7be249417b94a..292acdbbc3be8 100644 --- a/recipes/bioconductor-macat/meta.yaml +++ b/recipes/bioconductor-macat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "macat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f26ab5982050f5b89a52fd0ef72ba31e + md5: cad43ea7bcc92da57a4e5918581d0143 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-macat", max_pin="x.x") }}' noarch: generic # Suggests: hgu95av2.db, stjudem requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-macorrplot/meta.yaml b/recipes/bioconductor-macorrplot/meta.yaml index e08eeb78ddd2d..26005f13bc3d4 100644 --- a/recipes/bioconductor-macorrplot/meta.yaml +++ b/recipes/bioconductor-macorrplot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "maCorrPlot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad53b8a9ed8797daef76c81929eb25c8 + md5: 4d4be51b04e4ff3e09aff6643eeed215 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-macorrplot", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-macrophage/meta.yaml b/recipes/bioconductor-macrophage/meta.yaml index 66381d83d9755..54570f039c559 100644 --- a/recipes/bioconductor-macrophage/meta.yaml +++ b/recipes/bioconductor-macrophage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "macrophage" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 94a66e9f410a44d2aa240ebc4cf5c106 + md5: 5f83cf12d699a285cd228119b1d95cf0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-macrophage", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-macrophage/post-link.sh b/recipes/bioconductor-macrophage/post-link.sh index e21678c7de8a2..07ecd9410ed61 100644 --- a/recipes/bioconductor-macrophage/post-link.sh +++ b/recipes/bioconductor-macrophage/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "macrophage-1.16.0" +installBiocDataPackage.sh "macrophage-1.18.0" diff --git a/recipes/bioconductor-macsdata/meta.yaml b/recipes/bioconductor-macsdata/meta.yaml index e698607b03c87..9b6e64baa9952 100644 --- a/recipes/bioconductor-macsdata/meta.yaml +++ b/recipes/bioconductor-macsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MACSdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b5f6edbf074b1f0f5cb5d0d546cdbd0a + md5: 1d10f4fe6b20d5c09148b8011fb3183f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-macsdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-macsdata/post-link.sh b/recipes/bioconductor-macsdata/post-link.sh index eb83aa26c36d6..5b08e731f2aa8 100644 --- a/recipes/bioconductor-macsdata/post-link.sh +++ b/recipes/bioconductor-macsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "macsdata-1.8.0" +installBiocDataPackage.sh "macsdata-1.10.0" diff --git a/recipes/bioconductor-macsquantifyr/meta.yaml b/recipes/bioconductor-macsquantifyr/meta.yaml index b7f36ac6f8545..d34ebb85df598 100644 --- a/recipes/bioconductor-macsquantifyr/meta.yaml +++ b/recipes/bioconductor-macsquantifyr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MACSQuantifyR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a6252d72b886c783344a123b6b8b324a + md5: b0bc5dd3ddff22c28356a8af09704f82 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-macsquantifyr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, R.utils, spelling requirements: diff --git a/recipes/bioconductor-macsr/meta.yaml b/recipes/bioconductor-macsr/meta.yaml index d550c04c1780c..69879b8a4a240 100644 --- a/recipes/bioconductor-macsr/meta.yaml +++ b/recipes/bioconductor-macsr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MACSr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cee42ba19dbef311158effc2860c8ed6 + md5: bab4dacc8d41a2a47798bc740181f014 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-macsr", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle, MACSdata requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-reticulate run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-reticulate test: diff --git a/recipes/bioconductor-made4/meta.yaml b/recipes/bioconductor-made4/meta.yaml index 931cd5da58c55..924483d6772f8 100644 --- a/recipes/bioconductor-made4/meta.yaml +++ b/recipes/bioconductor-made4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "made4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6a9e234449f176b7ca00e61605dae1c5 + md5: ae8a8a420c5f5ebd8a729767baf0a762 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-made4", max_pin="x.x") }}' noarch: generic # Suggests: affy, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ade4 - r-base - r-gplots - r-rcolorbrewer - r-scatterplot3d run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ade4 - r-base - r-gplots diff --git a/recipes/bioconductor-madseq/meta.yaml b/recipes/bioconductor-madseq/meta.yaml index 928d177cace5f..54bf4e92bbf41 100644 --- a/recipes/bioconductor-madseq/meta.yaml +++ b/recipes/bioconductor-madseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "MADSEQ" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,50 +11,51 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f2e25b4e8cf74ac0ef392ddb4d7214b1 + md5: c64d51251670d105945b18d12dcd5fec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-madseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-coda - 'r-rjags >=4.6' - r-vcfr - r-vgam run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-coda - 'r-rjags >=4.6' diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml index be99ecb9bd161..2b6aa7f5d2729 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.1Kgenomes.phase1.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a20471906a41678ce710879e92d2a9dc build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.1kgenomes.phase1.grch38", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml index 38d35b744a3c0..370e667cdc070 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.1Kgenomes.phase1.hs37d5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ece6b758ca0e1a8a307b5cd5829671f4 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.1kgenomes.phase1.hs37d5", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml index 825c493200e85..1db40c302708a 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.1Kgenomes.phase3.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ee57d9cb6a1748932407d20b9bffd8a2 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.1kgenomes.phase3.grch38", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml index 4de3ba7d81011..e5eef7f32a86d 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.1Kgenomes.phase3.hs37d5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ac3cbbf52eb2026f067a4f42c6654555 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.1kgenomes.phase3.hs37d5", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml index b246266b6fe51..a96f0e68085a4 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.ExAC.r1.0.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 303332c918996d8cb3e7b7c74d694dd1 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.exac.r1.0.grch38", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml index dffd2da0880cd..8ee13e3ac78c2 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.ExAC.r1.0.hs37d5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4d523554a2b0eb296bada9d33a78eefc build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.exac.r1.0.hs37d5", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml index 2f42f1af107df..acc4810915163 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.ExAC.r1.0.nonTCGA.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: cf447f59cc8b1cd7ca395fd3fe6e4730 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.exac.r1.0.nontcga.grch38", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml index 1a7713ca04870..4e474b21e0b3f 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.ExAC.r1.0.nonTCGA.hs37d5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: da3a699e9776b0b769b3bc1e9fb742f0 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.exac.r1.0.nontcga.hs37d5", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/meta.yaml b/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/meta.yaml index 357433b83fe2e..6a2aeb3790b7b 100644 --- a/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.gnomAD.r2.1.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0e842b24476aeb834f57f9302a36ea18 build: - number: 7 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.gnomad.r2.1.grch38", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml index c18f6c455ea03..e55b30222e669 100644 --- a/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.gnomAD.r2.1.hs37d5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 12221c461930ae1ecfe925943a619d56 build: - number: 9 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.gnomad.r2.1.hs37d5", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/meta.yaml b/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/meta.yaml index 306a937c8d05c..0a1f9568b4c16 100644 --- a/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.gnomADex.r2.1.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a0ab5b74997669fabb8aecfd9ef7f767 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.gnomadex.r2.1.grch38", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml index f01decacb0e1e..9c24dd865ddc8 100644 --- a/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.gnomADex.r2.1.hs37d5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6ca4d742571687a13906d99cea2dbf1f build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.gnomadex.r2.1.hs37d5", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml b/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml index 2c94cbac23ecb..06fdf2b8407e8 100644 --- a/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml +++ b/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.TOPMed.freeze5.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7fdb58eb69187ade189689da58ca6266 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.topmed.freeze5.hg19", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml b/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml index b976d65bd270b..485f8cd9f87c6 100644 --- a/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml +++ b/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.TOPMed.freeze5.hg38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a3355623fde26b83dfd346a32829f073 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.topmed.freeze5.hg38", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafh5.gnomad.v3.1.1.grch38/meta.yaml b/recipes/bioconductor-mafh5.gnomad.v3.1.1.grch38/meta.yaml index 9a2a78841bcb4..a0ae0f400cc7a 100644 --- a/recipes/bioconductor-mafh5.gnomad.v3.1.1.grch38/meta.yaml +++ b/recipes/bioconductor-mafh5.gnomad.v3.1.1.grch38/meta.yaml @@ -41,7 +41,7 @@ requirements: - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20230706 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafh5.gnomad.v3.1.2.grch38/meta.yaml b/recipes/bioconductor-mafh5.gnomad.v3.1.2.grch38/meta.yaml index 22bb4faead093..906283e9f2b28 100644 --- a/recipes/bioconductor-mafh5.gnomad.v3.1.2.grch38/meta.yaml +++ b/recipes/bioconductor-mafh5.gnomad.v3.1.2.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.15.0" %} {% set name = "MafH5.gnomAD.v3.1.2.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,35 +13,36 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e9c85173866caf998cf1af7dd35aac0b build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafh5.gnomad.v3.1.2.grch38", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-maftools/meta.yaml b/recipes/bioconductor-maftools/meta.yaml index 86123ebc13b62..45bb795699803 100644 --- a/recipes/bioconductor-maftools/meta.yaml +++ b/recipes/bioconductor-maftools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "maftools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b54e39e3b9f5f9123ce2755efdd2cc92 + md5: 3dadc2b7f6f1693ae23a41b61f541db4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-maftools", max_pin="x.x") }}' # Suggests: berryFunctions, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr, mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment, rmarkdown, S4Vectors, pheatmap, curl # SystemRequirements: GNU make requirements: host: - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-data.table - r-rcolorbrewer @@ -31,9 +32,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-data.table - r-rcolorbrewer diff --git a/recipes/bioconductor-magar/meta.yaml b/recipes/bioconductor-magar/meta.yaml index 37aa9da557ce8..e87b79b60d97d 100644 --- a/recipes/bioconductor-magar/meta.yaml +++ b/recipes/bioconductor-magar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MAGAR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 17a56f640a48d9270666b77554644c7b + md5: 27ccb3bf6acaabe9b9d29b52f9d98213 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-magar", max_pin="x.x") }}' noarch: generic # Suggests: gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil, rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools, BiocGenerics, BiocManager requirements: host: - - 'bioconductor-crlmm >=1.58.0,<1.59.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-rnbeads >=2.18.0,<2.19.0' - - 'bioconductor-rnbeads.hg19 >=1.32.0,<1.33.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' + - 'bioconductor-crlmm >=1.60.0,<1.61.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-rnbeads >=2.20.0,<2.21.0' + - 'bioconductor-rnbeads.hg19 >=1.34.0,<1.35.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' - r-argparse - r-base - r-bigstatsr @@ -40,12 +41,12 @@ requirements: - r-rjson - r-upsetr run: - - 'bioconductor-crlmm >=1.58.0,<1.59.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-rnbeads >=2.18.0,<2.19.0' - - 'bioconductor-rnbeads.hg19 >=1.32.0,<1.33.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' + - 'bioconductor-crlmm >=1.60.0,<1.61.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-rnbeads >=2.20.0,<2.21.0' + - 'bioconductor-rnbeads.hg19 >=1.34.0,<1.35.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' - r-argparse - r-base - r-bigstatsr diff --git a/recipes/bioconductor-mageckflute/meta.yaml b/recipes/bioconductor-mageckflute/meta.yaml index a7b7a298d0692..3a485e0d36c7c 100644 --- a/recipes/bioconductor-mageckflute/meta.yaml +++ b/recipes/bioconductor-mageckflute/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "MAGeCKFlute" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3471b341d90f59e6ef5c9ae15ed4e6d0 + md5: 09a3c95fe59a959ce069f5ad56e75276 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mageckflute", max_pin="x.x") }}' noarch: generic # Suggests: biomaRt, BiocStyle, dendextend, graphics, knitr, pheatmap, png, scales, sva, BiocManager requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-depmap >=1.14.0,<1.15.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-depmap >=1.16.0,<1.17.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' - r-base - r-ggplot2 - r-ggrepel @@ -34,12 +35,12 @@ requirements: - r-msigdbr - r-reshape2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-depmap >=1.14.0,<1.15.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-depmap >=1.16.0,<1.17.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-magpie/meta.yaml b/recipes/bioconductor-magpie/meta.yaml index f600033cb56df..9b8edec7aca44 100644 --- a/recipes/bioconductor-magpie/meta.yaml +++ b/recipes/bioconductor-magpie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "magpie" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 52ffa8a06a288f5a51ea9337aa99733e + md5: 019cf9b038353b96851fe65fa55f3d08 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-magpie", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, kableExtra, RUnit, TBX20BamSubset, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tress >=1.6.0,<1.7.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tress >=1.8.0,<1.9.0' - r-aod - r-base - r-matrix @@ -39,16 +40,16 @@ requirements: - r-rcolorbrewer - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tress >=1.6.0,<1.7.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tress >=1.8.0,<1.9.0' - r-aod - r-base - r-matrix diff --git a/recipes/bioconductor-magrene/meta.yaml b/recipes/bioconductor-magrene/meta.yaml index 062f1bacc7482..54cc0f1df97ec 100644 --- a/recipes/bioconductor-magrene/meta.yaml +++ b/recipes/bioconductor-magrene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "magrene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: df1a679707bfc6783f48a7489c8e0c8b + md5: 7d02392d3081830451c4fae90ed50177 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-magrene", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base test: commands: diff --git a/recipes/bioconductor-mai/meta.yaml b/recipes/bioconductor-mai/meta.yaml index 4f88bbb8b24e2..e1039188b4612 100644 --- a/recipes/bioconductor-mai/meta.yaml +++ b/recipes/bioconductor-mai/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "MAI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 990f4687d2c061d10aea5f5d78795328 + md5: ac8dbd997d58657f8ed6b64f5cdee7a9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mai", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-caret - r-doparallel @@ -34,9 +35,9 @@ requirements: - r-missforest - r-tidyverse run: - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-caret - r-doparallel diff --git a/recipes/bioconductor-mait/meta.yaml b/recipes/bioconductor-mait/meta.yaml index 5351c8eb39d02..695444af43443 100644 --- a/recipes/bioconductor-mait/meta.yaml +++ b/recipes/bioconductor-mait/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "MAIT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37e3772801390dcf734e87c62b98471b + md5: f32e9e8e908202848634b26a5ece4d8f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mait", max_pin="x.x") }}' # Suggests: faahKO requirements: host: - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-agricolae - r-base - r-caret @@ -35,8 +36,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-agricolae - r-base - r-caret diff --git a/recipes/bioconductor-maizecdf/meta.yaml b/recipes/bioconductor-maizecdf/meta.yaml index 0e8d7a5d7b90b..d836b954f6903 100644 --- a/recipes/bioconductor-maizecdf/meta.yaml +++ b/recipes/bioconductor-maizecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "maizecdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f9dec9e46688d96daf1e07d4e815afb4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-maizecdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-maizeprobe/meta.yaml b/recipes/bioconductor-maizeprobe/meta.yaml index 5506099f48285..3c8eb2bfe896a 100644 --- a/recipes/bioconductor-maizeprobe/meta.yaml +++ b/recipes/bioconductor-maizeprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "maizeprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ef7ba47de2346b3552621263399c05d1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-maizeprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-makecdfenv/meta.yaml b/recipes/bioconductor-makecdfenv/meta.yaml index 1fc6c31d0e941..2271860f8f2bc 100644 --- a/recipes/bioconductor-makecdfenv/meta.yaml +++ b/recipes/bioconductor-makecdfenv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "makecdfenv" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4455ab7ea0c109310c0ef051acc9bf44 + md5: b5c8877fd5b09fbb4d3656490fa7eb64 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-makecdfenv", max_pin="x.x") }}' requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-malaria.db0/meta.yaml b/recipes/bioconductor-malaria.db0/meta.yaml index b0d07125ccc9e..ddff973edf6fe 100644 --- a/recipes/bioconductor-malaria.db0/meta.yaml +++ b/recipes/bioconductor-malaria.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "malaria.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b8064752fa55d249e89e1c94db04b434 + md5: 6f71b4ac69ae5237f3f5e1337d5073d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-malaria.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-malaria.db0/post-link.sh b/recipes/bioconductor-malaria.db0/post-link.sh index aa5c1fbc028d9..723835d617cfb 100644 --- a/recipes/bioconductor-malaria.db0/post-link.sh +++ b/recipes/bioconductor-malaria.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "malaria.db0-3.17.0" +installBiocDataPackage.sh "malaria.db0-3.18.0" diff --git a/recipes/bioconductor-mammaprintdata/meta.yaml b/recipes/bioconductor-mammaprintdata/meta.yaml index 9f531c2391d37..0ad3e9e516f38 100644 --- a/recipes/bioconductor-mammaprintdata/meta.yaml +++ b/recipes/bioconductor-mammaprintdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "mammaPrintData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfd6915395a6a2adeebac6854f3359c9 + md5: 08b3249a36d5f165a933bfab5eb05a2a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mammaprintdata", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, readxl, limma requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mammaprintdata/post-link.sh b/recipes/bioconductor-mammaprintdata/post-link.sh index b1a54fcddb5fa..ee220d325a5a0 100644 --- a/recipes/bioconductor-mammaprintdata/post-link.sh +++ b/recipes/bioconductor-mammaprintdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mammaprintdata-1.36.0" +installBiocDataPackage.sh "mammaprintdata-1.38.0" diff --git a/recipes/bioconductor-manor/meta.yaml b/recipes/bioconductor-manor/meta.yaml index d21c6e9c6b331..0b48ee35d2fea 100644 --- a/recipes/bioconductor-manor/meta.yaml +++ b/recipes/bioconductor-manor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "MANOR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fff1198e00300c326aec0b10f1243e7d + md5: a2d915a1904045acbe371b10102c8512 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-manor", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, bookdown requirements: host: - - 'bioconductor-glad >=2.64.0,<2.65.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' - r-base - libblas - liblapack run: - - 'bioconductor-glad >=2.64.0,<2.65.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-mantelcorr/meta.yaml b/recipes/bioconductor-mantelcorr/meta.yaml index 20ab63e20a1ab..5fe60a98bbc56 100644 --- a/recipes/bioconductor-mantelcorr/meta.yaml +++ b/recipes/bioconductor-mantelcorr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "MantelCorr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f20807432d60061faa0e788a6e98c84 + md5: 7ef5ee0a329a4cf218c340e9289fea32 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mantelcorr", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-mapkldata/meta.yaml b/recipes/bioconductor-mapkldata/meta.yaml index 50ea4875e03e4..8669aaad8b16f 100644 --- a/recipes/bioconductor-mapkldata/meta.yaml +++ b/recipes/bioconductor-mapkldata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "mAPKLData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d1b511c7be1a423450a153fc118e7cb + md5: ce6399a1c853cb4e78de226347c3dc5d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mapkldata", max_pin="x.x") }}' noarch: generic # Suggests: Biobase requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mapkldata/post-link.sh b/recipes/bioconductor-mapkldata/post-link.sh index d7a4cb29b019b..5c4a6533b73dc 100644 --- a/recipes/bioconductor-mapkldata/post-link.sh +++ b/recipes/bioconductor-mapkldata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mapkldata-1.32.0" +installBiocDataPackage.sh "mapkldata-1.34.0" diff --git a/recipes/bioconductor-mapredictdsc/meta.yaml b/recipes/bioconductor-mapredictdsc/meta.yaml index 98832a70410c7..88e0feda89173 100644 --- a/recipes/bioconductor-mapredictdsc/meta.yaml +++ b/recipes/bioconductor-mapredictdsc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "maPredictDSC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6478a774bba2457523926418168a45f2 + md5: b2a491a7c799fcc0efcaed0b3067aa66 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mapredictdsc", max_pin="x.x") }}' noarch: generic # Suggests: parallel requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-lungcanceracvssccgeo >=1.36.0,<1.37.0' - - 'bioconductor-roc >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-lungcanceracvssccgeo >=1.38.0,<1.39.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' - r-base - r-caret - r-class @@ -35,13 +36,13 @@ requirements: - r-mass - r-rocr run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-lungcanceracvssccgeo >=1.36.0,<1.37.0' - - 'bioconductor-roc >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-lungcanceracvssccgeo >=1.38.0,<1.39.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' - r-base - r-caret - r-class diff --git a/recipes/bioconductor-mapscape/meta.yaml b/recipes/bioconductor-mapscape/meta.yaml index 68bec68fe92d6..d0af3af41f6ed 100644 --- a/recipes/bioconductor-mapscape/meta.yaml +++ b/recipes/bioconductor-mapscape/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "mapscape" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fb51de837561beef21ffa11f723654f9 + md5: dc197aa43e86dc49fef0d85d2ead252c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mapscape", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-maqcexpression4plex/meta.yaml b/recipes/bioconductor-maqcexpression4plex/meta.yaml index 53bdea96b4749..58945237d3ad0 100644 --- a/recipes/bioconductor-maqcexpression4plex/meta.yaml +++ b/recipes/bioconductor-maqcexpression4plex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "maqcExpression4plex" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 761e3e1f398262f4c0cac3cd31979fc7 + md5: 8312b7fbcba763a33630effb8c3b5f10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-maqcexpression4plex", max_pin="x.x") }}' noarch: generic # Suggests: oligo, pdInfoBuilder requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-maqcexpression4plex/post-link.sh b/recipes/bioconductor-maqcexpression4plex/post-link.sh index fc90732c5d1fd..8a868702a088b 100644 --- a/recipes/bioconductor-maqcexpression4plex/post-link.sh +++ b/recipes/bioconductor-maqcexpression4plex/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "maqcexpression4plex-1.44.0" +installBiocDataPackage.sh "maqcexpression4plex-1.46.0" diff --git a/recipes/bioconductor-maqcsubset/meta.yaml b/recipes/bioconductor-maqcsubset/meta.yaml index 8f3a5ded5021c..4f5f9467649c3 100644 --- a/recipes/bioconductor-maqcsubset/meta.yaml +++ b/recipes/bioconductor-maqcsubset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "MAQCsubset" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eb3ea654ce6aa3db50c7a39c6d8cab28 + md5: 5757c11a1af2150b8fd17c3a8b8b0c0c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-maqcsubset", max_pin="x.x") }}' noarch: generic # Suggests: genefilter, codelink requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-maqcsubset/post-link.sh b/recipes/bioconductor-maqcsubset/post-link.sh index 270d828522f4e..2e61448c5748c 100644 --- a/recipes/bioconductor-maqcsubset/post-link.sh +++ b/recipes/bioconductor-maqcsubset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "maqcsubset-1.38.0" +installBiocDataPackage.sh "maqcsubset-1.40.0" diff --git a/recipes/bioconductor-maqcsubsetilm/meta.yaml b/recipes/bioconductor-maqcsubsetilm/meta.yaml index c1926f58f1dd3..8c1a687bc5053 100644 --- a/recipes/bioconductor-maqcsubsetilm/meta.yaml +++ b/recipes/bioconductor-maqcsubsetilm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "MAQCsubsetILM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4aaeddbd20f73e3f84dc630e9c02e219 + md5: 1c975db69a86cc80e99c5245998ee255 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-maqcsubsetilm", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-maqcsubsetilm/post-link.sh b/recipes/bioconductor-maqcsubsetilm/post-link.sh index 76cbbf1ec8f5a..20355734efcd0 100644 --- a/recipes/bioconductor-maqcsubsetilm/post-link.sh +++ b/recipes/bioconductor-maqcsubsetilm/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "maqcsubsetilm-1.38.0" +installBiocDataPackage.sh "maqcsubsetilm-1.40.0" diff --git a/recipes/bioconductor-mariner/meta.yaml b/recipes/bioconductor-mariner/meta.yaml index 9e1ea1bdda43a..faa6324855fb2 100644 --- a/recipes/bioconductor-mariner/meta.yaml +++ b/recipes/bioconductor-mariner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "mariner" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8e7440b7a29afb6f325512a65653b3b9 + md5: 6ed30878d03b8a17e8e7c4ee17218893 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mariner", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat (>= 3.0.0), dplyr, rmarkdown, ExperimentHub, marinerData requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plotgardener >=1.6.0,<1.7.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plotgardener >=1.8.0,<1.9.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-assertthat - r-base @@ -49,19 +50,19 @@ requirements: - r-rlang - 'r-strawr >=0.0.91' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plotgardener >=1.6.0,<1.7.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plotgardener >=1.8.0,<1.9.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-assertthat - r-base diff --git a/recipes/bioconductor-marinerdata/meta.yaml b/recipes/bioconductor-marinerdata/meta.yaml index c1961f6c744f6..1f58a93bd6ba5 100644 --- a/recipes/bioconductor-marinerdata/meta.yaml +++ b/recipes/bioconductor-marinerdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "marinerData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 88417144bbc4ae0164445918ce73376d + md5: 7875113ebb6baaaed6eb6fc762ba92ca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-marinerdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-marinerdata/post-link.sh b/recipes/bioconductor-marinerdata/post-link.sh index ddb0b82fcea0c..a1f63c4a9a63d 100644 --- a/recipes/bioconductor-marinerdata/post-link.sh +++ b/recipes/bioconductor-marinerdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "marinerdata-1.0.0" +installBiocDataPackage.sh "marinerdata-1.2.0" diff --git a/recipes/bioconductor-marr/meta.yaml b/recipes/bioconductor-marr/meta.yaml index 5f05cd664dbf4..cb6168d37a922 100644 --- a/recipes/bioconductor-marr/meta.yaml +++ b/recipes/bioconductor-marr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "marr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5034df18a1cb3deb55978997508feea8 + md5: 3b839d77065c34ddb5f5c2a8eee277ea build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-marr", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, testthat, covr requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -31,8 +32,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-marray/meta.yaml b/recipes/bioconductor-marray/meta.yaml index b0c13d578a065..d4701902cbd9a 100644 --- a/recipes/bioconductor-marray/meta.yaml +++ b/recipes/bioconductor-marray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "marray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3dc5ce3be06cf55e1e4c95f77f2acce0 + md5: 569b373e346d36964430d249d075cf07 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-marray", max_pin="x.x") }}' noarch: generic # Suggests: tkWidgets requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-martini/meta.yaml b/recipes/bioconductor-martini/meta.yaml index a5c17f5984402..707dd1d27a6ae 100644 --- a/recipes/bioconductor-martini/meta.yaml +++ b/recipes/bioconductor-martini/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "martini" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 400390c31bdbd7cc031fdf235683eb7d + md5: 85e3366daf7ac24c0f50261fafe8b274 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-martini", max_pin="x.x") }}' # Suggests: biomaRt (>= 2.34.1), circlize (>= 0.4.11), STRINGdb (>= 2.2.0), httr (>= 1.2.1), IRanges (>= 2.8.2), S4Vectors (>= 0.12.2), knitr, testthat, readr, rmarkdown requirements: host: - - 'bioconductor-snpstats >=1.50.0,<1.51.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' - r-base - 'r-igraph >=1.0.1' - r-matrix @@ -30,7 +31,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-snpstats >=1.50.0,<1.51.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' - r-base - 'r-igraph >=1.0.1' - r-matrix diff --git a/recipes/bioconductor-maser/meta.yaml b/recipes/bioconductor-maser/meta.yaml index 831d0c6a9612b..984e5476ff7d0 100644 --- a/recipes/bioconductor-maser/meta.yaml +++ b/recipes/bioconductor-maser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "maser" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 052306b8282c5b311639dfa2d5ef7045 + md5: 43be20847a05369476ccdb91cdd6ad4e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-maser", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle, AnnotationHub requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-dplyr @@ -34,12 +35,12 @@ requirements: - r-ggplot2 - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-masigpro/meta.yaml b/recipes/bioconductor-masigpro/meta.yaml index f932961901201..92ad4b2047ab2 100644 --- a/recipes/bioconductor-masigpro/meta.yaml +++ b/recipes/bioconductor-masigpro/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "maSigPro" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 712ae9a5e65afe3af9adb7b6b0701938 + md5: ab91a6a10122c6d1f28fee40be32c2b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-masigpro", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-mass - r-mclust - r-venn run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-mass - r-mclust diff --git a/recipes/bioconductor-maskbad/meta.yaml b/recipes/bioconductor-maskbad/meta.yaml index f0c5d696b39a6..e7cfd10db732a 100644 --- a/recipes/bioconductor-maskbad/meta.yaml +++ b/recipes/bioconductor-maskbad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "maskBAD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b331548e7096b6b3be7c7dec18ef8326 + md5: a5fc8482a4370f32fde7bc2b3e302c77 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-maskbad", max_pin="x.x") }}' noarch: generic # Suggests: hgu95av2probe, hgu95av2cdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' - r-base test: commands: diff --git a/recipes/bioconductor-massarray/meta.yaml b/recipes/bioconductor-massarray/meta.yaml index 3d6d46c569432..0afae7ac8c0e7 100644 --- a/recipes/bioconductor-massarray/meta.yaml +++ b/recipes/bioconductor-massarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "MassArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 10baaf1ef33e244057e4f36061412c28 + md5: 028fea456ce2e5b3820ad6dc0d1989c1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-massarray", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-massir/meta.yaml b/recipes/bioconductor-massir/meta.yaml index 9e0e03f5fb577..dbf9731aa509d 100644 --- a/recipes/bioconductor-massir/meta.yaml +++ b/recipes/bioconductor-massir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "massiR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 486b707284622849c02988e6cd5b82f9 + md5: f2dda0fb78f776b416af77100e902b55 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-massir", max_pin="x.x") }}' noarch: generic # Suggests: biomaRt, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-cluster - r-diptest - r-gplots run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-cluster - r-diptest diff --git a/recipes/bioconductor-massspecwavelet/meta.yaml b/recipes/bioconductor-massspecwavelet/meta.yaml index 96df2a5052c6d..3518c50e8a816 100644 --- a/recipes/bioconductor-massspecwavelet/meta.yaml +++ b/recipes/bioconductor-massspecwavelet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "MassSpecWavelet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ebb91cab5b3607ac2c59cd73e6e06c9 + md5: 387636ea7c674fe339c56a8af3458f8a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-massspecwavelet", max_pin="x.x") }}' # Suggests: signal, waveslim, BiocStyle, knitr, rmarkdown, RUnit, bench requirements: host: diff --git a/recipes/bioconductor-mast/meta.yaml b/recipes/bioconductor-mast/meta.yaml index 029f53b7473ce..1dd0a3e36a434 100644 --- a/recipes/bioconductor-mast/meta.yaml +++ b/recipes/bioconductor-mast/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "MAST" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9442a26a462745f9c9f05cdb036cc1df + md5: 5b2d5c6a33243cdf9c2e4440ba4bf1da build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mast", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, lme4(>= 1.0), blme, roxygen2(> 6.0.0), numDeriv, car, gdata, lattice, GGally, GSEABase, NMF, TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer, BiocStyle, scater, DelayedArray, HDF5Array, zinbwave, dplyr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-data.table @@ -36,11 +37,11 @@ requirements: - r-reshape2 - r-stringr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-data.table diff --git a/recipes/bioconductor-mastr/meta.yaml b/recipes/bioconductor-mastr/meta.yaml index 812d4bfc3fa77..d13e915d95790 100644 --- a/recipes/bioconductor-mastr/meta.yaml +++ b/recipes/bioconductor-mastr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "mastR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ce292ab282a5db42a4c0975bfd326640 + md5: be4cab3fb29097cb5dd34ee7ba1ce228 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mastr", max_pin="x.x") }}' noarch: generic # Suggests: BiocManager, BiocStyle, BisqueRNA, clusterProfiler, ComplexHeatmap, depmap, enrichplot, ggrepel, ggvenn, gridExtra, jsonlite, knitr, rmarkdown, RobustRankAggreg, rvest, scuttle, singscore, splatter, testthat (>= 3.0.0), UpSetR requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msigdb >=1.8.0,<1.9.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msigdb >=1.10.0,<1.11.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -39,15 +40,15 @@ requirements: - r-seuratobject - r-tidyr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msigdb >=1.8.0,<1.9.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msigdb >=1.10.0,<1.11.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-matchbox/meta.yaml b/recipes/bioconductor-matchbox/meta.yaml index 987d19e540765..0cb5c684cdaaa 100644 --- a/recipes/bioconductor-matchbox/meta.yaml +++ b/recipes/bioconductor-matchbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "matchBox" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e86b03f10e018b4c355da5ff1f8b17d0 + md5: b6e4b10ee38f433d1bce146a089a44ec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-matchbox", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-matrixgenerics/meta.yaml b/recipes/bioconductor-matrixgenerics/meta.yaml index 51d5c467ae836..4db7b3d78519a 100644 --- a/recipes/bioconductor-matrixgenerics/meta.yaml +++ b/recipes/bioconductor-matrixgenerics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.2" %} +{% set version = "1.14.0" %} {% set name = "MatrixGenerics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91a6ccc193831c76b3806c41b3ceed6d + md5: 18c3a5cc993ca5c2ad48dde1813105e6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-matrixgenerics", max_pin="x.x") }}' noarch: generic # Suggests: Matrix, sparseMatrixStats, SparseArray, DelayedArray, DelayedMatrixStats, SummarizedExperiment, testthat (>= 2.1.0) requirements: diff --git a/recipes/bioconductor-matrixqcvis/meta.yaml b/recipes/bioconductor-matrixqcvis/meta.yaml index 4042891f77548..39bd88b0aa423 100644 --- a/recipes/bioconductor-matrixqcvis/meta.yaml +++ b/recipes/bioconductor-matrixqcvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MatrixQCvis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3c78e12fc1b9c6bda807c330f86197e + md5: 21f91ace512d3afadd5fe42e93ba7fe9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-matrixqcvis", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics (>= 0.37.4), BiocStyle (>= 2.19.2), hexbin (>= 1.28.2), jpeg (>= 0.1-10), knitr (>= 1.33), statmod (>= 1.5.0), testthat (>= 3.0.2) requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-proda >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-proda >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - 'r-dplyr >=1.0.5' - 'r-ggplot2 >=3.3.3' @@ -49,14 +50,14 @@ requirements: - 'r-umap >=0.2.7.0' - 'r-upsetr >=1.4.0' run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-proda >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-proda >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - 'r-dplyr >=1.0.5' - 'r-ggplot2 >=3.3.3' diff --git a/recipes/bioconductor-matrixrider/meta.yaml b/recipes/bioconductor-matrixrider/meta.yaml index c0e2a75d98583..89be4c1d9d40e 100644 --- a/recipes/bioconductor-matrixrider/meta.yaml +++ b/recipes/bioconductor-matrixrider/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "MatrixRider" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9831760b8e5550b70367da373860cdd9 + md5: 2de2ee8befc7dcf6b84ea6630a0c089f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-matrixrider", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics, BiocStyle, JASPAR2014 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-matter/meta.yaml b/recipes/bioconductor-matter/meta.yaml index 37f67677cee07..631bf8eaa0512 100644 --- a/recipes/bioconductor-matter/meta.yaml +++ b/recipes/bioconductor-matter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "matter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9af0c8ea4ebd31da1bb4d27f0e610989 + md5: 08919bc0df5442e0916ee7cffbc23003 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-matter", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - r-base - r-biglm - r-digest @@ -31,9 +32,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - r-base - r-biglm - r-digest @@ -49,8 +50,8 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'A framework for rapid prototyping with file-based data structures' - description: 'Memory-efficient reading, writing, and manipulation of structured binary data as file-based vectors, matrices, arrays, lists, and data frames.' + summary: 'Out-of-memory dense and sparse signal arrays' + description: 'Memory-efficient file-based data structures for dense and sparse vectors, matrices, arrays, and lists with applications to nonuniformly sampled signals and spectra.' extra: identifiers: - biotools:matter diff --git a/recipes/bioconductor-mbamethyl/meta.yaml b/recipes/bioconductor-mbamethyl/meta.yaml index 9df037c318d99..d76d4dc6cc97c 100644 --- a/recipes/bioconductor-mbamethyl/meta.yaml +++ b/recipes/bioconductor-mbamethyl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "MBAmethyl" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c62ade813fcdb70923e320b12b345e16 + md5: 0b6ac0d76525c156606d08bcbf606709 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mbamethyl", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-mbased/meta.yaml b/recipes/bioconductor-mbased/meta.yaml index 2307cd01cdd85..02ada98f3ea95 100644 --- a/recipes/bioconductor-mbased/meta.yaml +++ b/recipes/bioconductor-mbased/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "MBASED" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a182ddefc6e826fc016a735e09a4dda + md5: 441d95c8a2670c6d5fd3488ed33aad2d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mbased", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-runit run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-runit test: diff --git a/recipes/bioconductor-mbcb/meta.yaml b/recipes/bioconductor-mbcb/meta.yaml index d4d4d3ad6c293..10a541c33c679 100644 --- a/recipes/bioconductor-mbcb/meta.yaml +++ b/recipes/bioconductor-mbcb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "MBCB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96f8ffc0fec24d84ad88762f060594ca + md5: 51a88491b8d5872a1088def3f6113466 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mbcb", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-tcltk2 run: - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-tcltk2 test: diff --git a/recipes/bioconductor-mbecs/meta.yaml b/recipes/bioconductor-mbecs/meta.yaml index 353e54f8d4950..027ca183cf4f5 100644 --- a/recipes/bioconductor-mbecs/meta.yaml +++ b/recipes/bioconductor-mbecs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "MBECS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ce3a45af4cc4421da87dbb1a2350be7 + md5: 5e7481e4bcd7fc20a2251635324035a4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mbecs", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-cluster - r-dplyr @@ -40,9 +41,9 @@ requirements: - r-tidyr - r-vegan run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-cluster - r-dplyr diff --git a/recipes/bioconductor-mbkmeans/meta.yaml b/recipes/bioconductor-mbkmeans/meta.yaml index f8b3093cd52f8..7d17593365b4e 100644 --- a/recipes/bioconductor-mbkmeans/meta.yaml +++ b/recipes/bioconductor-mbkmeans/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "mbkmeans" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7b6ff2a1ccf521fe1bf7a20e41b88d88 + md5: 1bd55f0f927fea250caa1a8264e3013c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mbkmeans", max_pin="x.x") }}' # Suggests: beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData, scater, DelayedMatrixStats, bluster, knitr, testthat, rmarkdown # SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-benchmarkme - r-clusterr @@ -37,13 +38,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-benchmarkme - r-clusterr diff --git a/recipes/bioconductor-mbpcr/meta.yaml b/recipes/bioconductor-mbpcr/meta.yaml index 350f2c9b1ecb9..bdcd2d19a5648 100644 --- a/recipes/bioconductor-mbpcr/meta.yaml +++ b/recipes/bioconductor-mbpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "mBPCR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d80f58ccbe4015bcdc599ba75d2a68d5 + md5: 1d48a3fd5a04c61ce96aa4da34d364a2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mbpcr", max_pin="x.x") }}' noarch: generic # Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gwastools >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gwastools >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gwastools >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gwastools >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base test: commands: diff --git a/recipes/bioconductor-mbqn/meta.yaml b/recipes/bioconductor-mbqn/meta.yaml index 201c9c2424cbf..37d730a8cbee4 100644 --- a/recipes/bioconductor-mbqn/meta.yaml +++ b/recipes/bioconductor-mbqn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "MBQN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af21afa905ec9efb9a8ae56c6c974e10 + md5: e48e4ebcd3b69b82559496b66ca4cf44 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mbqn", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-paireddata @@ -33,10 +34,10 @@ requirements: - r-rmarkdown - r-xml2 run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-paireddata diff --git a/recipes/bioconductor-mbqtl/meta.yaml b/recipes/bioconductor-mbqtl/meta.yaml index 7bb44f7edfa24..c92f3949b66e7 100644 --- a/recipes/bioconductor-mbqtl/meta.yaml +++ b/recipes/bioconductor-mbqtl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "mbQTL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d840e98993cc26ca1dbb216dacdda443 + md5: 5b8464d079a9297ed19fcdfade113190 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mbqtl", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base - r-broom - r-dplyr @@ -32,7 +33,7 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base - r-broom - r-dplyr diff --git a/recipes/bioconductor-mbttest/meta.yaml b/recipes/bioconductor-mbttest/meta.yaml index 5c77e8f2124b3..a9891797e564b 100644 --- a/recipes/bioconductor-mbttest/meta.yaml +++ b/recipes/bioconductor-mbttest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "MBttest" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa0087a2a95b5f53df47bea5d6076fd4 + md5: 35c603063456aab63ffa0ebfc67a3c16 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mbttest", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BiocGenerics requirements: diff --git a/recipes/bioconductor-mcbiclust/meta.yaml b/recipes/bioconductor-mcbiclust/meta.yaml index c34d3fb25fd94..ba83c329537ca 100644 --- a/recipes/bioconductor-mcbiclust/meta.yaml +++ b/recipes/bioconductor-mcbiclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "MCbiclust" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 975f96f64105c1969462273506b9d06e + md5: dd042cb41360eec094ff9596439d3aa6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mcbiclust", max_pin="x.x") }}' noarch: generic # Suggests: gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr, pander, devtools, testthat, GSVA requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-cluster - r-ggally @@ -32,10 +33,10 @@ requirements: - r-scales - r-wgcna run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-cluster - r-ggally diff --git a/recipes/bioconductor-mcsea/meta.yaml b/recipes/bioconductor-mcsea/meta.yaml index 8f97facbb1825..6e571eec95da3 100644 --- a/recipes/bioconductor-mcsea/meta.yaml +++ b/recipes/bioconductor-mcsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "mCSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91864cc204cc545d5bd60196c1176efd + md5: 8bac97f11934f91da5250521a7b26f75 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mcsea", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, BiocGenerics, BiocStyle, FlowSorted.Blood.450k, knitr, leukemiasEset, minfi, minfiData, rmarkdown, RUnit requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mcseadata >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mcseadata >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mcseadata >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mcseadata >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-mcseadata/meta.yaml b/recipes/bioconductor-mcseadata/meta.yaml index f8469dde6c5e9..08f1aea183985 100644 --- a/recipes/bioconductor-mcseadata/meta.yaml +++ b/recipes/bioconductor-mcseadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "mCSEAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43b69165fffc6652fc2df2395bd0b8e6 + md5: 11f8150e223a0e8d8fa5b9b8dedaa374 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mcseadata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230717 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mcseadata/post-link.sh b/recipes/bioconductor-mcseadata/post-link.sh index 2eeaf2308191f..eddebf7dac4c4 100644 --- a/recipes/bioconductor-mcseadata/post-link.sh +++ b/recipes/bioconductor-mcseadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mcseadata-1.20.1" +installBiocDataPackage.sh "mcseadata-1.22.0" diff --git a/recipes/bioconductor-mcsurvdata/meta.yaml b/recipes/bioconductor-mcsurvdata/meta.yaml index ec4f53953e076..07bb985fda8c3 100644 --- a/recipes/bioconductor-mcsurvdata/meta.yaml +++ b/recipes/bioconductor-mcsurvdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "mcsurvdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4e4b6fa4d49cfa4588d65cb3a22ab121 + md5: 0299258c7610f3675dc0b9f8e333eefa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mcsurvdata", max_pin="x.x") }}' noarch: generic -# Suggests: knitr +# Suggests: BiocStyle, knitr requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mcsurvdata/post-link.sh b/recipes/bioconductor-mcsurvdata/post-link.sh index f95e358811081..2585fbcb3d43f 100644 --- a/recipes/bioconductor-mcsurvdata/post-link.sh +++ b/recipes/bioconductor-mcsurvdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mcsurvdata-1.18.0" +installBiocDataPackage.sh "mcsurvdata-1.20.0" diff --git a/recipes/bioconductor-mdp/meta.yaml b/recipes/bioconductor-mdp/meta.yaml index b78f40966c9e2..b0c34a1dd0fdb 100644 --- a/recipes/bioconductor-mdp/meta.yaml +++ b/recipes/bioconductor-mdp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "mdp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2ffda81dd0c84bae56391e259a9b8e30 + md5: a947b52acd7f930a3babcdb4e429bb0c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mdp", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, fgsea, BiocManager requirements: diff --git a/recipes/bioconductor-mdqc/meta.yaml b/recipes/bioconductor-mdqc/meta.yaml index db49be2c8f742..1ffa27337522e 100644 --- a/recipes/bioconductor-mdqc/meta.yaml +++ b/recipes/bioconductor-mdqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "mdqc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b3ec385cc5a3e1239228514e209bcc3e + md5: a9dd8adf71b5fe15b4b5b444f0b43110 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mdqc", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-mdts/meta.yaml b/recipes/bioconductor-mdts/meta.yaml index d7b9e11c822c9..4f9602a0f22b3 100644 --- a/recipes/bioconductor-mdts/meta.yaml +++ b/recipes/bioconductor-mdts/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MDTS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c9c5c88b0658f84733f792cdd6bdaed + md5: a9ab8fa7a5e9ef7dcdb28fb553b895f6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mdts", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-stringr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-stringr test: diff --git a/recipes/bioconductor-meal/meta.yaml b/recipes/bioconductor-meal/meta.yaml index 247dfcfd6a427..3ab450a08d105 100644 --- a/recipes/bioconductor-meal/meta.yaml +++ b/recipes/bioconductor-meal/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "MEAL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9de73f065fd4e5bfad6f5b3d9aea5ea0 + md5: f157edf85ba036b17edb728a44e2e519 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-meal", max_pin="x.x") }}' noarch: generic # Suggests: testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData, BiocStyle, rmarkdown, brgedata requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-missmethyl >=1.34.0,<1.35.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-missmethyl >=1.36.0,<1.37.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-ggplot2 >=2.0.0' - r-isva @@ -40,17 +41,17 @@ requirements: - r-smartsva - r-vegan run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-missmethyl >=1.34.0,<1.35.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-missmethyl >=1.36.0,<1.37.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-ggplot2 >=2.0.0' - r-isva diff --git a/recipes/bioconductor-measurementerror.cor/meta.yaml b/recipes/bioconductor-measurementerror.cor/meta.yaml index 5a6ed80d42dd6..a008cdd80f4d1 100644 --- a/recipes/bioconductor-measurementerror.cor/meta.yaml +++ b/recipes/bioconductor-measurementerror.cor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "MeasurementError.cor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8d6f3c05b7e609ef2150c1bc1a294ea + md5: 7de3f5ca3749a7b1e80fdfa66204a252 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-measurementerror.cor", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-meat/meta.yaml b/recipes/bioconductor-meat/meta.yaml index 3043cdb47180e..084d2922cfced 100644 --- a/recipes/bioconductor-meat/meta.yaml +++ b/recipes/bioconductor-meat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "MEAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e3f19960d36b1330ef8aee3c8b0922fc + md5: ea3f3041f0bdfab3844cea85f8d28c9b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-meat", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown, rmarkdown, BiocStyle, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-watermelon >=2.6.0,<2.7.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-watermelon >=2.8.0,<2.9.0' - r-base - r-dplyr - 'r-dynamictreecut >=1.63' @@ -33,10 +34,10 @@ requirements: - r-stringr - r-tibble run: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-watermelon >=2.6.0,<2.7.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-watermelon >=2.8.0,<2.9.0' - r-base - r-dplyr - 'r-dynamictreecut >=1.63' diff --git a/recipes/bioconductor-meb/meta.yaml b/recipes/bioconductor-meb/meta.yaml index 74df08e06a995..fbe884a83a68b 100644 --- a/recipes/bioconductor-meb/meta.yaml +++ b/recipes/bioconductor-meb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MEB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d4d4b70c1d2127e1dd18241c6fabde2 + md5: b1785984524fee5b32976a5e768037d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-meb", max_pin="x.x") }}' noarch: generic # Suggests: knitr,rmarkdown,BiocStyle requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-wrswor run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-wrswor diff --git a/recipes/bioconductor-medicagocdf/meta.yaml b/recipes/bioconductor-medicagocdf/meta.yaml index f055eb8e01c78..4f18d4e92ad67 100644 --- a/recipes/bioconductor-medicagocdf/meta.yaml +++ b/recipes/bioconductor-medicagocdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "medicagocdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1fbb2e4c070344d18e65f1b3993867db build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-medicagocdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-medicagoprobe/meta.yaml b/recipes/bioconductor-medicagoprobe/meta.yaml index f508bc9f63561..64886de29099e 100644 --- a/recipes/bioconductor-medicagoprobe/meta.yaml +++ b/recipes/bioconductor-medicagoprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "medicagoprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 83b9887ad2ed26c704b0ca7115e5838d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-medicagoprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-medips/meta.yaml b/recipes/bioconductor-medips/meta.yaml index 314a6d555c7ca..fa842250f78ce 100644 --- a/recipes/bioconductor-medips/meta.yaml +++ b/recipes/bioconductor-medips/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "MEDIPS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f9d22ca90431583329f7bc0d04937b21 + md5: 088394b1864d37eba7ed1064a9d671e9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-medips", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, BiocStyle requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-gtools run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-gtools test: diff --git a/recipes/bioconductor-medipsdata/meta.yaml b/recipes/bioconductor-medipsdata/meta.yaml index 22526db86a800..898fea78b24ec 100644 --- a/recipes/bioconductor-medipsdata/meta.yaml +++ b/recipes/bioconductor-medipsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "MEDIPSData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d6d822abd5a2acc639cad1a270f03a2d + md5: 7b329ecedb2e9911b92ad669856abf2b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-medipsdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-medipsdata/post-link.sh b/recipes/bioconductor-medipsdata/post-link.sh index a62231fab4e43..82ae17809dfbd 100644 --- a/recipes/bioconductor-medipsdata/post-link.sh +++ b/recipes/bioconductor-medipsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "medipsdata-1.36.0" +installBiocDataPackage.sh "medipsdata-1.38.0" diff --git a/recipes/bioconductor-medme/meta.yaml b/recipes/bioconductor-medme/meta.yaml index 366e23083231d..83cc34d658330 100644 --- a/recipes/bioconductor-medme/meta.yaml +++ b/recipes/bioconductor-medme/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "MEDME" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b5459677fe2fd70028253a9a58f4caf5 + md5: 03868c2e2f04af9c9f33d48cc6abed08 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-medme", max_pin="x.x") }}' # Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-drc - r-mass - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-drc - r-mass diff --git a/recipes/bioconductor-meebodata/meta.yaml b/recipes/bioconductor-meebodata/meta.yaml index d31b64df4acf4..4f4e1ad5b8435 100644 --- a/recipes/bioconductor-meebodata/meta.yaml +++ b/recipes/bioconductor-meebodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "MEEBOdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0eb2ee76322ae64e44bb926769bd1f77 + md5: cd3b9bb8a918c9497903f6274f323904 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-meebodata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-meebodata/post-link.sh b/recipes/bioconductor-meebodata/post-link.sh index 7e37c76550466..f406ddac9857c 100644 --- a/recipes/bioconductor-meebodata/post-link.sh +++ b/recipes/bioconductor-meebodata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "meebodata-1.38.0" +installBiocDataPackage.sh "meebodata-1.40.0" diff --git a/recipes/bioconductor-megadepth/meta.yaml b/recipes/bioconductor-megadepth/meta.yaml index 6819b6c8c78ef..c3dc6063d66e7 100644 --- a/recipes/bioconductor-megadepth/meta.yaml +++ b/recipes/bioconductor-megadepth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "megadepth" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 51770a42690eedccaf6282e0b5dbdf61 + md5: 5fa04f9d4075030126388db419378304 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-megadepth", max_pin="x.x") }}' noarch: generic # Suggests: covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer, derfinder, GenomeInfoDb, tools, RefManageR, testthat # SystemRequirements: megadepth () requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-cmdfun - r-dplyr @@ -31,7 +32,7 @@ requirements: - r-readr - r-xfun run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-cmdfun - r-dplyr diff --git a/recipes/bioconductor-melissa/meta.yaml b/recipes/bioconductor-melissa/meta.yaml index 47c67940b57d9..c69b137991ec8 100644 --- a/recipes/bioconductor-melissa/meta.yaml +++ b/recipes/bioconductor-melissa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Melissa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1557389f567dcdd1cc017fc4bd688d16 + md5: 25f975650bec04b62c6e022b11cc33c6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-melissa", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-bprmeth >=1.26.0,<1.27.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-bprmeth >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-assertthat - r-base - r-cowplot @@ -39,9 +40,9 @@ requirements: - r-rocr - r-truncnorm run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-bprmeth >=1.26.0,<1.27.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-bprmeth >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-assertthat - r-base - r-cowplot diff --git a/recipes/bioconductor-memes/meta.yaml b/recipes/bioconductor-memes/meta.yaml index 7c654b09008a7..eb689687be72c 100644 --- a/recipes/bioconductor-memes/meta.yaml +++ b/recipes/bioconductor-memes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "memes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 637b0a3bf608e7dbdb5b909a53fb1815 + md5: c9b7baebb9608344040a4dc38a05dea3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-memes", max_pin="x.x") }}' noarch: generic # Suggests: cowplot, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Dmelanogaster.UCSC.dm6, forcats, testthat (>= 2.1.0), knitr, MotifDb, pheatmap, PMCMRplus, plyranges (>= 1.9.1), rmarkdown, covr # SystemRequirements: Meme Suite (v5.3.3 or above) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-universalmotif >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-universalmotif >=1.20.0,<1.21.0' - r-base - 'r-cmdfun >=1.0.2' - r-dplyr @@ -42,9 +43,9 @@ requirements: - r-usethis - r-xml2 run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-universalmotif >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-universalmotif >=1.20.0,<1.21.0' - r-base - 'r-cmdfun >=1.0.2' - r-dplyr diff --git a/recipes/bioconductor-merfishdata/meta.yaml b/recipes/bioconductor-merfishdata/meta.yaml index 7577ff46666b0..70f5bd162ef8c 100644 --- a/recipes/bioconductor-merfishdata/meta.yaml +++ b/recipes/bioconductor-merfishdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.1" %} {% set name = "MerfishData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d4e86b95520641c0d3f1b5c938d5a3b7 + md5: 05369f89c4e1a15bdab1ce5174facbe4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-merfishdata", max_pin="x.x") }}' noarch: generic -# Suggests: grid, ggplot2, ggpubr, knitr, rmarkdown, testthat, BiocStyle +# Suggests: grid, ggplot2, ggpubr, knitr, rmarkdown, testthat, BiocStyle, DropletUtils requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-bumpymatrix >=1.8.0,<1.9.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-bumpymatrix >=1.8.0,<1.9.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-merfishdata/post-link.sh b/recipes/bioconductor-merfishdata/post-link.sh index 96590c781dc87..d616f8e059879 100644 --- a/recipes/bioconductor-merfishdata/post-link.sh +++ b/recipes/bioconductor-merfishdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "merfishdata-1.2.0" +installBiocDataPackage.sh "merfishdata-1.4.1" diff --git a/recipes/bioconductor-mergeomics/meta.yaml b/recipes/bioconductor-mergeomics/meta.yaml index a8273f2a04cda..5284a10f7d961 100644 --- a/recipes/bioconductor-mergeomics/meta.yaml +++ b/recipes/bioconductor-mergeomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "Mergeomics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed07a8df123e4d35ec9671e2cad53bf5 + md5: 1b8f5bc8cf54fa99df988a83c71737d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mergeomics", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: diff --git a/recipes/bioconductor-meshdbi/meta.yaml b/recipes/bioconductor-meshdbi/meta.yaml index 2a2268ae1d56d..05e67cd414ef0 100644 --- a/recipes/bioconductor-meshdbi/meta.yaml +++ b/recipes/bioconductor-meshdbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "MeSHDbi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: acde95248b916ed0e3674a2d030c45b5 + md5: edb738bd5c18f7017ebd13bd0cce9d2f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-meshdbi", max_pin="x.x") }}' noarch: generic # Suggests: testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-rsqlite test: diff --git a/recipes/bioconductor-meshes/meta.yaml b/recipes/bioconductor-meshes/meta.yaml index c7227ce2fb5dc..860286dd24bc5 100644 --- a/recipes/bioconductor-meshes/meta.yaml +++ b/recipes/bioconductor-meshes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "meshes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f7b0ab25441510c48b40e9ab09a53615 + md5: 90be6eeeb3ced1146ddcba48e2ec6c6e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-meshes", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, prettydoc requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-meshdbi >=1.36.0,<1.37.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-meshdbi >=1.38.0,<1.39.0' - r-base - r-yulab.utils run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-meshdbi >=1.36.0,<1.37.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-meshdbi >=1.38.0,<1.39.0' - r-base - r-yulab.utils test: diff --git a/recipes/bioconductor-meshr/meta.yaml b/recipes/bioconductor-meshr/meta.yaml index b973725c15fa7..529a0bdbb3121 100644 --- a/recipes/bioconductor-meshr/meta.yaml +++ b/recipes/bioconductor-meshr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "meshr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7bcf4253b38df394c838c2cc477f84a9 + md5: 7809b970dabdb3c42112e6b3aad5b75b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-meshr", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-meshdbi >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-meshdbi >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fdrtool - r-knitr @@ -32,11 +33,11 @@ requirements: - r-rmarkdown - r-rsqlite run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-meshdbi >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-meshdbi >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fdrtool - r-knitr diff --git a/recipes/bioconductor-meskit/meta.yaml b/recipes/bioconductor-meskit/meta.yaml index efea8c2955c60..df270a05c0104 100644 --- a/recipes/bioconductor-meskit/meta.yaml +++ b/recipes/bioconductor-meskit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MesKit" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eac8c8557107d7d2efca76e50a999af0 + md5: 909ad92f34384c66c0e86f0f13ff7e71 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-meskit", max_pin="x.x") }}' noarch: generic # Suggests: shiny, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), org.Hs.eg.db, clusterProfiler, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'r-ape >=5.4.1' - r-base - r-circlize @@ -41,11 +42,11 @@ requirements: - r-rcolorbrewer - 'r-tidyr >=1.0.0' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'r-ape >=5.4.1' - r-base - r-circlize diff --git a/recipes/bioconductor-messina/meta.yaml b/recipes/bioconductor-messina/meta.yaml index 2a5a2a4501225..48739dc5c9b95 100644 --- a/recipes/bioconductor-messina/meta.yaml +++ b/recipes/bioconductor-messina/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "messina" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 62c9610704259aa1b9f838966beac394 + md5: ad9cfdec37597c8a312b49085f1ff124 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-messina", max_pin="x.x") }}' # Suggests: knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>= 2.22.0), BiocStyle requirements: host: diff --git a/recipes/bioconductor-metabcombiner/meta.yaml b/recipes/bioconductor-metabcombiner/meta.yaml index 7b6bcb0515d1d..9b9563bf04b9f 100644 --- a/recipes/bioconductor-metabcombiner/meta.yaml +++ b/recipes/bioconductor-metabcombiner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "metabCombiner" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb2078d2857b0824411b6d7942c469ef + md5: 9840a8f7cdc657e21d3ebc2a7b6b68b2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metabcombiner", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - 'r-dplyr >=1.0' @@ -31,7 +32,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - 'r-dplyr >=1.0' diff --git a/recipes/bioconductor-metabinr/meta.yaml b/recipes/bioconductor-metabinr/meta.yaml index c7e099f880000..67899dd2e1f85 100644 --- a/recipes/bioconductor-metabinr/meta.yaml +++ b/recipes/bioconductor-metabinr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "metabinR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 66c3ea5a3163579c070dde3a0a7fb1f7 + md5: 7080ae8eac49640aeae95bda1185ac7d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metabinr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, cvms, data.table, dplyr, ggplot2, gridExtra, knitr, R.utils, rmarkdown, sabre, spelling, testthat (>= 3.0.0) # SystemRequirements: Java (>= 8) diff --git a/recipes/bioconductor-metaboannotation/meta.yaml b/recipes/bioconductor-metaboannotation/meta.yaml index bcedfe552443b..4664b5262cd69 100644 --- a/recipes/bioconductor-metaboannotation/meta.yaml +++ b/recipes/bioconductor-metaboannotation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.1" %} {% set name = "MetaboAnnotation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ddd0682814407d9262bc9e82c223adb3 + md5: fee181fc1795a1e2bde1d1e551f1a45e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metaboannotation", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny, shinyjs, DT, AnnotationHub, microbenchmark, mzR +# Suggests: testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny, shinyjs, DT, microbenchmark, mzR requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-compounddb >=1.4.0,<1.5.0' - - 'bioconductor-metabocoreutils >=1.8.0,<1.9.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-compounddb >=1.6.0,<1.7.0' + - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-compounddb >=1.4.0,<1.5.0' - - 'bioconductor-metabocoreutils >=1.8.0,<1.9.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-compounddb >=1.6.0,<1.7.0' + - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-metabocoreutils/meta.yaml b/recipes/bioconductor-metabocoreutils/meta.yaml index 592a4adbde4b1..a73ae28540ebe 100644 --- a/recipes/bioconductor-metabocoreutils/meta.yaml +++ b/recipes/bioconductor-metabocoreutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MetaboCoreUtils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91404bfbcac731a6ee59e80d777e2148 + md5: e4b834af09aa89158b64b8586d4d15c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metabocoreutils", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - r-base test: commands: diff --git a/recipes/bioconductor-metaboliteidmapping/meta.yaml b/recipes/bioconductor-metaboliteidmapping/meta.yaml index d8785e941a169..e248f2cb8aadb 100644 --- a/recipes/bioconductor-metaboliteidmapping/meta.yaml +++ b/recipes/bioconductor-metaboliteidmapping/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "metaboliteIDmapping" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: bd78ec373ce90fac1a10d2c64c462e77 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metaboliteidmapping", max_pin="x.x") }}' noarch: generic # Suggests: magrittr, graphite, dplyr, tidyr, tibble, rappdirs, XML, readxl, stringr, utils, knitr, sets, R.utils, readr, conflicted, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-metabolomicsworkbenchr/meta.yaml b/recipes/bioconductor-metabolomicsworkbenchr/meta.yaml index e85a7ad245869..d4c21164ee6d0 100644 --- a/recipes/bioconductor-metabolomicsworkbenchr/meta.yaml +++ b/recipes/bioconductor-metabolomicsworkbenchr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "metabolomicsWorkbenchR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5501c9f3300368e1e579ddf3eb89b678 + md5: 7e8485177f5ad463ff6a0f6e573e74fb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metabolomicsworkbenchr", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, covr, knitr, HDF5Array, rmarkdown, structToolbox, testthat, pmp, grid, png +# Suggests: BiocStyle, covr, knitr, HDF5Array, httptest, rmarkdown, structToolbox, testthat, pmp, grid, png requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-struct >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-struct >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-httr - r-jsonlite run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-struct >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-struct >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-httr diff --git a/recipes/bioconductor-metabomxtr/meta.yaml b/recipes/bioconductor-metabomxtr/meta.yaml index 67917cf5d5f8e..1ab86aa0f3f66 100644 --- a/recipes/bioconductor-metabomxtr/meta.yaml +++ b/recipes/bioconductor-metabomxtr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "metabomxtr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9b3776d7ca5080f4c33fffbf74603ca8 + md5: ec247e3fe8099096d1bfcc8fff93f08d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metabomxtr", max_pin="x.x") }}' noarch: generic # Suggests: xtable, reshape2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-formula - r-ggplot2 - r-optimx - r-plyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-formula - r-ggplot2 diff --git a/recipes/bioconductor-metabosignal/meta.yaml b/recipes/bioconductor-metabosignal/meta.yaml index d737fef136bbb..01f312d812830 100644 --- a/recipes/bioconductor-metabosignal/meta.yaml +++ b/recipes/bioconductor-metabosignal/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.1" %} +{% set version = "1.32.0" %} {% set name = "MetaboSignal" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ff7b743e46475cfa8a60e92bcea0986 + md5: a8f1dc09626a1881461f987e726078bf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metabosignal", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0' - - 'bioconductor-hpar >=1.42.0,<1.43.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-mwastools >=1.24.0,<1.25.0' - - 'bioconductor-mygene >=1.36.0,<1.37.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-hpar >=1.44.0,<1.45.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-mwastools >=1.26.0,<1.27.0' + - 'bioconductor-mygene >=1.38.0,<1.39.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-igraph - r-rcurl run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0' - - 'bioconductor-hpar >=1.42.0,<1.43.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-mwastools >=1.24.0,<1.25.0' - - 'bioconductor-mygene >=1.36.0,<1.37.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-hpar >=1.44.0,<1.45.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-mwastools >=1.26.0,<1.27.0' + - 'bioconductor-mygene >=1.38.0,<1.39.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-igraph - r-rcurl diff --git a/recipes/bioconductor-metacca/meta.yaml b/recipes/bioconductor-metacca/meta.yaml index 4f5e4e50e1ea6..851175efd2c07 100644 --- a/recipes/bioconductor-metacca/meta.yaml +++ b/recipes/bioconductor-metacca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "metaCCA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94d27eb69649e28b07201192f1022a8e + md5: d5be58f253912b275964a681a508234d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metacca", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: diff --git a/recipes/bioconductor-metacyto/meta.yaml b/recipes/bioconductor-metacyto/meta.yaml index b5da01927e8db..e7c7260f307a2 100644 --- a/recipes/bioconductor-metacyto/meta.yaml +++ b/recipes/bioconductor-metacyto/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "MetaCyto" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 22428db1b2332f3d7fbde4f03fc5ffed + md5: 0cd04a831a226a35bdeb881c03d30193 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metacyto", max_pin="x.x") }}' noarch: generic # Suggests: knitr, dplyr, rmarkdown requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowsom >=2.8.0,<2.9.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowsom >=2.10.0,<2.11.0' - r-base - r-cluster - r-fastcluster @@ -30,8 +31,8 @@ requirements: - r-metafor - 'r-tidyr >=0.7' run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowsom >=2.8.0,<2.9.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowsom >=2.10.0,<2.11.0' - r-base - r-cluster - r-fastcluster diff --git a/recipes/bioconductor-metagene2/meta.yaml b/recipes/bioconductor-metagene2/meta.yaml index 9fdcbd6880db6..7b828dbbaba57 100644 --- a/recipes/bioconductor-metagene2/meta.yaml +++ b/recipes/bioconductor-metagene2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "metagene2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7b21feb21c30995a96cbec500bb9148a + md5: adef0ffd2a7cec30870a2b66eb2cb4f9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metagene2", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-dplyr @@ -37,13 +38,13 @@ requirements: - 'r-r6 >=2.0' - r-reshape2 run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-metagenomeseq/meta.yaml b/recipes/bioconductor-metagenomeseq/meta.yaml index f415ce2a68608..73137c6fc52d9 100644 --- a/recipes/bioconductor-metagenomeseq/meta.yaml +++ b/recipes/bioconductor-metagenomeseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.43.0" %} {% set name = "metagenomeSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 639ed9fe16c0bf887c363a66a1e8e5eb + md5: ea0139abb9cbcda1f445b3527e621345 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metagenomeseq", max_pin="x.x") }}' noarch: generic # Suggests: annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay, IHW requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-wrench >=1.18.0,<1.19.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-wrench >=1.20.0,<1.21.0' - r-base - r-foreach - r-glmnet @@ -32,9 +33,9 @@ requirements: - r-matrixstats - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-wrench >=1.18.0,<1.19.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-wrench >=1.20.0,<1.21.0' - r-base - r-foreach - r-glmnet diff --git a/recipes/bioconductor-metagxbreast/meta.yaml b/recipes/bioconductor-metagxbreast/meta.yaml index c75e7b63ed502..969e8d8c535ba 100644 --- a/recipes/bioconductor-metagxbreast/meta.yaml +++ b/recipes/bioconductor-metagxbreast/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MetaGxBreast" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 38b605d1c36990f9ae722ed9391afb75 + md5: e711302482bca1429de5fe2e5276c788 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metagxbreast", max_pin="x.x") }}' noarch: generic # Suggests: testthat, xtable, tinytex requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-lattice run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-lattice - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-metagxbreast/post-link.sh b/recipes/bioconductor-metagxbreast/post-link.sh index f778c7b5da540..e04b480c25fb1 100644 --- a/recipes/bioconductor-metagxbreast/post-link.sh +++ b/recipes/bioconductor-metagxbreast/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "metagxbreast-1.20.0" +installBiocDataPackage.sh "metagxbreast-1.22.0" diff --git a/recipes/bioconductor-metagxovarian/meta.yaml b/recipes/bioconductor-metagxovarian/meta.yaml index 7105fb8cdc088..a6cf76c8d62c9 100644 --- a/recipes/bioconductor-metagxovarian/meta.yaml +++ b/recipes/bioconductor-metagxovarian/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MetaGxOvarian" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 180366821492879a0fc25f4b4117b20f + md5: f76dc6c912d3a8936f81509ba6559286 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metagxovarian", max_pin="x.x") }}' noarch: generic # Suggests: testthat, xtable, rmarkdown, knitr, BiocStyle, markdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-lattice run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-lattice - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-metagxovarian/post-link.sh b/recipes/bioconductor-metagxovarian/post-link.sh index d364690daf944..a592b878de955 100644 --- a/recipes/bioconductor-metagxovarian/post-link.sh +++ b/recipes/bioconductor-metagxovarian/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "metagxovarian-1.20.0" +installBiocDataPackage.sh "metagxovarian-1.22.0" diff --git a/recipes/bioconductor-metagxpancreas/meta.yaml b/recipes/bioconductor-metagxpancreas/meta.yaml index 2bb9483835525..0486ab5f27c80 100644 --- a/recipes/bioconductor-metagxpancreas/meta.yaml +++ b/recipes/bioconductor-metagxpancreas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MetaGxPancreas" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 837617be22e87ee2716a5bd6888bb204 + md5: 0c1764dc18a9a180b2121649c98a26a1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metagxpancreas", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle, rmarkdown, markdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-metagxpancreas/post-link.sh b/recipes/bioconductor-metagxpancreas/post-link.sh index b2264e376b686..325b7237840e4 100644 --- a/recipes/bioconductor-metagxpancreas/post-link.sh +++ b/recipes/bioconductor-metagxpancreas/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "metagxpancreas-1.20.0" +installBiocDataPackage.sh "metagxpancreas-1.22.0" diff --git a/recipes/bioconductor-metahdep/build_failure.osx-64.yaml b/recipes/bioconductor-metahdep/build_failure.osx-64.yaml index a39539fdd7101..8f5e1414fd2f4 100644 --- a/recipes/bioconductor-metahdep/build_failure.osx-64.yaml +++ b/recipes/bioconductor-metahdep/build_failure.osx-64.yaml @@ -1,4 +1,4 @@ -recipe_sha: 2edfbb98f63d48d98994d4c4daecfd4678c9619a700efddca7297420a69e54f1 # The commit at which this recipe failed to build. +recipe_sha: 7d681cfa3280b3e2180df68fba6a82a10dab63dfb65f81b7020b5d2b80a134a9 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran @@ -102,3 +102,7 @@ log: |- raise subprocess.CalledProcessError(proc.returncode, _args) subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-metahdep_1689833451644/work/conda_build.sh']' returned non-zero exit status 1. # Last 100 lines of the build log. +reason: |- + 19:17:50 BIOCONDA INFO (ERR) metahdep.c:471:79: error: incompatible pointer to integer conversion passing 'const char *' to parameter of type 'char' [-Wint-conversion] +category: |- + compiler error diff --git a/recipes/bioconductor-metahdep/meta.yaml b/recipes/bioconductor-metahdep/meta.yaml index 42b9943246328..c8dc23a250052 100644 --- a/recipes/bioconductor-metahdep/meta.yaml +++ b/recipes/bioconductor-metahdep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "metahdep" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3a49994338fecd947fd4e144745b4a39 + md5: 578b66621982372185989aa8559f8293 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metahdep", max_pin="x.x") }}' # Suggests: affyPLM requirements: host: diff --git a/recipes/bioconductor-metams/meta.yaml b/recipes/bioconductor-metams/meta.yaml index 0551920c729ad..af42016d642d6 100644 --- a/recipes/bioconductor-metams/meta.yaml +++ b/recipes/bioconductor-metams/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "metaMS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d64ce34b47d681fb1064f1ff93f320ed + md5: c26507515ab859aa42dbea4acc8cacc3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metams", max_pin="x.x") }}' noarch: generic # Suggests: metaMSdata, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-matrix - r-robustbase run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-matrix - r-robustbase diff --git a/recipes/bioconductor-metamsdata/meta.yaml b/recipes/bioconductor-metamsdata/meta.yaml index 7d1d70162c264..b6730e4cfe2c3 100644 --- a/recipes/bioconductor-metamsdata/meta.yaml +++ b/recipes/bioconductor-metamsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "metaMSdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c4408ceda2098402daaa6c94bbd3768 + md5: aa7ca09c8f43104cb85f69fda0a1fc1a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metamsdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-metamsdata/post-link.sh b/recipes/bioconductor-metamsdata/post-link.sh index c93f33a23616f..6e2a1a56a7ab7 100644 --- a/recipes/bioconductor-metamsdata/post-link.sh +++ b/recipes/bioconductor-metamsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "metamsdata-1.36.0" +installBiocDataPackage.sh "metamsdata-1.38.0" diff --git a/recipes/bioconductor-metaneighbor/meta.yaml b/recipes/bioconductor-metaneighbor/meta.yaml index 67b3e6cb1a37b..cdd31dff18139 100644 --- a/recipes/bioconductor-metaneighbor/meta.yaml +++ b/recipes/bioconductor-metaneighbor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MetaNeighbor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d8a02ccc2353f4a830b1a600e6cb070 + md5: 4b42a5bac6ac46bdff32c5cce84e448d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metaneighbor", max_pin="x.x") }}' noarch: generic # Suggests: knitr (>= 1.17), rmarkdown (>= 1.6), testthat (>= 1.0.2), UpSetR requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-beanplot >=1.2' - r-dplyr @@ -35,8 +36,8 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-beanplot >=1.2' - r-dplyr diff --git a/recipes/bioconductor-metaphor/meta.yaml b/recipes/bioconductor-metaphor/meta.yaml index fb3841cdd3fe7..ee6d1a43d5289 100644 --- a/recipes/bioconductor-metaphor/meta.yaml +++ b/recipes/bioconductor-metaphor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "MetaPhOR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd33f344dadc728d1802df7f7596818b + md5: 311e286126427130d127b23a77b3b6f4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metaphor", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, kableExtra # SystemRequirements: Cytoscape (>= 3.9.0) for the cytoPath() examples requirements: host: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-ggplot2 - r-ggrepel @@ -31,8 +32,8 @@ requirements: - r-recordlinkage - r-stringr run: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-metapod/meta.yaml b/recipes/bioconductor-metapod/meta.yaml index 81f246e9c0d13..e354996b693d3 100644 --- a/recipes/bioconductor-metapod/meta.yaml +++ b/recipes/bioconductor-metapod/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "metapod" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ed81a84b379501af983bb5c25262b63f + md5: 49bf3f5df3f99c0d4068224a8f51eacc build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metapod", max_pin="x.x") }}' # Suggests: testthat, knitr, BiocStyle, rmarkdown # SystemRequirements: C++11 requirements: diff --git a/recipes/bioconductor-metapone/meta.yaml b/recipes/bioconductor-metapone/meta.yaml index f011d1814093c..491d13b08b3c4 100644 --- a/recipes/bioconductor-metapone/meta.yaml +++ b/recipes/bioconductor-metapone/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "metapone" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9a346aa647de2ac05f8f3494c5fa9c09 + md5: d53938772148968f88fab10130dbc905 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metapone", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' - r-base - r-fdrtool - r-fields @@ -30,8 +31,8 @@ requirements: - r-ggrepel - r-markdown run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' - r-base - r-fdrtool - r-fields diff --git a/recipes/bioconductor-metascope/meta.yaml b/recipes/bioconductor-metascope/meta.yaml index b0a892aca1284..4e41830dd7494 100644 --- a/recipes/bioconductor-metascope/meta.yaml +++ b/recipes/bioconductor-metascope/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "MetaScope" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aef272f5f78bc787f42bd9c47b923cfb + md5: 3e9dbacc12fa3bd332773ffa95325f0b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metascope", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, biomformat, knitr, lintr, plyr, rmarkdown, Rsubread, spelling, sys, testthat, usethis +# Suggests: BiocStyle, biomformat, knitr, lintr, plyr, R.utils, rmarkdown, Rsubread, spelling, sys, testthat, usethis requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rbowtie2 >=2.6.0,<2.7.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr @@ -35,20 +36,19 @@ requirements: - r-magrittr - r-matrix - r-qlcmatrix - - r-r.utils - r-readr - r-rlang - r-stringr - r-taxize - r-tidyr run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rbowtie2 >=2.6.0,<2.7.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr @@ -56,14 +56,13 @@ requirements: - r-magrittr - r-matrix - r-qlcmatrix - - r-r.utils - r-readr - r-rlang - r-stringr - r-taxize - r-tidyr - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' @@ -71,6 +70,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data' - description: 'This package contains tools and methods for preprocessing microbiome data. Functionality includes library generation, demultiplexing, alignment, and microbe identification. It is partly an R translation of the PathoScope 2.0 pipeline.' + description: 'This package contains tools and methods for preprocessing microbiome data. Functionality includes library generation, demultiplexing, alignment, and microbe identification. It is in part an R translation of the PathoScope 2.0 pipeline.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-metascope/post-link.sh b/recipes/bioconductor-metascope/post-link.sh index f94aeef0d0954..e3bd6b90fb0e0 100644 --- a/recipes/bioconductor-metascope/post-link.sh +++ b/recipes/bioconductor-metascope/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "metascope-1.0.0" +installBiocDataPackage.sh "metascope-1.2.0" diff --git a/recipes/bioconductor-metaseq/meta.yaml b/recipes/bioconductor-metaseq/meta.yaml index c229f390a9ea5..564aeea18d8a0 100644 --- a/recipes/bioconductor-metaseq/meta.yaml +++ b/recipes/bioconductor-metaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "metaSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7805af79576c88c0861543ebb4b731a0 + md5: 8c3ee60501395cc86ecda6817d0d5439 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metaseq", max_pin="x.x") }}' requirements: host: - - 'bioconductor-noiseq >=2.44.0,<2.45.0' + - 'bioconductor-noiseq >=2.46.0,<2.47.0' - r-base - r-rcpp - r-snow - libblas - liblapack run: - - 'bioconductor-noiseq >=2.44.0,<2.45.0' + - 'bioconductor-noiseq >=2.46.0,<2.47.0' - r-base - r-rcpp - r-snow diff --git a/recipes/bioconductor-metcirc/meta.yaml b/recipes/bioconductor-metcirc/meta.yaml index 89b5bb1a95cba..c70232ee98cfa 100644 --- a/recipes/bioconductor-metcirc/meta.yaml +++ b/recipes/bioconductor-metcirc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "MetCirc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 420d7e30089b00444306978ccac47184 + md5: c21a385245acf6911f5c762093ea6e0b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metcirc", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, graphics (>= 3.5), grDevices (>= 3.5), knitr (>= 1.11), testthat (>= 2.2.1) requirements: host: - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - 'r-amap >=0.8' - r-base - 'r-circlize >=0.3.9' @@ -31,9 +32,9 @@ requirements: - 'r-scales >=0.3.0' - 'r-shiny >=1.0.0' run: - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - 'r-amap >=0.8' - r-base - 'r-circlize >=0.3.9' diff --git a/recipes/bioconductor-methimpute/meta.yaml b/recipes/bioconductor-methimpute/meta.yaml index 110306a836ace..65d687e154683 100644 --- a/recipes/bioconductor-methimpute/meta.yaml +++ b/recipes/bioconductor-methimpute/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "methimpute" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: edb7a53f8b002f4b0d135381af736420 + md5: 7b2a598d7391c33c4ba82639616077e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methimpute", max_pin="x.x") }}' # Suggests: knitr, BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-data.table - r-ggplot2 @@ -33,10 +34,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-methinheritsim/meta.yaml b/recipes/bioconductor-methinheritsim/meta.yaml index e17311bc74346..d131c38563f89 100644 --- a/recipes/bioconductor-methinheritsim/meta.yaml +++ b/recipes/bioconductor-methinheritsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "methInheritSim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e84fe101c5de73da2e8764b71ec3e467 + md5: c695628dcb686ee7e6a3f4ee134481ff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methinheritsim", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, RUnit, methylInheritance requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-methylkit >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-methylkit >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-msm run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-methylkit >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-methylkit >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-msm test: diff --git a/recipes/bioconductor-methped/meta.yaml b/recipes/bioconductor-methped/meta.yaml index 1d52a997eacd3..ab47c7a890944 100644 --- a/recipes/bioconductor-methped/meta.yaml +++ b/recipes/bioconductor-methped/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "MethPed" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b811e3dcc16dd85f75fc300602d99845 + md5: 57b633da5d8548342b0a2071efe3c04d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methped", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, markdown, impute requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-randomforest run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-randomforest test: diff --git a/recipes/bioconductor-methreg/meta.yaml b/recipes/bioconductor-methreg/meta.yaml index 59fcc9250f4b5..639722859e243 100644 --- a/recipes/bioconductor-methreg/meta.yaml +++ b/recipes/bioconductor-methreg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MethReg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 33bbfd93bde253c973cc8324e4475bde + md5: 0c092ea7b8883b6c125e64e16030bca6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methreg", max_pin="x.x") }}' noarch: generic -# Suggests: rmarkdown, BiocStyle, testthat (>= 2.1.0), parallel, downloader, R.utils, doParallel, reshape2, JASPAR2022, TFBSTools, motifmatchr, matrixStats, biomaRt, dorothea, viper, stageR, BiocFileCache, png, htmltools, knitr, jpeg, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19 +# Suggests: rmarkdown, BiocStyle, testthat (>= 2.1.0), parallel, downloader, R.utils, doParallel, reshape2, JASPAR2022, TFBSTools, motifmatchr, matrixStats, biomaRt, dorothea, viper, stageR, BiocFileCache, png, htmltools, knitr, jpeg, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, openxlsx, data.table, downloader requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sesame >=1.18.0,<1.19.0' - - 'bioconductor-sesamedata >=1.18.0,<1.19.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sesame >=1.20.0,<1.21.0' + - 'bioconductor-sesamedata >=1.20.0,<1.21.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -46,15 +47,15 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sesame >=1.18.0,<1.19.0' - - 'bioconductor-sesamedata >=1.18.0,<1.19.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sesame >=1.20.0,<1.21.0' + - 'bioconductor-sesamedata >=1.20.0,<1.21.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-methrix/meta.yaml b/recipes/bioconductor-methrix/meta.yaml index 5f837225e9e2f..bd7c11532203f 100644 --- a/recipes/bioconductor-methrix/meta.yaml +++ b/recipes/bioconductor-methrix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "methrix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8e0de73ac035291e3328e4157b193997 + md5: 7bdda59fc802fc09d10ca9a4916cfe94 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methrix", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) +# Suggests: knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, BSgenome.Hsapiens.UCSC.hg19, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-data.table >=1.12.4' - r-ggplot2 - r-matrixstats run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-data.table >=1.12.4' - r-ggplot2 diff --git a/recipes/bioconductor-methtargetedngs/meta.yaml b/recipes/bioconductor-methtargetedngs/meta.yaml index 6193170be0067..fb49f0aa6445e 100644 --- a/recipes/bioconductor-methtargetedngs/meta.yaml +++ b/recipes/bioconductor-methtargetedngs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "MethTargetedNGS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c6777e1517295425bd1b7e6763d58793 + md5: 0bce9edc9682a9ca23653409301d7225 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methtargetedngs", max_pin="x.x") }}' noarch: generic # SystemRequirements: HMMER3 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-gplots - r-seqinr - r-stringr - 'hmmer >=3' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-gplots - r-seqinr diff --git a/recipes/bioconductor-methylaid/meta.yaml b/recipes/bioconductor-methylaid/meta.yaml index 11cefa78cfba2..d6bdffb88c0f7 100644 --- a/recipes/bioconductor-methylaid/meta.yaml +++ b/recipes/bioconductor-methylaid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "MethylAid" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8f44cf538be4d026ac332365de6063c + md5: 8e5139726d6384208be410a794ba6388 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylaid", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-gridbase @@ -34,11 +35,11 @@ requirements: - r-rcolorbrewer - r-shiny run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-gridbase diff --git a/recipes/bioconductor-methylaiddata/meta.yaml b/recipes/bioconductor-methylaiddata/meta.yaml index 2c6f2f3bc4f90..9d93dbaa10899 100644 --- a/recipes/bioconductor-methylaiddata/meta.yaml +++ b/recipes/bioconductor-methylaiddata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "MethylAidData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43ab55538e535cab63f2594898cfbda4 + md5: 95cc72b436067e4a8046564381101e04 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylaiddata", max_pin="x.x") }}' noarch: generic # Suggests: BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC requirements: host: - - 'bioconductor-methylaid >=1.34.0,<1.35.0' + - 'bioconductor-methylaid >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-methylaid >=1.34.0,<1.35.0' + - 'bioconductor-methylaid >=1.36.0,<1.37.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-methylaiddata/post-link.sh b/recipes/bioconductor-methylaiddata/post-link.sh index bfc7879f10589..05ddd59e85e4c 100644 --- a/recipes/bioconductor-methylaiddata/post-link.sh +++ b/recipes/bioconductor-methylaiddata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "methylaiddata-1.32.0" +installBiocDataPackage.sh "methylaiddata-1.34.0" diff --git a/recipes/bioconductor-methylcc/meta.yaml b/recipes/bioconductor-methylcc/meta.yaml index ef779d73a8837..55e496807a54b 100644 --- a/recipes/bioconductor-methylcc/meta.yaml +++ b/recipes/bioconductor-methylcc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "methylCC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f599be86fb37a9d8f95f7e3113facccb + md5: 77566e7338f615ca5305d6e00465908b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylcc", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-flowsorted.blood.450k >=1.38.0,<1.39.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-flowsorted.blood.450k >=1.40.0,<1.41.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-magrittr - r-quadprog run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-flowsorted.blood.450k >=1.38.0,<1.39.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-flowsorted.blood.450k >=1.40.0,<1.41.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-magrittr diff --git a/recipes/bioconductor-methylclock/meta.yaml b/recipes/bioconductor-methylclock/meta.yaml index 981a365aa2e6a..16024462c189f 100644 --- a/recipes/bioconductor-methylclock/meta.yaml +++ b/recipes/bioconductor-methylclock/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "methylclock" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 770a4eeb0cb8da839fe57d6a42e317c3 + md5: b6151e23d6086f38d6489dcc277c81c9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylclock", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, GEOquery, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-methylclockdata >=1.8.0,<1.9.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-planet >=1.8.0,<1.9.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-methylclockdata >=1.10.0,<1.11.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-planet >=1.10.0,<1.11.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-devtools - r-dplyr @@ -45,13 +46,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-methylclockdata >=1.8.0,<1.9.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-planet >=1.8.0,<1.9.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-methylclockdata >=1.10.0,<1.11.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-planet >=1.10.0,<1.11.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-devtools - r-dplyr diff --git a/recipes/bioconductor-methylclockdata/meta.yaml b/recipes/bioconductor-methylclockdata/meta.yaml index 0f81c2bd0f5c3..771be08cf1782 100644 --- a/recipes/bioconductor-methylclockdata/meta.yaml +++ b/recipes/bioconductor-methylclockdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "methylclockData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c211da6ed8d39ba8cee6d4d630691bad + md5: 633d9cc6c028025090e12004484fada1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylclockdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-experimenthubdata >=1.26.0,<1.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-experimenthubdata >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-experimenthubdata >=1.26.0,<1.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-experimenthubdata >=1.28.0,<1.29.0' - r-base - curl - - bioconductor-data-packages>=20230717 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-methylclockdata/post-link.sh b/recipes/bioconductor-methylclockdata/post-link.sh index 744cc5a5c07e4..16f98ea792eb3 100644 --- a/recipes/bioconductor-methylclockdata/post-link.sh +++ b/recipes/bioconductor-methylclockdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "methylclockdata-1.8.1" +installBiocDataPackage.sh "methylclockdata-1.10.0" diff --git a/recipes/bioconductor-methylgsa/meta.yaml b/recipes/bioconductor-methylgsa/meta.yaml index d10d0d4ad8fc6..9858e7286e22e 100644 --- a/recipes/bioconductor-methylgsa/meta.yaml +++ b/recipes/bioconductor-methylgsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "methylGSA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c9287c45585ad0f59e2dc67c738a787e + md5: e802fab6abc1a9bac64bc36dd588c19d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylgsa", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, enrichplot requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-missmethyl >=1.34.0,<1.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' + - 'bioconductor-missmethyl >=1.36.0,<1.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - r-base - r-ggplot2 - r-robustrankaggreg - r-shiny - r-stringr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-missmethyl >=1.34.0,<1.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' + - 'bioconductor-missmethyl >=1.36.0,<1.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - r-base - r-ggplot2 - r-robustrankaggreg diff --git a/recipes/bioconductor-methylinheritance/meta.yaml b/recipes/bioconductor-methylinheritance/meta.yaml index 6041af6f4b285..c3fcbcbda2b35 100644 --- a/recipes/bioconductor-methylinheritance/meta.yaml +++ b/recipes/bioconductor-methylinheritance/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "methylInheritance" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed652748487f26ee71332e443e3f3a80 + md5: 0242605800daea10c810fa356cb2cf0c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylinheritance", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-methylkit >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-methylkit >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-gridextra - r-rebus run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-methylkit >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-methylkit >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-gridextra diff --git a/recipes/bioconductor-methylkit/meta.yaml b/recipes/bioconductor-methylkit/meta.yaml index 7582763615f42..05fa1c56fc358 100644 --- a/recipes/bioconductor-methylkit/meta.yaml +++ b/recipes/bioconductor-methylkit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "methylKit" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37ac13b36487394b54e843d5f0b1c4d3 + md5: 5e21ca2558b439a2f542492eeec0f99d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylkit", max_pin="x.x") }}' # Suggests: testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager # SystemRequirements: GNU make requirements: host: - - 'bioconductor-fastseg >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-fastseg >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - 'r-data.table >=1.9.6' - r-emdbook @@ -44,17 +45,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-fastseg >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-fastseg >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - 'r-data.table >=1.9.6' - r-emdbook diff --git a/recipes/bioconductor-methylmix/meta.yaml b/recipes/bioconductor-methylmix/meta.yaml index 83ed80dadb3c8..80533398aa225 100644 --- a/recipes/bioconductor-methylmix/meta.yaml +++ b/recipes/bioconductor-methylmix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "MethylMix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 752979d4cb82fa14d6408b323f93005f + md5: 4a716254f6aff8e65daf63cdcd939704 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylmix", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-data.table - r-digest @@ -33,8 +34,8 @@ requirements: - r-rcurl - r-rpmm run: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-data.table - r-digest diff --git a/recipes/bioconductor-methylmnm/meta.yaml b/recipes/bioconductor-methylmnm/meta.yaml index 233e752251688..86b480b3cdd61 100644 --- a/recipes/bioconductor-methylmnm/meta.yaml +++ b/recipes/bioconductor-methylmnm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "methylMnM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dfc25779d379687166c7a894b52086eb + md5: 3d6c83c4fa30daea5b1c91e70f67c6b5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylmnm", max_pin="x.x") }}' requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - r-statmod - libblas - liblapack run: - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - r-statmod build: diff --git a/recipes/bioconductor-methylpipe/meta.yaml b/recipes/bioconductor-methylpipe/meta.yaml index d49eb3e1ee37f..fe35aeaa5f55b 100644 --- a/recipes/bioconductor-methylpipe/meta.yaml +++ b/recipes/bioconductor-methylpipe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.1" %} +{% set version = "1.36.0" %} {% set name = "methylPipe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,43 +11,44 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9fc26ce4cc91e60ef63712f165615294 + md5: bd41f308a3d5e58c4e05ce38c28f17f9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylpipe", max_pin="x.x") }}' # Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-gplots - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-gplots diff --git a/recipes/bioconductor-methylscaper/meta.yaml b/recipes/bioconductor-methylscaper/meta.yaml index 9ccf2ccb044a2..2dd87a797efc1 100644 --- a/recipes/bioconductor-methylscaper/meta.yaml +++ b/recipes/bioconductor-methylscaper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.4" %} +{% set version = "1.10.0" %} {% set name = "methylscaper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c2bae24f7f0fd7284a2faf5f6fea4f09 + md5: 0fae72e2aac98ec4a55d8aa4343039ba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylscaper", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, devtools, R.utils requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-rfast @@ -33,9 +34,9 @@ requirements: - r-shinyfiles - r-shinyjs run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-rfast diff --git a/recipes/bioconductor-methylseekr/meta.yaml b/recipes/bioconductor-methylseekr/meta.yaml index 4c02b0e12be43..49c54a3395fbc 100644 --- a/recipes/bioconductor-methylseekr/meta.yaml +++ b/recipes/bioconductor-methylseekr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "MethylSeekR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9caa87128143195fc74e45aea4c58142 + md5: 02bba9cfe7502e55a26e0ac76ba63457 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylseekr", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg18 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - 'r-mhsmm >=0.4.4' run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - 'r-mhsmm >=0.4.4' test: diff --git a/recipes/bioconductor-methylseqdata/meta.yaml b/recipes/bioconductor-methylseqdata/meta.yaml index 145e934653d1d..136355ee746c8 100644 --- a/recipes/bioconductor-methylseqdata/meta.yaml +++ b/recipes/bioconductor-methylseqdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MethylSeqData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d1a6bd69401032cbdba32519c02fdf4c + md5: ded280784f55a6ebec42069160de26ad build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylseqdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocFileCache, BiocStyle, data.table, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-methylseqdata/post-link.sh b/recipes/bioconductor-methylseqdata/post-link.sh index 7de3f110ab6e7..a095ba9151fb9 100644 --- a/recipes/bioconductor-methylseqdata/post-link.sh +++ b/recipes/bioconductor-methylseqdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "methylseqdata-1.10.0" +installBiocDataPackage.sh "methylseqdata-1.12.0" diff --git a/recipes/bioconductor-methylumi/meta.yaml b/recipes/bioconductor-methylumi/meta.yaml index 422e651866f92..52c8312d6006e 100644 --- a/recipes/bioconductor-methylumi/meta.yaml +++ b/recipes/bioconductor-methylumi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "methylumi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 19a426ce620cab5722a42b3ab54c3ac7 + md5: eb3792c8c9c2a778cf41e9bb7b95232b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylumi", max_pin="x.x") }}' noarch: generic # Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-fdb.infiniummethylation.hg19 >=2.2.0,<2.3.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-lattice @@ -42,20 +43,20 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-fdb.infiniummethylation.hg19 >=2.2.0,<2.3.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-lattice diff --git a/recipes/bioconductor-metid/meta.yaml b/recipes/bioconductor-metid/meta.yaml index 0fc4c8446b6e2..3b7cbc31f2086 100644 --- a/recipes/bioconductor-metid/meta.yaml +++ b/recipes/bioconductor-metid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "MetID" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80066250bcfc764f96ff4f3d3aed3154 + md5: 873920da0ab3c4e6a3bcd9e580097b86 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metid", max_pin="x.x") }}' noarch: generic # Suggests: knitr (>= 1.19), rmarkdown (>= 1.8) requirements: host: - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - 'r-devtools >=1.13.0' - 'r-igraph >=1.2.1' - 'r-matrix >=1.2-12' - 'r-stringr >=1.3.0' run: - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - 'r-devtools >=1.13.0' - 'r-igraph >=1.2.1' diff --git a/recipes/bioconductor-metnet/meta.yaml b/recipes/bioconductor-metnet/meta.yaml index e1de4c58763cb..78ede31d4fedc 100644 --- a/recipes/bioconductor-metnet/meta.yaml +++ b/recipes/bioconductor-metnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "MetNet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67d052b6ddc20ce093c5205bd21113c4 + md5: 0e03ec28e1272f094758907923a0226f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metnet", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), glmnet (>= 4.1-1), igraph (>= 1.1.2), knitr (>= 1.11), rmarkdown (>= 1.15), testthat (>= 2.2.1), Spectra (>= 1.4.1), MsCoreUtils (>= 1.6.0) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genie3 >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genie3 >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-bnlearn >=4.3' - 'r-corpcor >=1.6.10' @@ -38,10 +39,10 @@ requirements: - 'r-tibble >=3.0.5' - 'r-tidyr >=1.1.2' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genie3 >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genie3 >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-bnlearn >=4.3' - 'r-corpcor >=1.6.10' diff --git a/recipes/bioconductor-mfa/meta.yaml b/recipes/bioconductor-mfa/meta.yaml index 1986448c2f204..5da35eaca5908 100644 --- a/recipes/bioconductor-mfa/meta.yaml +++ b/recipes/bioconductor-mfa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "mfa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a47205412204ffd49737d41b7b78574d + md5: 37fa2e82d83636458e9a20cc72069dcd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mfa", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-coda - r-dplyr @@ -34,7 +35,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-coda - r-dplyr diff --git a/recipes/bioconductor-mfuzz/meta.yaml b/recipes/bioconductor-mfuzz/meta.yaml index 3a69ac72e50d2..a85698f9f0ed3 100644 --- a/recipes/bioconductor-mfuzz/meta.yaml +++ b/recipes/bioconductor-mfuzz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.60.0" %} +{% set version = "2.62.0" %} {% set name = "Mfuzz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8997e343fab679b0005f7cb9eb95be1d + md5: 03a765bd452d34b166f85cdfee8063ae build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mfuzz", max_pin="x.x") }}' noarch: generic # Suggests: marray requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-tkwidgets >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-tkwidgets >=1.80.0,<1.81.0' - r-base - r-e1071 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-tkwidgets >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-tkwidgets >=1.80.0,<1.81.0' - r-base - r-e1071 test: diff --git a/recipes/bioconductor-mgfm/meta.yaml b/recipes/bioconductor-mgfm/meta.yaml index 1212b35df01a2..7b05b8cea6a81 100644 --- a/recipes/bioconductor-mgfm/meta.yaml +++ b/recipes/bioconductor-mgfm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "MGFM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 87e2aeabf70fe5c98af8b31fc7eb87a8 + md5: 893a9f574fe4e023d3c4d3b99d58ae78 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgfm", max_pin="x.x") }}' noarch: generic # Suggests: hgu133a.db requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base test: commands: diff --git a/recipes/bioconductor-mgfr/meta.yaml b/recipes/bioconductor-mgfr/meta.yaml index 48dfafef2cb6b..988ffb8e7853e 100644 --- a/recipes/bioconductor-mgfr/meta.yaml +++ b/recipes/bioconductor-mgfr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "MGFR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b2461c46ec06a15eb25e35e645a9332 + md5: 73cad34ad523499dbdcfb3746b519b48 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgfr", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-mgsa/meta.yaml b/recipes/bioconductor-mgsa/meta.yaml index f3f84f49ee018..18c113cd156d3 100644 --- a/recipes/bioconductor-mgsa/meta.yaml +++ b/recipes/bioconductor-mgsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "mgsa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 29e5cee310a2610a0167f448d39c0206 + md5: 1a0667a9a3b9c3e973a47a49249b08db build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgsa", max_pin="x.x") }}' # Suggests: DBI, RSQLite, GO.db, testthat requirements: host: diff --git a/recipes/bioconductor-mgu74a.db/meta.yaml b/recipes/bioconductor-mgu74a.db/meta.yaml index 5282b2deaa29a..c2dd2b0ae3b6f 100644 --- a/recipes/bioconductor-mgu74a.db/meta.yaml +++ b/recipes/bioconductor-mgu74a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mgu74a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9fb75c159c50e2ae316ee5a8abe1a48c build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74acdf/meta.yaml b/recipes/bioconductor-mgu74acdf/meta.yaml index 790af0f291883..6d1e5d9376af7 100644 --- a/recipes/bioconductor-mgu74acdf/meta.yaml +++ b/recipes/bioconductor-mgu74acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74acdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ed6e86398e51c7b0ddca4431797ecbc0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74acdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74aprobe/meta.yaml b/recipes/bioconductor-mgu74aprobe/meta.yaml index e82292a4a259d..01606e9b7cee0 100644 --- a/recipes/bioconductor-mgu74aprobe/meta.yaml +++ b/recipes/bioconductor-mgu74aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74aprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7fea6d44856203e6293e0cd9fe1ad066 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74aprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74av2.db/meta.yaml b/recipes/bioconductor-mgu74av2.db/meta.yaml index b67f4f55511e5..405b9aa9777a8 100644 --- a/recipes/bioconductor-mgu74av2.db/meta.yaml +++ b/recipes/bioconductor-mgu74av2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mgu74av2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3205856d0c7725acded5238415e907bc build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74av2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74av2cdf/meta.yaml b/recipes/bioconductor-mgu74av2cdf/meta.yaml index d066d7b144da8..e72145c2c0482 100644 --- a/recipes/bioconductor-mgu74av2cdf/meta.yaml +++ b/recipes/bioconductor-mgu74av2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74av2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 35e2abb9fbfd68d90dc32a2faae00c95 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74av2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74av2probe/meta.yaml b/recipes/bioconductor-mgu74av2probe/meta.yaml index 0caa9eac2a672..8e2e4ecec00f0 100644 --- a/recipes/bioconductor-mgu74av2probe/meta.yaml +++ b/recipes/bioconductor-mgu74av2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74av2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ac540b0e26b14a411740233b02d3e11c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74av2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74b.db/meta.yaml b/recipes/bioconductor-mgu74b.db/meta.yaml index 7d8d7d5a2a75c..3063cdc54e8e1 100644 --- a/recipes/bioconductor-mgu74b.db/meta.yaml +++ b/recipes/bioconductor-mgu74b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mgu74b.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 205577a6e41d56910f221ffb940ee25b build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74b.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74bcdf/meta.yaml b/recipes/bioconductor-mgu74bcdf/meta.yaml index bf1d3d00be458..f44812422b044 100644 --- a/recipes/bioconductor-mgu74bcdf/meta.yaml +++ b/recipes/bioconductor-mgu74bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74bcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a1f0f98f29d34a421622447252113e1e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74bcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74bprobe/meta.yaml b/recipes/bioconductor-mgu74bprobe/meta.yaml index db2bc9262a391..29fd25ee76e40 100644 --- a/recipes/bioconductor-mgu74bprobe/meta.yaml +++ b/recipes/bioconductor-mgu74bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74bprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 224d606e6fc87592d387dbaabe5cd353 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74bprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74bv2.db/meta.yaml b/recipes/bioconductor-mgu74bv2.db/meta.yaml index a686c73cb696c..84c103d1c0982 100644 --- a/recipes/bioconductor-mgu74bv2.db/meta.yaml +++ b/recipes/bioconductor-mgu74bv2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mgu74bv2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4ec0fbed7343f0578ef11e2330d0d12a build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74bv2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74bv2cdf/meta.yaml b/recipes/bioconductor-mgu74bv2cdf/meta.yaml index 40247022fe1d4..1e5b584de6c4a 100644 --- a/recipes/bioconductor-mgu74bv2cdf/meta.yaml +++ b/recipes/bioconductor-mgu74bv2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74bv2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 45c48d11af03633dc10f8682b7ad74c5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74bv2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74bv2probe/meta.yaml b/recipes/bioconductor-mgu74bv2probe/meta.yaml index 3f5bfd9f4b642..2c0bd49a0fabb 100644 --- a/recipes/bioconductor-mgu74bv2probe/meta.yaml +++ b/recipes/bioconductor-mgu74bv2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74bv2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f6a12f88ea3c43a3e885c7e9b3fd03d2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74bv2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74c.db/meta.yaml b/recipes/bioconductor-mgu74c.db/meta.yaml index ae87a17b48e1b..f645da667a7cf 100644 --- a/recipes/bioconductor-mgu74c.db/meta.yaml +++ b/recipes/bioconductor-mgu74c.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mgu74c.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6c4f183e6ed5f0b5735596e7544746ae build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74c.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74ccdf/meta.yaml b/recipes/bioconductor-mgu74ccdf/meta.yaml index 2b1644415aad6..80c910bd5ffb7 100644 --- a/recipes/bioconductor-mgu74ccdf/meta.yaml +++ b/recipes/bioconductor-mgu74ccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74ccdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 172e626b0e3072edc65c4efff35fe998 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74ccdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74cprobe/meta.yaml b/recipes/bioconductor-mgu74cprobe/meta.yaml index 38cf65f888fc5..2e2b2ca35ed51 100644 --- a/recipes/bioconductor-mgu74cprobe/meta.yaml +++ b/recipes/bioconductor-mgu74cprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74cprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 186992992708f0071fd552ef92b9e25c build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74cprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74cv2.db/meta.yaml b/recipes/bioconductor-mgu74cv2.db/meta.yaml index 3175d01f69550..997784f9be6fd 100644 --- a/recipes/bioconductor-mgu74cv2.db/meta.yaml +++ b/recipes/bioconductor-mgu74cv2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mgu74cv2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1f860dfbf4400ede54eb30d9a70ec131 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74cv2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74cv2cdf/meta.yaml b/recipes/bioconductor-mgu74cv2cdf/meta.yaml index bfe25f12a1f9d..e03108fc7e228 100644 --- a/recipes/bioconductor-mgu74cv2cdf/meta.yaml +++ b/recipes/bioconductor-mgu74cv2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74cv2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9ef62b4b28f97770859db24393a07ed5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74cv2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74cv2probe/meta.yaml b/recipes/bioconductor-mgu74cv2probe/meta.yaml index 957ceff230bbe..ca9038a77b902 100644 --- a/recipes/bioconductor-mgu74cv2probe/meta.yaml +++ b/recipes/bioconductor-mgu74cv2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74cv2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0373496c817a1c1a153114047cfa7c5b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74cv2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mguatlas5k.db/meta.yaml b/recipes/bioconductor-mguatlas5k.db/meta.yaml index 7f8f9eb126727..22485ecde8e5b 100644 --- a/recipes/bioconductor-mguatlas5k.db/meta.yaml +++ b/recipes/bioconductor-mguatlas5k.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mguatlas5k.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 826093fe7228c08962aff36ad89af28e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mguatlas5k.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgug4104a.db/meta.yaml b/recipes/bioconductor-mgug4104a.db/meta.yaml index 511cc22eba5e0..23f2e33b36284 100644 --- a/recipes/bioconductor-mgug4104a.db/meta.yaml +++ b/recipes/bioconductor-mgug4104a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgug4104a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7b1cef094a226257cd657ed8d61e9ef1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgug4104a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgug4120a.db/meta.yaml b/recipes/bioconductor-mgug4120a.db/meta.yaml index c12a333d6504d..5029a19397f6f 100644 --- a/recipes/bioconductor-mgug4120a.db/meta.yaml +++ b/recipes/bioconductor-mgug4120a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgug4120a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bb57e8b2efe3d038ec2a0ace0313a4e7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgug4120a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgug4121a.db/meta.yaml b/recipes/bioconductor-mgug4121a.db/meta.yaml index f9b9edd4bd897..f58dbc5d4a23b 100644 --- a/recipes/bioconductor-mgug4121a.db/meta.yaml +++ b/recipes/bioconductor-mgug4121a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgug4121a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6b5cc321d5175356c383b91e30e120b7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgug4121a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgug4122a.db/meta.yaml b/recipes/bioconductor-mgug4122a.db/meta.yaml index 11a080bd0e856..f28449f09300b 100644 --- a/recipes/bioconductor-mgug4122a.db/meta.yaml +++ b/recipes/bioconductor-mgug4122a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgug4122a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5fcdce909ac1c0ccbf06bf6411f6fe52 build: - number: 16 + number: 17 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgug4122a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mi16cod.db/meta.yaml b/recipes/bioconductor-mi16cod.db/meta.yaml index dcb98323413d3..8fb4d0203848f 100644 --- a/recipes/bioconductor-mi16cod.db/meta.yaml +++ b/recipes/bioconductor-mi16cod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "mi16cod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f3a8e6f45ce5c298c1b1c5b32bf2630c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mi16cod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mia/meta.yaml b/recipes/bioconductor-mia/meta.yaml index b2031393678e7..919a3676af018 100644 --- a/recipes/bioconductor-mia/meta.yaml +++ b/recipes/bioconductor-mia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "mia" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4e6cd405049a4a4f7890047dd0e3ad9d + md5: 73446335fd354444f38c4e8cf793d520 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mia", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, patchwork, BiocStyle, yaml, phyloseq, dada2, stringr, biomformat, reldist, ade4, microbiomeDataSets, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-decontam >=1.20.0,<1.21.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-dirichletmultinomial >=1.42.0,<1.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bluster >=1.12.0,<1.13.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-decontam >=1.22.0,<1.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-dirichletmultinomial >=1.44.0,<1.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-ape - r-base - r-dplyr @@ -46,22 +49,24 @@ requirements: - r-tidyr - r-vegan run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-decontam >=1.20.0,<1.21.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-dirichletmultinomial >=1.42.0,<1.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bluster >=1.12.0,<1.13.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-decontam >=1.22.0,<1.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-dirichletmultinomial >=1.44.0,<1.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-ape - r-base - r-dplyr diff --git a/recipes/bioconductor-miasim/meta.yaml b/recipes/bioconductor-miasim/meta.yaml index 91f6fb97a3046..01006e0284875 100644 --- a/recipes/bioconductor-miasim/meta.yaml +++ b/recipes/bioconductor-miasim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "miaSim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 36d959599bdaf1bce1bc6f3302022ddc + md5: 0867c6e7b7cae5acbfd6154b8af06d41 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-miasim", max_pin="x.x") }}' noarch: generic -# Suggests: ape, cluster, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy +# Suggests: ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy requirements: host: - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-desolve - r-powerlaw run: - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-desolve - r-powerlaw diff --git a/recipes/bioconductor-miaviz/meta.yaml b/recipes/bioconductor-miaviz/meta.yaml index f76a198ae67f3..5d98581a6690d 100644 --- a/recipes/bioconductor-miaviz/meta.yaml +++ b/recipes/bioconductor-miaviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "miaViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 12187467cffef6ea27c17e3fce3a336a + md5: 8388770fbcfce7b95040dc84f02938bc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-miaviz", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, BiocStyle, testthat, patchwork, vegan, microbiomeDataSets +# Suggests: knitr, rmarkdown, BiocStyle, testthat, patchwork, vegan, microbiomeDataSets, bluster requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-dirichletmultinomial >=1.42.0,<1.43.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-mia >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-dirichletmultinomial >=1.44.0,<1.45.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-mia >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-ape - r-base - r-dplyr - r-ggnewscale - r-ggplot2 - 'r-ggraph >=2.0' + - r-ggrepel - r-purrr - r-rlang - r-tibble @@ -45,22 +48,24 @@ requirements: - r-tidytree - r-viridis run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-dirichletmultinomial >=1.42.0,<1.43.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-mia >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-dirichletmultinomial >=1.44.0,<1.45.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-mia >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-ape - r-base - r-dplyr - r-ggnewscale - r-ggplot2 - 'r-ggraph >=2.0' + - r-ggrepel - r-purrr - r-rlang - r-tibble diff --git a/recipes/bioconductor-michip/meta.yaml b/recipes/bioconductor-michip/meta.yaml index 91c869251363f..cafafc492b65d 100644 --- a/recipes/bioconductor-michip/meta.yaml +++ b/recipes/bioconductor-michip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "MiChip" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1fa83d7ff43b635845b8718f63d52c4c + md5: 28daafdf6588314a9fad7a75b1671c10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-michip", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-microbiome/meta.yaml b/recipes/bioconductor-microbiome/meta.yaml index 97851a11b7c02..1a8d53b4a4491 100644 --- a/recipes/bioconductor-microbiome/meta.yaml +++ b/recipes/bioconductor-microbiome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "microbiome" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f6a3ca6428df676e03c3b34d64f4fc88 + md5: 2d185cf8b8bf7d23f295dee1af621a0f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microbiome", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-compositions - r-dplyr @@ -34,8 +35,8 @@ requirements: - r-tidyr - r-vegan run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-compositions - r-dplyr diff --git a/recipes/bioconductor-microbiomebenchmarkdata/meta.yaml b/recipes/bioconductor-microbiomebenchmarkdata/meta.yaml index 3fdbe1071c43f..4738a600749e6 100644 --- a/recipes/bioconductor-microbiomebenchmarkdata/meta.yaml +++ b/recipes/bioconductor-microbiomebenchmarkdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "MicrobiomeBenchmarkData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1116445da1265ebf3e4bf29678bd6cc3 + md5: c6c791669de95bf2dc108798770ea5be build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microbiomebenchmarkdata", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0), mia, ggplot2, tidyr, dplyr, magrittr, tibble, purrr requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-ape - r-base run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-ape - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-microbiomebenchmarkdata/post-link.sh b/recipes/bioconductor-microbiomebenchmarkdata/post-link.sh index 25fe021fab244..b41c09486c6b4 100644 --- a/recipes/bioconductor-microbiomebenchmarkdata/post-link.sh +++ b/recipes/bioconductor-microbiomebenchmarkdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "microbiomebenchmarkdata-1.2.0" +installBiocDataPackage.sh "microbiomebenchmarkdata-1.4.0" diff --git a/recipes/bioconductor-microbiomedasim/meta.yaml b/recipes/bioconductor-microbiomedasim/meta.yaml index 159e119977f81..1bf6caba4a6b5 100644 --- a/recipes/bioconductor-microbiomedasim/meta.yaml +++ b/recipes/bioconductor-microbiomedasim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "microbiomeDASim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 39fb498f8346fa9914285ad4b7790a73 + md5: 9ddf99ab393766f7bcb9dee13b3707f9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microbiomedasim", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), knitr, devtools requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-ggplot2 - r-mass @@ -32,9 +33,9 @@ requirements: - r-pbapply - r-tmvtnorm run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-ggplot2 - r-mass diff --git a/recipes/bioconductor-microbiomedatasets/meta.yaml b/recipes/bioconductor-microbiomedatasets/meta.yaml index 45bed4d640d18..4fcdb8454b7a9 100644 --- a/recipes/bioconductor-microbiomedatasets/meta.yaml +++ b/recipes/bioconductor-microbiomedatasets/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "microbiomeDataSets" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 084634f8885e50e157bbaef972b7ad8f + md5: 90cd4bb36dafcef8f6eb0e0232afdcd0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microbiomedatasets", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-ape - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-ape - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-microbiomedatasets/post-link.sh b/recipes/bioconductor-microbiomedatasets/post-link.sh index aa74335043872..a7009b824d2c1 100644 --- a/recipes/bioconductor-microbiomedatasets/post-link.sh +++ b/recipes/bioconductor-microbiomedatasets/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "microbiomedatasets-1.8.0" +installBiocDataPackage.sh "microbiomedatasets-1.10.0" diff --git a/recipes/bioconductor-microbiomeexplorer/meta.yaml b/recipes/bioconductor-microbiomeexplorer/meta.yaml index 046802c402141..87c2c126866f1 100644 --- a/recipes/bioconductor-microbiomeexplorer/meta.yaml +++ b/recipes/bioconductor-microbiomeexplorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "microbiomeExplorer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a899b212f5888fd3d9b11ee585a8119 + md5: c1e966728a968697ad53fd6405c156c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microbiomeexplorer", max_pin="x.x") }}' noarch: generic # Suggests: V8, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomformat >=1.28.0,<1.29.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomformat >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base - r-broom - r-car @@ -54,11 +55,11 @@ requirements: - r-tidyr - r-vegan run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomformat >=1.28.0,<1.29.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomformat >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base - r-broom - r-car diff --git a/recipes/bioconductor-microbiomemarker/meta.yaml b/recipes/bioconductor-microbiomemarker/meta.yaml index f845014d8b090..6b50c7ac62de1 100644 --- a/recipes/bioconductor-microbiomemarker/meta.yaml +++ b/recipes/bioconductor-microbiomemarker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "microbiomeMarker" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 548c6c090fa44c0a03d1dbdfe4ae4415 + md5: facf2f8071da6049b688fe3d16efb0e2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microbiomemarker", max_pin="x.x") }}' noarch: generic # Suggests: testthat, covr, glmnet, Matrix, kernlab, e1071, ranger, knitr, rmarkdown, BiocStyle, withr requirements: host: - - 'bioconductor-aldex2 >=1.32.0,<1.33.0' - - 'bioconductor-ancombc >=2.2.0,<2.3.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomformat >=1.28.0,<1.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-aldex2 >=1.34.0,<1.35.0' + - 'bioconductor-ancombc >=2.4.0,<2.5.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomformat >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - r-coin @@ -57,23 +58,23 @@ requirements: - r-vegan - r-yaml run: - - 'bioconductor-aldex2 >=1.32.0,<1.33.0' - - 'bioconductor-ancombc >=2.2.0,<2.3.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomformat >=1.28.0,<1.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-aldex2 >=1.34.0,<1.35.0' + - 'bioconductor-ancombc >=2.4.0,<2.5.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomformat >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - r-coin diff --git a/recipes/bioconductor-microbiomeprofiler/meta.yaml b/recipes/bioconductor-microbiomeprofiler/meta.yaml index 0b262d73b3fcf..7a31e5d435166 100644 --- a/recipes/bioconductor-microbiomeprofiler/meta.yaml +++ b/recipes/bioconductor-microbiomeprofiler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "MicrobiomeProfiler" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 47b4023245daeb0e51c9aa1e543f1d49 + md5: 47851ff17ed03e5b448a09513c7bf122 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microbiomeprofiler", max_pin="x.x") }}' noarch: generic -# Suggests: rmarkdown, knitr, prettydoc, testthat (>= 3.0.0) +# Suggests: rmarkdown, knitr, testthat (>= 3.0.0), prettydoc requirements: host: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - r-base - r-config - r-dt @@ -35,8 +36,8 @@ requirements: - r-shinycustomloader - r-shinywidgets run: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - r-base - r-config - r-dt diff --git a/recipes/bioconductor-microbiotaprocess/meta.yaml b/recipes/bioconductor-microbiotaprocess/meta.yaml index 509f549b57693..448857a29ab05 100644 --- a/recipes/bioconductor-microbiotaprocess/meta.yaml +++ b/recipes/bioconductor-microbiotaprocess/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.2" %} +{% set version = "1.14.0" %} {% set name = "MicrobiotaProcess" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5e400f9a6b55f6e01b6438f36ff42a18 + md5: 104b99004b64b664131ddea6462cbabc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microbiotaprocess", max_pin="x.x") }}' noarch: generic -# Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, corrr, ggupset, ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial +# Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, ggupset, ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial, ggpp, BiocManager requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-ggtreeextra >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treeio >=1.24.0,<1.25.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-ggtreeextra >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treeio >=1.26.0,<1.27.0' - r-ape - r-base - r-cli @@ -34,6 +35,7 @@ requirements: - r-dplyr - r-dtplyr - r-foreach + - 'r-ggfun >=0.1.1' - r-ggplot2 - r-ggrepel - r-ggsignif @@ -51,11 +53,11 @@ requirements: - r-vegan - r-zoo run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-ggtreeextra >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treeio >=1.24.0,<1.25.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-ggtreeextra >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treeio >=1.26.0,<1.27.0' - r-ape - r-base - r-cli @@ -64,6 +66,7 @@ requirements: - r-dplyr - r-dtplyr - r-foreach + - 'r-ggfun >=0.1.1' - r-ggplot2 - r-ggrepel - r-ggsignif diff --git a/recipes/bioconductor-microrna/meta.yaml b/recipes/bioconductor-microrna/meta.yaml index ee9067d643879..cc92ab37669ca 100644 --- a/recipes/bioconductor-microrna/meta.yaml +++ b/recipes/bioconductor-microrna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "microRNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 166bcf7edb5ded052551b53db0fe6b9f + md5: 04b7af542581242a8e6ba5d4f19c14ca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microrna", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-micrornaome/meta.yaml b/recipes/bioconductor-micrornaome/meta.yaml index cf47ca13893f9..20251ad808f38 100644 --- a/recipes/bioconductor-micrornaome/meta.yaml +++ b/recipes/bioconductor-micrornaome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "microRNAome" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04f1271bdd22d4cc2dabd9e8db57e006 + md5: 12d3baf395e82975bbcacfb9ff61a715 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-micrornaome", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, RUnit requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-micrornaome/post-link.sh b/recipes/bioconductor-micrornaome/post-link.sh index 6708b196917f9..2c965f7636c8d 100644 --- a/recipes/bioconductor-micrornaome/post-link.sh +++ b/recipes/bioconductor-micrornaome/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "micrornaome-1.22.0" +installBiocDataPackage.sh "micrornaome-1.24.0" diff --git a/recipes/bioconductor-microstasis/meta.yaml b/recipes/bioconductor-microstasis/meta.yaml index abc37a8a4fdb7..52e1c42705ee5 100644 --- a/recipes/bioconductor-microstasis/meta.yaml +++ b/recipes/bioconductor-microstasis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "microSTASIS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a5e65e09dd41f9734e4ce715a6ebf564 + md5: 7b9b67613eb5e6b69918dffc9d4060d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microstasis", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, gghighlight, knitr, rmarkdown, methods, RefManageR, sessioninfo, SingleCellExperiment, SummarizedExperiment, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-ggplot2 - r-ggside - r-rlang - r-stringr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-ggplot2 - r-ggside diff --git a/recipes/bioconductor-micsqtl/build.sh b/recipes/bioconductor-micsqtl/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-micsqtl/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-micsqtl/build_failure.linux-64.yaml b/recipes/bioconductor-micsqtl/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..3fe5e63aee6a4 --- /dev/null +++ b/recipes/bioconductor-micsqtl/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 48da45ce49c1641d3245866b89ddd5bb41be17df6a5b307fcbb400bb8ebd78e7 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + dependency issue +log: |2- + - r-ggplot2 + - r-tca + - r-glue + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - r-dirmult + - r-nnls + - r-magrittr + - r-purrr + - r-base 4.3.* + - r-ggridges + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested r-tca + - + + Leaving build/test directories: + Work: + /opt/conda/conda-bld/work + Test: + /opt/conda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + Build: + source activate /opt/conda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - bioconductor-toast >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - r-ggpubr + - r-ggplot2 + - r-tca + - r-glue + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - r-dirmult + - r-nnls + - r-magrittr + - r-purrr + - r-base 4.3.* + - r-ggridges + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested r-tca + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-tca")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-micsqtl/meta.yaml b/recipes/bioconductor-micsqtl/meta.yaml new file mode 100644 index 0000000000000..33eb7aa2e58cf --- /dev/null +++ b/recipes/bioconductor-micsqtl/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.0.0" %} +{% set name = "MICSQTL" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ec49e08df014da6955d2b6ab7dc77d3b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-micsqtl", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle +requirements: + host: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-toast >=1.16.0,<1.17.0' + - r-base + - r-dirmult + - r-ggplot2 + - r-ggpubr + - r-ggridges + - r-glue + - r-magrittr + - r-nnls + - r-purrr + - r-tca + run: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-toast >=1.16.0,<1.17.0' + - r-base + - r-dirmult + - r-ggplot2 + - r-ggpubr + - r-ggridges + - r-glue + - r-magrittr + - r-nnls + - r-purrr + - r-tca +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)' + description: 'Our pipeline, MICSQTL, utilizes scRNA-seq reference and bulk transcriptomes to estimate cellular composition in the matched bulk proteomes. The expression of genes and proteins at either bulk level or cell type level can be integrated by Angle-based Joint and Individual Variation Explained (AJIVE) framework. Meanwhile, MICSQTL can perform cell-type-specic quantitative trait loci (QTL) mapping to proteins or transcripts based on the input of bulk expression data and the estimated cellular composition per molecule type, without the need for single cell sequencing. We use matched transcriptome-proteome from human brain frontal cortex tissue samples to demonstrate the input and output of our tool.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-midashla/meta.yaml b/recipes/bioconductor-midashla/meta.yaml index 37868a12e2dfb..99330f8c5b329 100644 --- a/recipes/bioconductor-midashla/meta.yaml +++ b/recipes/bioconductor-midashla/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "midasHLA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 408626a1272bac5201d96f5992d1baab + md5: 7d77f1bda1bff8d67de91e02cb985519 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-midashla", max_pin="x.x") }}' noarch: generic # Suggests: broom.mixed (>= 0.2.4), cowplot (>= 1.0.0), devtools (>= 2.0.1), ggplot2 (>= 3.1.0), ggpubr (>= 0.2.5), rmarkdown, seqinr (>= 3.4-5), survival (>= 2.43-3), testthat (>= 2.0.1), tidyr (>= 1.1.2) requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'r-assertthat >=0.2.0' - r-base - 'r-broom >=0.5.1' @@ -38,9 +39,9 @@ requirements: - 'r-stringi >=1.2.4' - 'r-tibble >=2.0.1' run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'r-assertthat >=0.2.0' - r-base - 'r-broom >=0.5.1' diff --git a/recipes/bioconductor-migsadata/meta.yaml b/recipes/bioconductor-migsadata/meta.yaml index 189ec9574258d..9a6355a9d9d3f 100644 --- a/recipes/bioconductor-migsadata/meta.yaml +++ b/recipes/bioconductor-migsadata/meta.yaml @@ -25,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20230706 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-milor/meta.yaml b/recipes/bioconductor-milor/meta.yaml index e1011a151d562..85f159f4f472b 100644 --- a/recipes/bioconductor-milor/meta.yaml +++ b/recipes/bioconductor-milor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "miloR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bb65889883141ecec6c2ebc66cae0160 + md5: 9ab9a4a2fe26786cd8fef69354bfa08f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-milor", max_pin="x.x") }}' noarch: generic # Suggests: testthat, MASS, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData, MouseThymusAgeing, magick, RCurl, curl, graphics requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-dplyr @@ -48,15 +49,15 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-dplyr diff --git a/recipes/bioconductor-mimager/meta.yaml b/recipes/bioconductor-mimager/meta.yaml index 43bbfc9c7cd82..648f2f64bb6d4 100644 --- a/recipes/bioconductor-mimager/meta.yaml +++ b/recipes/bioconductor-mimager/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "mimager" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f6ed0e16875e23c4b287c4a82daaea68 + md5: 2a9eaf36345d24dc2d44a65c1f8640a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mimager", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind, affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1 requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyplm >=1.76.0,<1.77.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyplm >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-gtable - r-scales run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyplm >=1.76.0,<1.77.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyplm >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-gtable diff --git a/recipes/bioconductor-mina/meta.yaml b/recipes/bioconductor-mina/meta.yaml index dfccfbf55bae1..1f816fb2b240f 100644 --- a/recipes/bioconductor-mina/meta.yaml +++ b/recipes/bioconductor-mina/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "mina" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3cfb81237b29c98fd414eadcc05c74d3 + md5: d6578736bef864eef8f89958a849137b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mina", max_pin="x.x") }}' # Suggests: knitr, rmarkdown requirements: host: diff --git a/recipes/bioconductor-mineica/meta.yaml b/recipes/bioconductor-mineica/meta.yaml index 2e5774e5b900e..4f8e58766912f 100644 --- a/recipes/bioconductor-mineica/meta.yaml +++ b/recipes/bioconductor-mineica/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "MineICA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3bfbe3946133ce2be4c18c146f906f67 + md5: d08aa74cfe4d20f4ad26235e0695d555 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mineica", max_pin="x.x") }}' noarch: generic # Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX, future, future.apply requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - 'bioconductor-lumihumanall.db >=1.22.0,<1.23.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-cluster - r-colorspace @@ -49,17 +50,17 @@ requirements: - r-scales - r-xtable run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - 'bioconductor-lumihumanall.db >=1.22.0,<1.23.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-cluster - r-colorspace diff --git a/recipes/bioconductor-minet/meta.yaml b/recipes/bioconductor-minet/meta.yaml index 5ff3aea1feff8..430543b54eca5 100644 --- a/recipes/bioconductor-minet/meta.yaml +++ b/recipes/bioconductor-minet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.58.0" %} +{% set version = "3.60.0" %} {% set name = "minet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c19e497a170c61859a7f850c18a64829 + md5: 8aaab67519352be115568a301e98ef99 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-minet", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-minfi/meta.yaml b/recipes/bioconductor-minfi/meta.yaml index ef3788c157bc2..6ed741d14afee 100644 --- a/recipes/bioconductor-minfi/meta.yaml +++ b/recipes/bioconductor-minfi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "minfi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f2346d9ef5bd96b0715c47402ce585d8 + md5: 3c1998eee0aabbfab3c3796c82339a18 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-minfi", max_pin="x.x") }}' noarch: generic # Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-siggenes >=1.74.0,<1.75.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-beanplot - r-data.table @@ -52,25 +53,25 @@ requirements: - r-rcolorbrewer - r-reshape run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-siggenes >=1.74.0,<1.75.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-beanplot - r-data.table diff --git a/recipes/bioconductor-minfidata/meta.yaml b/recipes/bioconductor-minfidata/meta.yaml index 7168cbc79995f..f41037aeece26 100644 --- a/recipes/bioconductor-minfidata/meta.yaml +++ b/recipes/bioconductor-minfidata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.46.0" %} +{% set version = "0.48.0" %} {% set name = "minfiData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a5edb94dae6adb108bd94fdf4e0e8c3d + md5: 1ca7578aeab1a54db146c443870be6e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-minfidata", max_pin="x.x") }}' noarch: generic requirements: host: - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-minfidata/post-link.sh b/recipes/bioconductor-minfidata/post-link.sh index a14bd53842e17..7dbdb4780ea5f 100644 --- a/recipes/bioconductor-minfidata/post-link.sh +++ b/recipes/bioconductor-minfidata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "minfidata-0.46.0" +installBiocDataPackage.sh "minfidata-0.48.0" diff --git a/recipes/bioconductor-minfidataepic/meta.yaml b/recipes/bioconductor-minfidataepic/meta.yaml index d65e802545a06..d9429ed793030 100644 --- a/recipes/bioconductor-minfidataepic/meta.yaml +++ b/recipes/bioconductor-minfidataepic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "minfiDataEPIC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f61984902e4c4c2d0c01f375a3533935 + md5: bcb0b01d571c5308e02db4c6b5c0d1ce build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-minfidataepic", max_pin="x.x") }}' noarch: generic requirements: host: - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-minfidataepic/post-link.sh b/recipes/bioconductor-minfidataepic/post-link.sh index 7b5637a02d804..506358fd0d0de 100644 --- a/recipes/bioconductor-minfidataepic/post-link.sh +++ b/recipes/bioconductor-minfidataepic/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "minfidataepic-1.26.0" +installBiocDataPackage.sh "minfidataepic-1.28.0" diff --git a/recipes/bioconductor-minimumdistance/meta.yaml b/recipes/bioconductor-minimumdistance/meta.yaml index 7dbd68965a2b4..46b1638468be4 100644 --- a/recipes/bioconductor-minimumdistance/meta.yaml +++ b/recipes/bioconductor-minimumdistance/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "MinimumDistance" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c4a44703f30e7bfa7c4e7b02004a0f4c + md5: ab96e788a4152b80b7a685f3fc8fcd9c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-minimumdistance", max_pin="x.x") }}' noarch: generic # Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-vanillaice >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-vanillaice >=1.64.0,<1.65.0' - r-base - r-data.table - r-ff @@ -39,17 +40,17 @@ requirements: - r-lattice - r-matrixstats run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-vanillaice >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-vanillaice >=1.64.0,<1.65.0' - r-base - r-data.table - r-ff diff --git a/recipes/bioconductor-minionsummarydata/meta.yaml b/recipes/bioconductor-minionsummarydata/meta.yaml index e8c6a477792c0..f09a52c37ecc6 100644 --- a/recipes/bioconductor-minionsummarydata/meta.yaml +++ b/recipes/bioconductor-minionsummarydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "minionSummaryData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cab7c2dd789ebe23e1c9410bdbc259c6 + md5: 1679c45541b2d76094c3894abe9c011d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-minionsummarydata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-minionsummarydata/post-link.sh b/recipes/bioconductor-minionsummarydata/post-link.sh index cd6445be0f12a..9e9250e8eedd7 100644 --- a/recipes/bioconductor-minionsummarydata/post-link.sh +++ b/recipes/bioconductor-minionsummarydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "minionsummarydata-1.30.0" +installBiocDataPackage.sh "minionsummarydata-1.32.0" diff --git a/recipes/bioconductor-mipp/meta.yaml b/recipes/bioconductor-mipp/meta.yaml index 5f900be73ec9b..50af592ccbaa4 100644 --- a/recipes/bioconductor-mipp/meta.yaml +++ b/recipes/bioconductor-mipp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "MiPP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 79698b2acaac85272c49ff931598336b + md5: ce412e2a72891fcc7969faee078b2be3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mipp", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-e1071 - r-mass run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-e1071 - r-mass diff --git a/recipes/bioconductor-miqc/meta.yaml b/recipes/bioconductor-miqc/meta.yaml index 7d4a13b6656fa..6c084decec07f 100644 --- a/recipes/bioconductor-miqc/meta.yaml +++ b/recipes/bioconductor-miqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "miQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 031d41e099bf5babd6b0f8d32d9f0d1e + md5: e1246c2b5dcb83059d6887b35db543a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-miqc", max_pin="x.x") }}' noarch: generic # Suggests: scRNAseq, scater, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-flexmix - r-ggplot2 run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-flexmix - r-ggplot2 diff --git a/recipes/bioconductor-mira/meta.yaml b/recipes/bioconductor-mira/meta.yaml index 604ac4269053c..93e25f1a9c765 100644 --- a/recipes/bioconductor-mira/meta.yaml +++ b/recipes/bioconductor-mira/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "MIRA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 58cb07316068a920e02e241d1bfe8beb + md5: 670cb42f275d260b28e0e2d140cacda2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mira", max_pin="x.x") }}' noarch: generic # Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-ggplot2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-mirage/meta.yaml b/recipes/bioconductor-mirage/meta.yaml index 9b622e3b83db0..45a443bde1f58 100644 --- a/recipes/bioconductor-mirage/meta.yaml +++ b/recipes/bioconductor-mirage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "MiRaGE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d1ff8ce3f0bd0633b2d4fae52b4eec14 + md5: c86c12c042052eb4d558bdff55e8c47a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirage", max_pin="x.x") }}' noarch: generic # Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager test: diff --git a/recipes/bioconductor-mirbase.db/meta.yaml b/recipes/bioconductor-mirbase.db/meta.yaml index 15bfae93c86f9..a51ede2582bcd 100644 --- a/recipes/bioconductor-mirbase.db/meta.yaml +++ b/recipes/bioconductor-mirbase.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.2.0" %} {% set name = "mirbase.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 316bc12cee8c2dd9240b7fc30cd1619e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirbase.db", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirbaseversions.db/meta.yaml b/recipes/bioconductor-mirbaseversions.db/meta.yaml index 560259e831959..a66ca195291ed 100644 --- a/recipes/bioconductor-mirbaseversions.db/meta.yaml +++ b/recipes/bioconductor-mirbaseversions.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "miRBaseVersions.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,27 +13,28 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9944ab7a474f84a40100c56298f9cb77 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirbaseversions.db", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, annotate requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - r-dbi - r-gtools - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - r-dbi - r-gtools - r-rsqlite - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mircomp/meta.yaml b/recipes/bioconductor-mircomp/meta.yaml index 9d93697dfe47d..465227f2e2975 100644 --- a/recipes/bioconductor-mircomp/meta.yaml +++ b/recipes/bioconductor-mircomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "miRcomp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c16b1d3d79f266d11691bc93c44c2236 + md5: 06b97d8829ca13b60dd4869a48b684ab build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mircomp", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-mircompdata >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-mircompdata >=1.32.0,<1.33.0' - r-base - r-kernsmooth run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-mircompdata >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-mircompdata >=1.32.0,<1.33.0' - r-base - r-kernsmooth test: diff --git a/recipes/bioconductor-mircompdata/meta.yaml b/recipes/bioconductor-mircompdata/meta.yaml index 02fc8b1e898c3..95ae5ae333c25 100644 --- a/recipes/bioconductor-mircompdata/meta.yaml +++ b/recipes/bioconductor-mircompdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "miRcompData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df2f1f8eb6489db9c0e242224b47be36 + md5: 0b091222ebe8ac1a3a2c59384931393b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mircompdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mircompdata/post-link.sh b/recipes/bioconductor-mircompdata/post-link.sh index d25f90ae9ebeb..5d104e9b53a6d 100644 --- a/recipes/bioconductor-mircompdata/post-link.sh +++ b/recipes/bioconductor-mircompdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mircompdata-1.30.0" +installBiocDataPackage.sh "mircompdata-1.32.0" diff --git a/recipes/bioconductor-mirintegrator/meta.yaml b/recipes/bioconductor-mirintegrator/meta.yaml index 01a5af4f2e768..e122769fc894f 100644 --- a/recipes/bioconductor-mirintegrator/meta.yaml +++ b/recipes/bioconductor-mirintegrator/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "mirIntegrator" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df82dd0262aefe9230e29a27c67f760e + md5: 9ec5789f159dfc3880ce8369af20c27a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirintegrator", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rontotools >=2.28.0,<2.29.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rontotools >=2.30.0,<2.31.0' - r-base - r-ggplot2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rontotools >=2.28.0,<2.29.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rontotools >=2.30.0,<2.31.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-mirlab/meta.yaml b/recipes/bioconductor-mirlab/meta.yaml index e61b67c915ad2..02d028c863d44 100644 --- a/recipes/bioconductor-mirlab/meta.yaml +++ b/recipes/bioconductor-mirlab/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "miRLAB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 744b41ef84de2faa12cad1caefcae543 + md5: 3347a99a17fc2caade03a35471a79ad0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirlab", max_pin="x.x") }}' noarch: generic # Suggests: knitr,BiocGenerics, AnnotationDbi,RUnit,rmarkdown requirements: host: - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-ctc >=1.74.0,<1.75.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgabiolinks >=2.28.0,<2.29.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-ctc >=1.76.0,<1.77.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgabiolinks >=2.30.0,<2.31.0' - r-base - r-dplyr - r-energy @@ -42,14 +43,14 @@ requirements: - r-rcurl - r-stringr run: - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-ctc >=1.74.0,<1.75.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgabiolinks >=2.28.0,<2.29.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-ctc >=1.76.0,<1.77.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgabiolinks >=2.30.0,<2.31.0' - r-base - r-dplyr - r-energy diff --git a/recipes/bioconductor-mirna102xgaincdf/meta.yaml b/recipes/bioconductor-mirna102xgaincdf/meta.yaml index 8616bcbf2acdd..c2998928a01d0 100644 --- a/recipes/bioconductor-mirna102xgaincdf/meta.yaml +++ b/recipes/bioconductor-mirna102xgaincdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mirna102xgaincdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9091a45c2ac15c2de0263743ab334f97 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirna102xgaincdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirna10cdf/meta.yaml b/recipes/bioconductor-mirna10cdf/meta.yaml index b29f31fb1a81c..657e2d588c9fe 100644 --- a/recipes/bioconductor-mirna10cdf/meta.yaml +++ b/recipes/bioconductor-mirna10cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mirna10cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 814da2a2e298e132f4db0b2e8ab814be build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirna10cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirna10probe/meta.yaml b/recipes/bioconductor-mirna10probe/meta.yaml index cb6bf10f733c7..ad500280b4d55 100644 --- a/recipes/bioconductor-mirna10probe/meta.yaml +++ b/recipes/bioconductor-mirna10probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mirna10probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8bfa6cdfeee1c563b4881214bd5d4ce1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirna10probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirna20cdf/meta.yaml b/recipes/bioconductor-mirna20cdf/meta.yaml index 7a6ca0f379587..3d81b3981f94a 100644 --- a/recipes/bioconductor-mirna20cdf/meta.yaml +++ b/recipes/bioconductor-mirna20cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mirna20cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 56f7807673ff108427ae7f6bdf85ae1c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirna20cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirnameconverter/meta.yaml b/recipes/bioconductor-mirnameconverter/meta.yaml index ba45c1803c37d..5e214021c777c 100644 --- a/recipes/bioconductor-mirnameconverter/meta.yaml +++ b/recipes/bioconductor-mirnameconverter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "miRNAmeConverter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 159e14aa90692f18e70bd6b8ab4de62e + md5: cfc6563f669ecbc03292cccba919fe05 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirnameconverter", max_pin="x.x") }}' noarch: generic # Suggests: methods, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - 'bioconductor-mirbaseversions.db >=1.1.0,<1.2.0' - r-base - r-dbi - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - 'bioconductor-mirbaseversions.db >=1.1.0,<1.2.0' - r-base - r-dbi diff --git a/recipes/bioconductor-mirnapath/meta.yaml b/recipes/bioconductor-mirnapath/meta.yaml index 8c1ceb8ee5cc6..9438bd5588098 100644 --- a/recipes/bioconductor-mirnapath/meta.yaml +++ b/recipes/bioconductor-mirnapath/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "miRNApath" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7d5b6049d846a3e3d6bfed44c779e70d + md5: 94aad8a3b57b070cb5c559d9d1f14726 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirnapath", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-mirnatap.db/meta.yaml b/recipes/bioconductor-mirnatap.db/meta.yaml index 2de40cf5aa5d9..b8f95f3419969 100644 --- a/recipes/bioconductor-mirnatap.db/meta.yaml +++ b/recipes/bioconductor-mirnatap.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.10" %} {% set name = "miRNAtap.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,26 +13,27 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 48010280b68d6f1ddbff3b374132ce0a build: - number: 14 + number: 15 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirnatap.db", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-mirnatap >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-mirnatap >=1.36.0,<1.37.0' - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-mirnatap >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-mirnatap >=1.36.0,<1.37.0' - r-base - r-dbi - r-rsqlite - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirnatap/meta.yaml b/recipes/bioconductor-mirnatap/meta.yaml index df8230d80281b..6a542792493d7 100644 --- a/recipes/bioconductor-mirnatap/meta.yaml +++ b/recipes/bioconductor-mirnatap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "miRNAtap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a8119335b7deb36dd6f674bc005fe77 + md5: f09289c10d9e5e916cc1b95e79bf504f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirnatap", max_pin="x.x") }}' noarch: generic # Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - r-dbi - r-plyr @@ -29,7 +30,7 @@ requirements: - r-sqldf - r-stringr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - r-dbi - r-plyr diff --git a/recipes/bioconductor-mirnatarget/meta.yaml b/recipes/bioconductor-mirnatarget/meta.yaml index bc6f79cce1728..130d1f40deaf8 100644 --- a/recipes/bioconductor-mirnatarget/meta.yaml +++ b/recipes/bioconductor-mirnatarget/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "miRNATarget" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7418be6b97608cabc13f0812caf9301 + md5: f1988a96af5f0232abfbe507854d49bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirnatarget", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirnatarget/post-link.sh b/recipes/bioconductor-mirnatarget/post-link.sh index 2dc55d0f7b4f3..cca9ffdc3448c 100644 --- a/recipes/bioconductor-mirnatarget/post-link.sh +++ b/recipes/bioconductor-mirnatarget/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mirnatarget-1.38.0" +installBiocDataPackage.sh "mirnatarget-1.40.0" diff --git a/recipes/bioconductor-mirtarrnaseq/meta.yaml b/recipes/bioconductor-mirtarrnaseq/meta.yaml index c9e30b0034f70..5a9e793f0b0a7 100644 --- a/recipes/bioconductor-mirtarrnaseq/meta.yaml +++ b/recipes/bioconductor-mirtarrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "mirTarRnaSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e5293fd7139409c1f97be415ff33cfdb + md5: b8cac8c363bddb02eb97e6009bb91f4e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirtarrnaseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, R.cache, SPONGE requirements: diff --git a/recipes/bioconductor-missmethyl/meta.yaml b/recipes/bioconductor-missmethyl/meta.yaml index 0d0e59a147311..73c8b2a6314ae 100644 --- a/recipes/bioconductor-missmethyl/meta.yaml +++ b/recipes/bioconductor-missmethyl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "missMethyl" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,54 +11,55 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14f5ef67dfb35d45507cf6d89aa482b3 + md5: 4773cfc60c545bb0a04dac0b6cc0ac4e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-missmethyl", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biasedurn - r-ruv - r-statmod - r-stringr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biasedurn - r-ruv diff --git a/recipes/bioconductor-missrows/meta.yaml b/recipes/bioconductor-missrows/meta.yaml index 202971b260664..95759b50cdab7 100644 --- a/recipes/bioconductor-missrows/meta.yaml +++ b/recipes/bioconductor-missrows/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "missRows" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b83ec2b5bd3f9395ff1ed60e1da40868 + md5: d076124257e06505c39064a9dcddd695 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-missrows", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-gtools - r-plyr run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-gtools diff --git a/recipes/bioconductor-mistyr/meta.yaml b/recipes/bioconductor-mistyr/meta.yaml index 4eaa178821c74..ab71622892ea4 100644 --- a/recipes/bioconductor-mistyr/meta.yaml +++ b/recipes/bioconductor-mistyr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "mistyR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2e7371ef1a22dcb63add2f2e680deff0 + md5: f21483e1d8c9575d0c27a9fa544cfb3c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mistyr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, earth, future, igraph (>= 1.2.7), iml, kernlab, knitr, MASS, rmarkdown, RSNNS, testthat (>= 3.0.0), xgboost requirements: diff --git a/recipes/bioconductor-mitch/meta.yaml b/recipes/bioconductor-mitch/meta.yaml index 906e0da288dcc..0a18ed1cd6dfa 100644 --- a/recipes/bioconductor-mitch/meta.yaml +++ b/recipes/bioconductor-mitch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "mitch" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 58be0f0e3a1e2fae1812b39cf31ae3d4 + md5: c21044d7d878482677fcb758acf0a650 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mitch", max_pin="x.x") }}' noarch: generic # Suggests: stringi, testthat (>= 2.1.0) requirements: diff --git a/recipes/bioconductor-mitoclone2/build_failure.osx-64.yaml b/recipes/bioconductor-mitoclone2/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..6dc0ac91eab34 --- /dev/null +++ b/recipes/bioconductor-mitoclone2/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 60f475e5bda7669f78635653dbdbbc6ac8818393a7bc525552f7d723c69c6571 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + source download error +log: |2- + tapi: 1100.0.11-h9ce4665_0 conda-forge + tk: 8.6.13-h1abcd95_1 conda-forge + tktable: 2.10-ha166976_5 conda-forge + toml: 0.10.2-pyhd8ed1ab_0 conda-forge + tomlkit: 0.12.3-pyha770c72_0 conda-forge + tzdata: 2023c-h71feb2d_0 conda-forge + xmltodict: 0.13.0-pyhd8ed1ab_0 conda-forge + xz: 5.2.6-h775f41a_0 conda-forge + yaml: 0.2.5-h0d85af4_2 conda-forge + yq: 3.2.3-pyhd8ed1ab_0 conda-forge + zlib: 1.2.13-h8a1eda9_5 conda-forge + zstd: 1.5.5-h829000d_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld + Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-mitoclone2_1703020590195/_build_env + + + The following NEW packages will be INSTALLED: + + ca-certificates: 2023.11.17-h8857fd0_0 conda-forge + cctools_osx-64: 973.0.1-habff3f6_15 conda-forge + clang: 15.0.7-hac416ee_4 conda-forge + clang-15: 15.0.7-default_h6b1ee41_4 conda-forge + clang_impl_osx-64: 15.0.7-h03d6864_7 conda-forge + clang_osx-64: 15.0.7-hb91bd55_7 conda-forge + clangxx: 15.0.7-default_h6b1ee41_4 conda-forge + clangxx_impl_osx-64: 15.0.7-h2133e9c_7 conda-forge + clangxx_osx-64: 15.0.7-hb91bd55_7 conda-forge + compiler-rt: 15.0.7-ha38d28d_2 conda-forge + compiler-rt_osx-64: 15.0.7-ha38d28d_2 conda-forge + icu: 73.2-hf5e326d_0 conda-forge + ld64_osx-64: 609-h0fd476b_15 conda-forge + libclang-cpp15: 15.0.7-default_h6b1ee41_4 conda-forge + libcxx: 16.0.6-hd57cbcb_0 conda-forge + libiconv: 1.17-hd75f5a5_2 conda-forge + libllvm15: 15.0.7-hbedff68_4 conda-forge + libxml2: 2.12.3-hc0ae0f7_0 conda-forge + libzlib: 1.2.13-h8a1eda9_5 conda-forge + llvm-tools: 15.0.7-hbedff68_4 conda-forge + make: 4.3-h22f3db7_1 conda-forge + openssl: 3.2.0-hd75f5a5_1 conda-forge + sigtool: 0.1.3-h88f4db0_0 conda-forge + tapi: 1100.0.11-h9ce4665_0 conda-forge + xz: 5.2.6-h775f41a_0 conda-forge + zstd: 1.5.5-h829000d_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + INFO:conda_build.source:Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + Downloading source to cache: mitoClone2_1.8.1_22c58ba6ed.tar.gz + INFO:conda_build.source:Downloading source to cache: mitoClone2_1.8.1_22c58ba6ed.tar.gz + Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/mitoClone2_1.8.1.tar.gz + INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/mitoClone2_1.8.1.tar.gz + Success + INFO:conda_build.source:Success + Extracting download + Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/bioconductor-mitoclone2/gamma.patch + Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/bioconductor-mitoclone2/gamma.patch with args: + ['-Np1', '-i', '/var/folders/qv/pdh5wsgn0lq3dp77zj602b5c0000gn/T/tmpz0brhpff/gamma.patch.native', '--binary'] + checking file inst/SCITEpkg/findBestTrees.cpp + Hunk #1 succeeded at 55 (offset 2 lines). + Hunk #2 FAILED at 97. + Hunk #3 succeeded at 264 (offset 2 lines). + 1 out of 3 hunks FAILED + checking file inst/SCITEpkg/mcmc.cpp + Hunk #1 FAILED at 41. + Hunk #2 succeeded at 98 (offset 2 lines). + Hunk #3 succeeded at 121 (offset 2 lines). + 1 out of 3 hunks FAILED + checking file inst/SCITEpkg/mcmc.h + Hunk #1 FAILED at 8. + 1 out of 1 hunk FAILED + Warning: failed to download source. If building, will try again after downloading recipe dependencies. + Error was: + Command '['/opt/mambaforge/envs/bioconda/bin/patch', '--no-backup-if-mismatch', '--batch', '-Np1', '-i', '/var/folders/qv/pdh5wsgn0lq3dp77zj602b5c0000gn/T/tmpz0brhpff/gamma.patch.native', '--binary', '--dry-run']' returned non-zero exit status 1. + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2125, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 663, in try_download + raise RuntimeError("Failed to download or patch source. Please see build log for info.") + RuntimeError: Failed to download or patch source. Please see build log for info. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-mitoclone2/meta.yaml b/recipes/bioconductor-mitoclone2/meta.yaml index 099174a4e3d3c..5d35d4e370509 100644 --- a/recipes/bioconductor-mitoclone2/meta.yaml +++ b/recipes/bioconductor-mitoclone2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.1" %} {% set name = "mitoClone2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,7 +11,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f92e5f2d2688b3584be28e0aa21b8b90 + md5: 22c58ba6ed0a51f10714551935477355 patches: - gamma.patch build: @@ -19,14 +19,15 @@ build: rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mitoclone2", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, Biostrings, testthat # SystemRequirements: GNU make, PhISCS (optional) requirements: host: - - 'bioconductor-deepsnv >=1.46.0,<1.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-deepsnv >=1.48.0,<1.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-pheatmap @@ -34,10 +35,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-deepsnv >=1.46.0,<1.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-deepsnv >=1.48.0,<1.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-pheatmap diff --git a/recipes/bioconductor-mixomics/meta.yaml b/recipes/bioconductor-mixomics/meta.yaml index a151268aed52f..d86404b99b5ef 100644 --- a/recipes/bioconductor-mixomics/meta.yaml +++ b/recipes/bioconductor-mixomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "6.24.0" %} +{% set version = "6.26.0" %} {% set name = "mixOmics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0002176b6d102e7b6c4e64f8f98b6df9 + md5: d735d1aec6a3576238256244e87031ff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mixomics", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, rgl requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-corpcor - r-dplyr @@ -38,7 +39,7 @@ requirements: - r-reshape2 - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-corpcor - r-dplyr diff --git a/recipes/bioconductor-mlinterfaces/meta.yaml b/recipes/bioconductor-mlinterfaces/meta.yaml index bf434ef950404..fe32e07d825f8 100644 --- a/recipes/bioconductor-mlinterfaces/meta.yaml +++ b/recipes/bioconductor-mlinterfaces/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.80.0" %} +{% set version = "1.82.0" %} {% set name = "MLInterfaces" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a88e54ac37f4c267ee6c033b1d84a08 + md5: acb5f91abaa05ef8c6b156b2cc7df846 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mlinterfaces", max_pin="x.x") }}' # Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party, klaR, BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-fpc @@ -45,11 +46,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-fpc diff --git a/recipes/bioconductor-mlp/meta.yaml b/recipes/bioconductor-mlp/meta.yaml index 704803aa1b5d6..2a506c09f0e69 100644 --- a/recipes/bioconductor-mlp/meta.yaml +++ b/recipes/bioconductor-mlp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "MLP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8456e51613e4fca3b957e9d6d0393414 + md5: 5ed5a850807679b4baa1c5d4d88f48d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mlp", max_pin="x.x") }}' noarch: generic # Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, org.Mmu.eg.db, KEGGREST, annotate, Rgraphviz, GOstats, graph, limma, mouse4302.db, reactome.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - r-gplots run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - r-gplots test: diff --git a/recipes/bioconductor-mlseq/meta.yaml b/recipes/bioconductor-mlseq/meta.yaml index d9aa91b142ad4..f6a2d8f85b768 100644 --- a/recipes/bioconductor-mlseq/meta.yaml +++ b/recipes/bioconductor-mlseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "MLSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6407c67b3d4879d54a1311c5b2e27f5f + md5: 07ebcff7e7a474bc21b783a6ebc2605b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mlseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, e1071, kernlab requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-sseq >=1.38.0,<1.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sseq >=1.40.0,<1.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-caret - r-foreach @@ -37,12 +38,12 @@ requirements: - r-venndiagram - r-xtable run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-sseq >=1.38.0,<1.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sseq >=1.40.0,<1.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-caret - r-foreach diff --git a/recipes/bioconductor-mm24kresogen.db/meta.yaml b/recipes/bioconductor-mm24kresogen.db/meta.yaml index fa0455eab640b..13b54d2ee5b24 100644 --- a/recipes/bioconductor-mm24kresogen.db/meta.yaml +++ b/recipes/bioconductor-mm24kresogen.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.5.0" %} {% set name = "mm24kresogen.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 437f5d4bc225ee500af1ecc2d4da472b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mm24kresogen.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml b/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml index 87aa088134e08..316ebba0491be 100644 --- a/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml +++ b/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "MmAgilentDesign026655.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7ef619bd2c74f22ea4f3c2b2c4131fe9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mmagilentdesign026655.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mmappr2data/meta.yaml b/recipes/bioconductor-mmappr2data/meta.yaml index 178b222d06b81..5d3faebe25bb7 100644 --- a/recipes/bioconductor-mmappr2data/meta.yaml +++ b/recipes/bioconductor-mmappr2data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MMAPPR2data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ea459c418711fc37e694b10789d03ae + md5: 5b4772746766de5c40448c865fa2d60d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mmappr2data", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, roxygen2, seqinr, readr requirements: host: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base run: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mmappr2data/post-link.sh b/recipes/bioconductor-mmappr2data/post-link.sh index 4dd7748e61a2e..6cbdc2a4f1170 100644 --- a/recipes/bioconductor-mmappr2data/post-link.sh +++ b/recipes/bioconductor-mmappr2data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mmappr2data-1.14.0" +installBiocDataPackage.sh "mmappr2data-1.16.0" diff --git a/recipes/bioconductor-mmdiff2/meta.yaml b/recipes/bioconductor-mmdiff2/meta.yaml index 5d7d9ff1f6c61..ad1ed95691e31 100644 --- a/recipes/bioconductor-mmdiff2/meta.yaml +++ b/recipes/bioconductor-mmdiff2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "MMDiff2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 59a85253ca552a7e3140890cf5470067 + md5: 6d14e03f2d5842c403a50c41f30c82d1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mmdiff2", max_pin="x.x") }}' noarch: generic # Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-locfit - r-rcolorbrewer - r-shiny run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-locfit diff --git a/recipes/bioconductor-mmdiffbamsubset/meta.yaml b/recipes/bioconductor-mmdiffbamsubset/meta.yaml index 48e87f668f0c6..c8687b937206b 100644 --- a/recipes/bioconductor-mmdiffbamsubset/meta.yaml +++ b/recipes/bioconductor-mmdiffbamsubset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "MMDiffBamSubset" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b9a590f3dc54a5b5b4e36232ca7e2538 + md5: 0becc66301b49b58a99efa19577ee27c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mmdiffbamsubset", max_pin="x.x") }}' noarch: generic # Suggests: MMDiff2 requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mmdiffbamsubset/post-link.sh b/recipes/bioconductor-mmdiffbamsubset/post-link.sh index c6ea938925a92..41d02cf30eea3 100644 --- a/recipes/bioconductor-mmdiffbamsubset/post-link.sh +++ b/recipes/bioconductor-mmdiffbamsubset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mmdiffbamsubset-1.36.0" +installBiocDataPackage.sh "mmdiffbamsubset-1.38.0" diff --git a/recipes/bioconductor-mmuphin/meta.yaml b/recipes/bioconductor-mmuphin/meta.yaml index c674a0d4a3eca..40529f7cbcec9 100644 --- a/recipes/bioconductor-mmuphin/meta.yaml +++ b/recipes/bioconductor-mmuphin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MMUPHin" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef1929535164bd5dbb8e6b764a90d141 + md5: 51f094480eb1629226dc1da59902ab32 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mmuphin", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter # SystemRequirements: glpk (>= 4.57) requirements: host: - - 'bioconductor-maaslin2 >=1.14.0,<1.15.0' + - 'bioconductor-maaslin2 >=1.16.0,<1.17.0' - r-base - r-cowplot - r-dplyr @@ -33,7 +34,7 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-maaslin2 >=1.14.0,<1.15.0' + - 'bioconductor-maaslin2 >=1.16.0,<1.17.0' - r-base - r-cowplot - r-dplyr diff --git a/recipes/bioconductor-mnem/meta.yaml b/recipes/bioconductor-mnem/meta.yaml index 0332f413204d8..10fae6b84f0a8 100644 --- a/recipes/bioconductor-mnem/meta.yaml +++ b/recipes/bioconductor-mnem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "mnem" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: df7fca9a51f7c89a2f846cf070e03341 + md5: 630cb52a48148dc82038613aacb4e834 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mnem", max_pin="x.x") }}' # Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM, BiocStyle requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-linnorm >=2.24.0,<2.25.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-linnorm >=2.26.0,<2.27.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-cluster - r-data.table @@ -40,9 +41,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-linnorm >=2.24.0,<2.25.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-linnorm >=2.26.0,<2.27.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-cluster - r-data.table diff --git a/recipes/bioconductor-moanin/meta.yaml b/recipes/bioconductor-moanin/meta.yaml index 231bfbbaf8cd4..896119d5f8400 100644 --- a/recipes/bioconductor-moanin/meta.yaml +++ b/recipes/bioconductor-moanin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "moanin" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 47abaa04774cc2d70389e1dde355e8b9 + md5: 74f0ff5d927d538a2b41cdc9c1ee9fd9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moanin", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 1.0.0), timecoursedata, knitr, rmarkdown, markdown, covr, BiocStyle requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-clusterr - 'r-mass >=1.0.0' @@ -35,11 +36,11 @@ requirements: - r-viridis - r-zoo run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-clusterr - 'r-mass >=1.0.0' diff --git a/recipes/bioconductor-mobilitytransformr/meta.yaml b/recipes/bioconductor-mobilitytransformr/meta.yaml index 59a78638e061e..5d8c9210a5279 100644 --- a/recipes/bioconductor-mobilitytransformr/meta.yaml +++ b/recipes/bioconductor-mobilitytransformr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "MobilityTransformR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: feaa92c6a8c2d5c9145dfde034172797 + md5: 1d0f7904be49e25235092248b757df19 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mobilitytransformr", max_pin="x.x") }}' noarch: generic # Suggests: testthat, msdata (>= 0.35.3), knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown requirements: host: - - 'bioconductor-metabocoreutils >=1.8.0,<1.9.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base run: - - 'bioconductor-metabocoreutils >=1.8.0,<1.9.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base test: commands: diff --git a/recipes/bioconductor-moda/meta.yaml b/recipes/bioconductor-moda/meta.yaml index aa8aa54d1e1ed..f0c112fc22b46 100644 --- a/recipes/bioconductor-moda/meta.yaml +++ b/recipes/bioconductor-moda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "MODA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dee62b28e674b74f2ee50a7413256fdb + md5: 5f48d76fbd7f8905725dbd2db1bc6fee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moda", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-amountain >=1.26.0,<1.27.0' + - 'bioconductor-amountain >=1.28.0,<1.29.0' - r-base - r-cluster - r-dynamictreecut @@ -29,7 +30,7 @@ requirements: - r-rcolorbrewer - r-wgcna run: - - 'bioconductor-amountain >=1.26.0,<1.27.0' + - 'bioconductor-amountain >=1.28.0,<1.29.0' - r-base - r-cluster - r-dynamictreecut diff --git a/recipes/bioconductor-modcon/meta.yaml b/recipes/bioconductor-modcon/meta.yaml index 7dc0070ac4bae..b45ecc4ebeb3c 100644 --- a/recipes/bioconductor-modcon/meta.yaml +++ b/recipes/bioconductor-modcon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ModCon" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 30a6c15c8ebc53114e7f411b9aa54bdc + md5: bdb0634e890917a01325519cf6e53f90 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-modcon", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, dplyr, shinycssloaders, shiny, shinyFiles, shinydashboard, shinyjs # SystemRequirements: Perl diff --git a/recipes/bioconductor-modstrings/meta.yaml b/recipes/bioconductor-modstrings/meta.yaml index ace9febb26799..41aab942018f8 100644 --- a/recipes/bioconductor-modstrings/meta.yaml +++ b/recipes/bioconductor-modstrings/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Modstrings" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 005a6307ac499c539b9d7b44d7d85eb2 + md5: 04e7bccc20c165b4d1317e995a0b1de2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-modstrings", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-crayon - r-stringi - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-crayon - r-stringi diff --git a/recipes/bioconductor-moe430a.db/meta.yaml b/recipes/bioconductor-moe430a.db/meta.yaml index b11256886105a..07af16105b075 100644 --- a/recipes/bioconductor-moe430a.db/meta.yaml +++ b/recipes/bioconductor-moe430a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "moe430a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2bcdace3c55437bc8428b99064e486b1 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moe430a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moe430acdf/meta.yaml b/recipes/bioconductor-moe430acdf/meta.yaml index a0309689ab273..269ad39177873 100644 --- a/recipes/bioconductor-moe430acdf/meta.yaml +++ b/recipes/bioconductor-moe430acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "moe430acdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b03f1295fc483f0d782a4615e8ca0137 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moe430acdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moe430aprobe/meta.yaml b/recipes/bioconductor-moe430aprobe/meta.yaml index 0229d3b8e3a92..bb37dab84d098 100644 --- a/recipes/bioconductor-moe430aprobe/meta.yaml +++ b/recipes/bioconductor-moe430aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "moe430aprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0aa83189d04599a65211d1a2f0a51c8f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moe430aprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moe430b.db/meta.yaml b/recipes/bioconductor-moe430b.db/meta.yaml index 8580ce349d001..1ca12a8892d3c 100644 --- a/recipes/bioconductor-moe430b.db/meta.yaml +++ b/recipes/bioconductor-moe430b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "moe430b.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2d8a80b9d3342fb943087cc327c824e7 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moe430b.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moe430bcdf/meta.yaml b/recipes/bioconductor-moe430bcdf/meta.yaml index ad821650817a3..e59a11f6dde96 100644 --- a/recipes/bioconductor-moe430bcdf/meta.yaml +++ b/recipes/bioconductor-moe430bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "moe430bcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b7112dcf8ccfe4e079ca67ff62046f2e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moe430bcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moe430bprobe/meta.yaml b/recipes/bioconductor-moe430bprobe/meta.yaml index e84ca437bcf8d..cc36302889064 100644 --- a/recipes/bioconductor-moe430bprobe/meta.yaml +++ b/recipes/bioconductor-moe430bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "moe430bprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1368e6f4225babe7a693ccd39a3a436a build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moe430bprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moex10stprobeset.db/meta.yaml b/recipes/bioconductor-moex10stprobeset.db/meta.yaml index eb27513f5a45b..cfb5fa806324b 100644 --- a/recipes/bioconductor-moex10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-moex10stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "moex10stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b1c12c80a4424e2854beab9dc796cb00 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moex10stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml index feb6e978b0de1..224ad7a7dc909 100644 --- a/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "moex10sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bc3357b3c77ab7bf1dfb66f5f7da36ec build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moex10sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moexexonprobesetlocation/meta.yaml b/recipes/bioconductor-moexexonprobesetlocation/meta.yaml index 7db924e5850a4..60209c1317491 100644 --- a/recipes/bioconductor-moexexonprobesetlocation/meta.yaml +++ b/recipes/bioconductor-moexexonprobesetlocation/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.15.0" %} {% set name = "MoExExonProbesetLocation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 07eea205fce2a8cf4585fa7e71fb0057 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moexexonprobesetlocation", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mofa2/meta.yaml b/recipes/bioconductor-mofa2/meta.yaml index 45435aa0c80a0..5040a7de17019 100644 --- a/recipes/bioconductor-mofa2/meta.yaml +++ b/recipes/bioconductor-mofa2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MOFA2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 534a7aee62498651a346619081e8d819 + md5: 0ce3c0d9a65e9e3f18d387af8a86ef6e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mofa2", max_pin="x.x") }}' # Suggests: knitr, testthat, Seurat, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown, data.table, tidyverse, BiocStyle, Matrix, markdown # SystemRequirements: Python (>=3), numpy, pandas, h5py, scipy, argparse, sklearn, mofapy2 requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-corrplot - r-cowplot @@ -42,10 +43,10 @@ requirements: - r-tidyr - r-uwot run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-corrplot - r-cowplot diff --git a/recipes/bioconductor-mofadata/meta.yaml b/recipes/bioconductor-mofadata/meta.yaml index ba73ea609b4be..3105056f66ed7 100644 --- a/recipes/bioconductor-mofadata/meta.yaml +++ b/recipes/bioconductor-mofadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "MOFAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c3605011c45bfe05471c35727cf9896 + md5: 23e46e209a43d7e62cfd6accc6a6fb44 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mofadata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, MultiAssayExperiment, rmarkdown, BiocStyle requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mofadata/post-link.sh b/recipes/bioconductor-mofadata/post-link.sh index d8d3db7951bff..b927a90f23c04 100644 --- a/recipes/bioconductor-mofadata/post-link.sh +++ b/recipes/bioconductor-mofadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mofadata-1.16.1" +installBiocDataPackage.sh "mofadata-1.18.0" diff --git a/recipes/bioconductor-mogamun/meta.yaml b/recipes/bioconductor-mogamun/meta.yaml index 2d1af7529d78f..ec048725b40a6 100644 --- a/recipes/bioconductor-mogamun/meta.yaml +++ b/recipes/bioconductor-mogamun/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MOGAMUN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ce6bc4ff332cffdd506ab91cd5246055 + md5: 8e2d5c06b9fc3d7e294b154f7efb83b3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogamun", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-igraph - r-runit - r-stringr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-igraph - r-runit diff --git a/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml b/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml index 6d9d7efb92d10..99400c2a549a3 100644 --- a/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml +++ b/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "mogene.1.0.st.v1frmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b46f76903d0f19b85e8fa30347813ff5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene.1.0.st.v1frmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene10stprobeset.db/meta.yaml b/recipes/bioconductor-mogene10stprobeset.db/meta.yaml index 150788d2deaab..98460dd552e38 100644 --- a/recipes/bioconductor-mogene10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-mogene10stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mogene10stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 570d4cf3fcc42d1e9b54237b9e4eb5f7 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene10stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml index 9b1a33769b847..b7365dee5c39e 100644 --- a/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mogene10sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9553a8ecefad2baa7241c6b6bb8013f5 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene10sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene10stv1cdf/meta.yaml b/recipes/bioconductor-mogene10stv1cdf/meta.yaml index 1fe199e259fc5..842e7b799689e 100644 --- a/recipes/bioconductor-mogene10stv1cdf/meta.yaml +++ b/recipes/bioconductor-mogene10stv1cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mogene10stv1cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9c0271f5d6493290fc47f041a8c3f925 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene10stv1cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene10stv1probe/meta.yaml b/recipes/bioconductor-mogene10stv1probe/meta.yaml index 2c76031f6e705..7df09b6409c4e 100644 --- a/recipes/bioconductor-mogene10stv1probe/meta.yaml +++ b/recipes/bioconductor-mogene10stv1probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mogene10stv1probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 63cba1e2a0edee9f201267057fddb0fa build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene10stv1probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene11stprobeset.db/meta.yaml b/recipes/bioconductor-mogene11stprobeset.db/meta.yaml index 1674014284721..d6a7c91a56257 100644 --- a/recipes/bioconductor-mogene11stprobeset.db/meta.yaml +++ b/recipes/bioconductor-mogene11stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mogene11stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1fba63da3f550e814a58c09d24d61cc0 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene11stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml index 68b1d94d06bd2..e973216aa7b66 100644 --- a/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mogene11sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2a3bf07a4794e2349b7d09368dcb7d18 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene11sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene20stprobeset.db/meta.yaml b/recipes/bioconductor-mogene20stprobeset.db/meta.yaml index ee52a6e528392..d2fae2f15b125 100644 --- a/recipes/bioconductor-mogene20stprobeset.db/meta.yaml +++ b/recipes/bioconductor-mogene20stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mogene20stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a64ddbf33e4f2b96301452e808d0e81a build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene20stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml index f852ea0bff57e..192560f9dbc55 100644 --- a/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mogene20sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e00e56d47bd19169875690e8e2129156 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene20sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene21stprobeset.db/meta.yaml b/recipes/bioconductor-mogene21stprobeset.db/meta.yaml index ca1fbc8d88889..fae2795386efa 100644 --- a/recipes/bioconductor-mogene21stprobeset.db/meta.yaml +++ b/recipes/bioconductor-mogene21stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mogene21stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d6b3c352329b46493a20f6c27db05d43 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene21stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml index 775a5abc82d65..d36ffcbf36338 100644 --- a/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mogene21sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 10aaecc97bf06bfe770496b99612837a build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene21sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogsa/meta.yaml b/recipes/bioconductor-mogsa/meta.yaml index 4340dde6e1703..d9ec395d1b4f8 100644 --- a/recipes/bioconductor-mogsa/meta.yaml +++ b/recipes/bioconductor-mogsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "mogsa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 97374d3cdbd264479ec1188d20ddc51f + md5: 177b003a38a7dc7ce3fb238369d1b6e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogsa", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, org.Hs.eg.db requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-cluster - r-corpcor - r-gplots - r-svd run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-cluster - r-corpcor diff --git a/recipes/bioconductor-moleculeexperiment/meta.yaml b/recipes/bioconductor-moleculeexperiment/meta.yaml index 1aa49271ff42a..995c26bed8b41 100644 --- a/recipes/bioconductor-moleculeexperiment/meta.yaml +++ b/recipes/bioconductor-moleculeexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.2" %} {% set name = "MoleculeExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94c764955d2e47687932b60877afec83 + md5: d8fef705349bc9464ae152cd47bb9a58 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moleculeexperiment", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base + - r-cli - r-data.table - 'r-dplyr >=1.1.1' - r-ggplot2 @@ -31,11 +37,15 @@ requirements: - r-purrr - r-rjson - r-rlang - - r-sp - r-terra run: - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base + - r-cli - r-data.table - 'r-dplyr >=1.1.1' - r-ggplot2 @@ -44,7 +54,6 @@ requirements: - r-purrr - r-rjson - r-rlang - - r-sp - r-terra test: commands: diff --git a/recipes/bioconductor-moma/meta.yaml b/recipes/bioconductor-moma/meta.yaml index 72b4f034a14c9..82fa380418cee 100644 --- a/recipes/bioconductor-moma/meta.yaml +++ b/recipes/bioconductor-moma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "MOMA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 375d2de012590d80009625c8bdc11217 + md5: ce4cf6dab5fea53127b5b980756ef5db build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moma", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, viper requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-circlize - r-cluster @@ -39,9 +40,9 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-circlize - r-cluster diff --git a/recipes/bioconductor-monalisa/meta.yaml b/recipes/bioconductor-monalisa/meta.yaml index 4fe4192f03b03..a8dbdc4c4bbc7 100644 --- a/recipes/bioconductor-monalisa/meta.yaml +++ b/recipes/bioconductor-monalisa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "monaLisa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,46 +11,47 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4e0c35f87fe09e20036c129bc9e1e736 + md5: fc86eb3743fc47252a4420cd850ead9e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-monalisa", max_pin="x.x") }}' noarch: generic # Suggests: JASPAR2020, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, testthat, BiocStyle, gridExtra requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-circlize - r-glmnet - r-stabs - r-vioplot run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-circlize - r-glmnet diff --git a/recipes/bioconductor-monocle/meta.yaml b/recipes/bioconductor-monocle/meta.yaml index 08bf12a037b44..1877a38efe4cf 100644 --- a/recipes/bioconductor-monocle/meta.yaml +++ b/recipes/bioconductor-monocle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "monocle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 32a002f0d1231c13af5da03fc43f1401 + md5: 8b3a3d5cd2698b4cef4396c388250658 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-monocle", max_pin="x.x") }}' # Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-hsmmsinglecell >=1.20.0,<1.21.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-hsmmsinglecell >=1.22.0,<1.23.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-cluster - r-combinat @@ -54,11 +55,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-hsmmsinglecell >=1.20.0,<1.21.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-hsmmsinglecell >=1.22.0,<1.23.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-cluster - r-combinat diff --git a/recipes/bioconductor-moonlight2r/build.sh b/recipes/bioconductor-moonlight2r/build.sh new file mode 100644 index 0000000000000..497f7b5bdb678 --- /dev/null +++ b/recipes/bioconductor-moonlight2r/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +export LD_LIBRARY_PATH=${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-moonlight2r/meta.yaml b/recipes/bioconductor-moonlight2r/meta.yaml new file mode 100644 index 0000000000000..0bfdabb5af5a6 --- /dev/null +++ b/recipes/bioconductor-moonlight2r/meta.yaml @@ -0,0 +1,108 @@ +{% set version = "1.0.0" %} +{% set name = "Moonlight2R" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 45af1bc580f9231cb2a83eae7517d3b8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moonlight2r", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), devtools, roxygen2, png +# SystemRequirements: CScapeSomatic +requirements: + host: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - r-base + - r-circlize + - r-doparallel + - r-dplyr + - r-easypubmed + - r-foreach + - r-fuzzyjoin + - r-gplots + - r-hiver + - r-magrittr + - r-parmigene + - r-purrr + - r-qpdf + - r-randomforest + - r-rcolorbrewer + - r-readr + - r-rismed + - r-seqminer + - r-stringr + - r-tibble + - r-tidyheatmap + - r-tidyr + run: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - r-base + - r-circlize + - r-doparallel + - r-dplyr + - r-easypubmed + - r-foreach + - r-fuzzyjoin + - r-gplots + - r-hiver + - r-magrittr + - r-parmigene + - r-purrr + - r-qpdf + - r-randomforest + - r-rcolorbrewer + - r-readr + - r-rismed + - r-seqminer + - r-stringr + - r-tibble + - r-tidyheatmap + - r-tidyr + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] +test: + commands: + - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Identify oncogenes and tumor suppressor genes from omics data' + description: 'The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role (notably oncogenes and tumor suppressors). We present an updated version of the R/bioconductor package called MoonlightR, namely Moonlight2R, which returns a list of candidate driver genes for specific cancer types on the basis of omics data integration. The Moonlight framework contains a primary layer where gene expression data and information about biological processes are integrated to predict genes called oncogenic mediators, divided into putative tumor suppressors and putative oncogenes. This is done through functional enrichment analyses, gene regulatory networks and upstream regulator analyses to score the importance of well-known biological processes with respect to the studied cancer type. By evaluating the effect of the oncogenic mediators on biological processes or through random forests, the primary layer predicts two putative roles for the oncogenic mediators: i) tumor suppressor genes (TSGs) and ii) oncogenes (OCGs). As gene expression data alone is not enough to explain the deregulation of the genes, a second layer of evidence is needed. We have automated the integration of a secondary mutational layer through new functionalities in Moonlight2R. These functionalities analyze mutations in the cancer cohort and classifies these into driver and passenger mutations using the driver mutation prediction tool, CScape-somatic. Those oncogenic mediators with at least one driver mutation are retained as the driver genes. As a consequence, this methodology does not only identify genes playing a dual role (e.g. TSG in one cancer type and OCG in another) but also helps in elucidating the biological processes underlying their specific roles. In particular, Moonlight2R can be used to discover OCGs and TSGs in the same cancer type. This may for instance help in answering the question whether some genes change role between early stages (I, II) and late stages (III, IV). In the future, this analysis could be useful to determine the causes of different resistances to chemotherapeutic treatments.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' +extra: + container: + extended-base: true + diff --git a/recipes/bioconductor-moonlightr/meta.yaml b/recipes/bioconductor-moonlightr/meta.yaml index a7f5cc135260a..c20170c048746 100644 --- a/recipes/bioconductor-moonlightr/meta.yaml +++ b/recipes/bioconductor-moonlightr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "MoonlightR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6dc98a013d9a14f5fb86143343d1d102 + md5: 2a389ad9b7fe5ffc5e2c47717eb0b4c0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moonlightr", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png +# Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png, edgeR requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgabiolinks >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgabiolinks >=2.30.0,<2.31.0' - r-base - r-circlize - r-doparallel @@ -39,13 +40,13 @@ requirements: - r-rcolorbrewer - r-rismed run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgabiolinks >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgabiolinks >=2.30.0,<2.31.0' - r-base - r-circlize - r-doparallel diff --git a/recipes/bioconductor-mosaics/meta.yaml b/recipes/bioconductor-mosaics/meta.yaml index 931647a8ef049..a9598eaacbb9c 100644 --- a/recipes/bioconductor-mosaics/meta.yaml +++ b/recipes/bioconductor-mosaics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.38.0" %} +{% set version = "2.40.0" %} {% set name = "mosaics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e8ea8871c14e28559be2f8ccb77837ff + md5: 0648fcfd9fd595974e0602fbb2a37cac build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mosaics", max_pin="x.x") }}' # Suggests: mosaicsExample # SystemRequirements: Perl requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-lattice - r-mass @@ -35,12 +36,12 @@ requirements: - liblapack - 'perl >=5.6.0' run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-lattice - r-mass diff --git a/recipes/bioconductor-mosaicsexample/meta.yaml b/recipes/bioconductor-mosaicsexample/meta.yaml index 28c25085fd5ee..ff93401dec058 100644 --- a/recipes/bioconductor-mosaicsexample/meta.yaml +++ b/recipes/bioconductor-mosaicsexample/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "mosaicsExample" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dbbc0ae50f0d93a64a45efe4bb848a71 + md5: 8852ad56f152a138367e7630b6b21efb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mosaicsexample", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mosaicsexample/post-link.sh b/recipes/bioconductor-mosaicsexample/post-link.sh index 67a72782b8979..b88c16fdb3cce 100644 --- a/recipes/bioconductor-mosaicsexample/post-link.sh +++ b/recipes/bioconductor-mosaicsexample/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mosaicsexample-1.38.0" +installBiocDataPackage.sh "mosaicsexample-1.40.0" diff --git a/recipes/bioconductor-mosbi/meta.yaml b/recipes/bioconductor-mosbi/meta.yaml index 6651c91f23fc6..4206531beddd4 100644 --- a/recipes/bioconductor-mosbi/meta.yaml +++ b/recipes/bioconductor-mosbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "mosbi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b333ac572e9c67bf00a326e4be6cec60 + md5: f34159f8140d9fe59ea7fe2546e9cdce build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mosbi", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat (>= 3.0.0) # SystemRequirements: C++17, GNU make requirements: host: - - 'bioconductor-fabia >=2.46.0,<2.47.0' - - 'bioconductor-qubic >=1.28.0,<1.29.0' + - 'bioconductor-fabia >=2.48.0,<2.49.0' + - 'bioconductor-qubic >=1.30.0,<1.31.0' - r-akmbiclust - r-base - r-bh @@ -36,8 +37,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-fabia >=2.46.0,<2.47.0' - - 'bioconductor-qubic >=1.28.0,<1.29.0' + - 'bioconductor-fabia >=2.48.0,<2.49.0' + - 'bioconductor-qubic >=1.30.0,<1.31.0' - r-akmbiclust - r-base - r-bh diff --git a/recipes/bioconductor-mosim/meta.yaml b/recipes/bioconductor-mosim/meta.yaml index 045faf97a8da1..b7ae429633a46 100644 --- a/recipes/bioconductor-mosim/meta.yaml +++ b/recipes/bioconductor-mosim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MOSim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ece9e267f663dd2ff82200594d6d59fa + md5: 67f131b000a6d50361f61b4a78835d47 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mosim", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ggplot2 @@ -39,9 +40,9 @@ requirements: - r-tidyr - r-zoo run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-motif2site/meta.yaml b/recipes/bioconductor-motif2site/meta.yaml index 16140537eb5e7..d941340b40832 100644 --- a/recipes/bioconductor-motif2site/meta.yaml +++ b/recipes/bioconductor-motif2site/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "Motif2Site" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 594b23135d3e5f26922687fb1c328655 + md5: e8228f1deb42f2d4b3867a90a6eba14c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-motif2site", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-mass - r-mixtools run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-mass - r-mixtools diff --git a/recipes/bioconductor-motifbreakr/meta.yaml b/recipes/bioconductor-motifbreakr/meta.yaml index d83aaeb709ed2..ac68355c1531a 100644 --- a/recipes/bioconductor-motifbreakr/meta.yaml +++ b/recipes/bioconductor-motifbreakr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.13.7" %} +{% set version = "2.16.0" %} {% set name = "motifbreakR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,49 +11,50 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b47582e0b811ea6ec5a2e46456e1d7db + md5: fd2ed6098a4bade8948f237753404006 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-motifbreakr", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP155.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-motifdb >=1.42.0,<1.43.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-motifdb >=1.44.0,<1.45.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-matrixstats - r-stringr - r-tfmpvalue run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-motifdb >=1.42.0,<1.43.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-motifdb >=1.44.0,<1.45.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-matrixstats - r-stringr diff --git a/recipes/bioconductor-motifcounter/meta.yaml b/recipes/bioconductor-motifcounter/meta.yaml index a6ee87d58aa3a..a8167142b3b79 100644 --- a/recipes/bioconductor-motifcounter/meta.yaml +++ b/recipes/bioconductor-motifcounter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "motifcounter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 74707d361ecee0670ee22449f0bd3479 + md5: f093ba4ac3fe6bcf19d9d46bfb084290 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-motifcounter", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-motifdb/meta.yaml b/recipes/bioconductor-motifdb/meta.yaml index 63e63c09db371..ccbbed4686d7d 100644 --- a/recipes/bioconductor-motifdb/meta.yaml +++ b/recipes/bioconductor-motifdb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "MotifDb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 816f2af600528aae335542318f7ead0f + md5: 0aa63f3bc133dc0fa6c8cf88ebae383b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-motifdb", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR, markdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-splitstackshape run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-splitstackshape test: diff --git a/recipes/bioconductor-motifmatchr/meta.yaml b/recipes/bioconductor-motifmatchr/meta.yaml index b18da3e965dc7..77a5618b3748d 100644 --- a/recipes/bioconductor-motifmatchr/meta.yaml +++ b/recipes/bioconductor-motifmatchr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "motifmatchr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cc0571d16d56335905d347e7967a7308 + md5: 23c63cb97f5e359a4fb9e5e6751e037d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-motifmatchr", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-matrix - r-rcpp @@ -37,15 +38,15 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-motifstack/meta.yaml b/recipes/bioconductor-motifstack/meta.yaml index 547e310dd4115..2475f81526c68 100644 --- a/recipes/bioconductor-motifstack/meta.yaml +++ b/recipes/bioconductor-motifstack/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.1" %} +{% set version = "1.46.0" %} {% set name = "motifStack" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a907c93e9a990ab341e7ed4ce5a29bc + md5: b3306b32c8722e6d63ee1a37165a572e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-motifstack", max_pin="x.x") }}' noarch: generic # Suggests: Cairo, grImport, grImport2, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr, RUnit, rmarkdown, JASPAR2020 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-ade4 - r-base - r-ggplot2 - r-htmlwidgets - r-xml run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-ade4 - r-base - r-ggplot2 diff --git a/recipes/bioconductor-mouse.db0/meta.yaml b/recipes/bioconductor-mouse.db0/meta.yaml index 8cdf1d8f11550..ae26bfd28f0fd 100644 --- a/recipes/bioconductor-mouse.db0/meta.yaml +++ b/recipes/bioconductor-mouse.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "mouse.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 132244baa13685fdb259ecaecd9535af + md5: 1ef6bb1d25e53443871e0e8c975b36c0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse.db0/post-link.sh b/recipes/bioconductor-mouse.db0/post-link.sh index 7602a0e166383..b17f1a0a17b14 100644 --- a/recipes/bioconductor-mouse.db0/post-link.sh +++ b/recipes/bioconductor-mouse.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mouse.db0-3.17.0" +installBiocDataPackage.sh "mouse.db0-3.18.0" diff --git a/recipes/bioconductor-mouse4302.db/meta.yaml b/recipes/bioconductor-mouse4302.db/meta.yaml index 8fb2201559542..0a61e3af5ee7a 100644 --- a/recipes/bioconductor-mouse4302.db/meta.yaml +++ b/recipes/bioconductor-mouse4302.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mouse4302.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4ecaa53d32faca4199ba712c0e8ee570 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse4302.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse4302barcodevecs/meta.yaml b/recipes/bioconductor-mouse4302barcodevecs/meta.yaml index f8719b767f2a7..027726e25334e 100644 --- a/recipes/bioconductor-mouse4302barcodevecs/meta.yaml +++ b/recipes/bioconductor-mouse4302barcodevecs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "mouse4302barcodevecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bb60f755fb3fc86b8dbb769bbe6f06c4 + md5: 365757fba17dae1ed483e184d2c9fcdb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse4302barcodevecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse4302barcodevecs/post-link.sh b/recipes/bioconductor-mouse4302barcodevecs/post-link.sh index 3b8b8dba1b88a..ed7160125db4e 100644 --- a/recipes/bioconductor-mouse4302barcodevecs/post-link.sh +++ b/recipes/bioconductor-mouse4302barcodevecs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mouse4302barcodevecs-1.38.0" +installBiocDataPackage.sh "mouse4302barcodevecs-1.40.0" diff --git a/recipes/bioconductor-mouse4302cdf/meta.yaml b/recipes/bioconductor-mouse4302cdf/meta.yaml index 8ab265eec436f..57eb77636c347 100644 --- a/recipes/bioconductor-mouse4302cdf/meta.yaml +++ b/recipes/bioconductor-mouse4302cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mouse4302cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bda3463613f958de35c58777db05cec2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse4302cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse4302frmavecs/meta.yaml b/recipes/bioconductor-mouse4302frmavecs/meta.yaml index f7e7a74083c32..22c8cdff80066 100644 --- a/recipes/bioconductor-mouse4302frmavecs/meta.yaml +++ b/recipes/bioconductor-mouse4302frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "mouse4302frmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ec144b381abbe54d696356c1c124e372 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse4302frmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse4302probe/meta.yaml b/recipes/bioconductor-mouse4302probe/meta.yaml index c2556746c00f9..6da34b4b12cbc 100644 --- a/recipes/bioconductor-mouse4302probe/meta.yaml +++ b/recipes/bioconductor-mouse4302probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mouse4302probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7116787a7db241a545e79e419a8cfa0d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse4302probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse430a2.db/meta.yaml b/recipes/bioconductor-mouse430a2.db/meta.yaml index 4a05a16ffe54c..29f8490359d73 100644 --- a/recipes/bioconductor-mouse430a2.db/meta.yaml +++ b/recipes/bioconductor-mouse430a2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mouse430a2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0f1d053517af5f973f3cc49289cca1e5 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse430a2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse430a2cdf/meta.yaml b/recipes/bioconductor-mouse430a2cdf/meta.yaml index b120d005cf0e3..e6b2a4871edaf 100644 --- a/recipes/bioconductor-mouse430a2cdf/meta.yaml +++ b/recipes/bioconductor-mouse430a2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mouse430a2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1114c0415d1200bc21ad205e0830b075 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse430a2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse430a2frmavecs/meta.yaml b/recipes/bioconductor-mouse430a2frmavecs/meta.yaml index b15791ee611b3..885f3133c6c45 100644 --- a/recipes/bioconductor-mouse430a2frmavecs/meta.yaml +++ b/recipes/bioconductor-mouse430a2frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.0" %} {% set name = "mouse430a2frmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3bcb8de9182bbb8de5d560748eafa0cc build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse430a2frmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse430a2probe/meta.yaml b/recipes/bioconductor-mouse430a2probe/meta.yaml index b6d9a39038733..9891dca3ac191 100644 --- a/recipes/bioconductor-mouse430a2probe/meta.yaml +++ b/recipes/bioconductor-mouse430a2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mouse430a2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bb3c34477d4fcf03a539772011118795 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse430a2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mousechrloc/meta.yaml b/recipes/bioconductor-mousechrloc/meta.yaml index 0be1b73b5ae0c..97f1bb6f99725 100644 --- a/recipes/bioconductor-mousechrloc/meta.yaml +++ b/recipes/bioconductor-mousechrloc/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.1.6" %} {% set name = "mouseCHRLOC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0b81d7391e628cc355af4de3c5585a5f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mousechrloc", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mousefm/meta.yaml b/recipes/bioconductor-mousefm/meta.yaml index 895f5a44886b4..c7958d978dad0 100644 --- a/recipes/bioconductor-mousefm/meta.yaml +++ b/recipes/bioconductor-mousefm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MouseFM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 146c8308ce2ca568d5aed58b37471960 + md5: 02947a619a95abf1ad58bb781953a22d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mousefm", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-curl - r-data.table @@ -38,10 +39,10 @@ requirements: - r-scales - r-tidyr run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-curl - r-data.table diff --git a/recipes/bioconductor-mousegastrulationdata/meta.yaml b/recipes/bioconductor-mousegastrulationdata/meta.yaml index e3a086be85ff4..c6470676bb06c 100644 --- a/recipes/bioconductor-mousegastrulationdata/meta.yaml +++ b/recipes/bioconductor-mousegastrulationdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MouseGastrulationData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 671b5016215ff92409c4aba1f4a59c16 + md5: 4af06fb157942c6cfd9f24494bd7ae1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mousegastrulationdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bumpymatrix >=1.8.0,<1.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bumpymatrix >=1.8.0,<1.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mousegastrulationdata/post-link.sh b/recipes/bioconductor-mousegastrulationdata/post-link.sh index 8e592cd3fa57a..62b2c9b8a5dae 100644 --- a/recipes/bioconductor-mousegastrulationdata/post-link.sh +++ b/recipes/bioconductor-mousegastrulationdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mousegastrulationdata-1.14.0" +installBiocDataPackage.sh "mousegastrulationdata-1.16.0" diff --git a/recipes/bioconductor-mousethymusageing/meta.yaml b/recipes/bioconductor-mousethymusageing/meta.yaml index ced8a4b35d2a2..0f159f50427ac 100644 --- a/recipes/bioconductor-mousethymusageing/meta.yaml +++ b/recipes/bioconductor-mousethymusageing/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MouseThymusAgeing" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e5453bec0eab9aa18f7f438bbfd63c27 + md5: cf1889c22fa9e5ac5899a4d911907a90 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mousethymusageing", max_pin="x.x") }}' noarch: generic # Suggests: knitr, scuttle, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mousethymusageing/post-link.sh b/recipes/bioconductor-mousethymusageing/post-link.sh index abdcde4f7eb4f..f63c5f266662c 100644 --- a/recipes/bioconductor-mousethymusageing/post-link.sh +++ b/recipes/bioconductor-mousethymusageing/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mousethymusageing-1.8.0" +installBiocDataPackage.sh "mousethymusageing-1.10.0" diff --git a/recipes/bioconductor-mpedbarray.db/meta.yaml b/recipes/bioconductor-mpedbarray.db/meta.yaml index ae5e294805f59..b919b9c2456b9 100644 --- a/recipes/bioconductor-mpedbarray.db/meta.yaml +++ b/recipes/bioconductor-mpedbarray.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mpedbarray.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7bcd1fee1554b6f8844c9bf30b7db4ef build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mpedbarray.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mpfe/meta.yaml b/recipes/bioconductor-mpfe/meta.yaml index 22a5c1def59bb..b632910f132e4 100644 --- a/recipes/bioconductor-mpfe/meta.yaml +++ b/recipes/bioconductor-mpfe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "MPFE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d9941cf06f60869ff2770e087bf835ab + md5: 4f86c179f9bc43d1e16295df91c07cb8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mpfe", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-mpo.db/meta.yaml b/recipes/bioconductor-mpo.db/meta.yaml new file mode 100644 index 0000000000000..1e7309a1611e8 --- /dev/null +++ b/recipes/bioconductor-mpo.db/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "0.99.7" %} +{% set name = "MPO.db" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1f1b83d5d03d69a82ca2b9e7179b537f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mpo.db", max_pin="x.x") }}' + noarch: generic +# Suggests: rmarkdown, knitr, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - r-base + - r-dbi + run: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - r-base + - r-dbi + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A set of annotation maps describing the Mouse Phenotype Ontology' + description: 'We have developed the human disease ontology R package HDO.db, which provides the semantic relationship between human diseases. Relying on the DOSE and GOSemSim packages we developed, we can carry out disease enrichment and semantic similarity analyses. Many biological studies are achieved through mouse models, and a large number of data indicate the association between genotypes and phenotypes or diseases. The study of model organisms can be transformed into useful knowledge about normal human biology and disease to facilitate treatment and early screening for diseases. Organism-specific genotype-phenotypic associations can be applied to cross-species phenotypic studies to clarify previously unknown phenotypic connections in other species. Using the same principle to diseases can identify genetic associations and even help to identify disease associations that are not obvious. Therefore, as a supplement to HDO.db and DOSE, we developed mouse phenotypic ontology R package MPO.db.' + diff --git a/recipes/bioconductor-mpo.db/post-link.sh b/recipes/bioconductor-mpo.db/post-link.sh new file mode 100644 index 0000000000000..e54b8c62eb857 --- /dev/null +++ b/recipes/bioconductor-mpo.db/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "mpo.db-0.99.7" diff --git a/recipes/bioconductor-mpo.db/pre-unlink.sh b/recipes/bioconductor-mpo.db/pre-unlink.sh new file mode 100644 index 0000000000000..0a46c236ab5a1 --- /dev/null +++ b/recipes/bioconductor-mpo.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MPO.db diff --git a/recipes/bioconductor-mpra/meta.yaml b/recipes/bioconductor-mpra/meta.yaml index feca4df94b4aa..c7695063b2da4 100644 --- a/recipes/bioconductor-mpra/meta.yaml +++ b/recipes/bioconductor-mpra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "mpra" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 46586d5c53b2dd30ac5c51ca48ffc54a + md5: ee3c8c16534188d568ee8f0e01afb894 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mpra", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-scales - r-statmod run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-scales - r-statmod diff --git a/recipes/bioconductor-mpranalyze/meta.yaml b/recipes/bioconductor-mpranalyze/meta.yaml index 8bbc71f1d89ef..d750c44c0fcf3 100644 --- a/recipes/bioconductor-mpranalyze/meta.yaml +++ b/recipes/bioconductor-mpranalyze/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "MPRAnalyze" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7fefa718bdfc973d4d43150fc54848e0 + md5: 63ae4121bc319692b51499a1b151dffc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mpranalyze", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-progress run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-progress test: diff --git a/recipes/bioconductor-mqmetrics/meta.yaml b/recipes/bioconductor-mqmetrics/meta.yaml index 573e3690b8c3c..22405f3ac0796 100644 --- a/recipes/bioconductor-mqmetrics/meta.yaml +++ b/recipes/bioconductor-mqmetrics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MQmetrics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c4519a7303cf121235ab8028b6ed775d + md5: 6c0c8bd3d356ed2db8d6329fd21958d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mqmetrics", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), BiocStyle requirements: diff --git a/recipes/bioconductor-msa/meta.yaml b/recipes/bioconductor-msa/meta.yaml index fdd875fa6c032..d7f0231460388 100644 --- a/recipes/bioconductor-msa/meta.yaml +++ b/recipes/bioconductor-msa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "msa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 261f13d3751fe96b50e9745091278ca0 + md5: 78eba41452ffe497e1a7c72116335b3e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msa", max_pin="x.x") }}' # Suggests: Biobase, knitr, seqinr, ape (>= 5.1), phangorn # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-rcpp >=0.11.1' - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-rcpp >=0.11.1' build: diff --git a/recipes/bioconductor-msa2dist/meta.yaml b/recipes/bioconductor-msa2dist/meta.yaml index dd53d926e5525..64b19c561480a 100644 --- a/recipes/bioconductor-msa2dist/meta.yaml +++ b/recipes/bioconductor-msa2dist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "MSA2dist" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 69cf471088b61e2f4ce253992ace214a + md5: 8a0d1c303af72c93a1810488010c2e6f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msa2dist", max_pin="x.x") }}' # Suggests: rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-ape - r-base - r-doparallel @@ -40,9 +41,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-ape - r-base - r-doparallel diff --git a/recipes/bioconductor-msbackendmassbank/meta.yaml b/recipes/bioconductor-msbackendmassbank/meta.yaml index e74c7a50c242d..dc48b7c227b93 100644 --- a/recipes/bioconductor-msbackendmassbank/meta.yaml +++ b/recipes/bioconductor-msbackendmassbank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.1" %} {% set name = "MsBackendMassbank" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bbf939d9164027370b91ee2f052dd7af + md5: a929aebecff77108bc62891bc397f057 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msbackendmassbank", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base - r-dbi run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base - r-dbi test: diff --git a/recipes/bioconductor-msbackendmgf/meta.yaml b/recipes/bioconductor-msbackendmgf/meta.yaml index b023175e1c9c3..87335b6ed47d8 100644 --- a/recipes/bioconductor-msbackendmgf/meta.yaml +++ b/recipes/bioconductor-msbackendmgf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MsBackendMgf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 161fa6e31b677cc2e2f9f9a505f7365b + md5: a8b5cc0b0f9c2da6222c217ae8a4c44f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msbackendmgf", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base test: commands: diff --git a/recipes/bioconductor-msbackendmsp/meta.yaml b/recipes/bioconductor-msbackendmsp/meta.yaml index 75f54a1b70ccb..34df8b380d30c 100644 --- a/recipes/bioconductor-msbackendmsp/meta.yaml +++ b/recipes/bioconductor-msbackendmsp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "MsBackendMsp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b0c87f4dd11f453f3fdd531640413d4 + md5: 805d831547106b2f232bb9eda75172bc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msbackendmsp", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base test: commands: diff --git a/recipes/bioconductor-msbackendrawfilereader/meta.yaml b/recipes/bioconductor-msbackendrawfilereader/meta.yaml index e6d27818945ae..ebd428e4ee072 100644 --- a/recipes/bioconductor-msbackendrawfilereader/meta.yaml +++ b/recipes/bioconductor-msbackendrawfilereader/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.1" %} {% set name = "MsBackendRawFileReader" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3e2d39d098ace938f7b5e26b18045acc + md5: b933c2e4fbd38b9cc8298a9cb397b5ad build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msbackendrawfilereader", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 2.5), ExperimentHub, MsBackendMgf, knitr, lattice, mzR, protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat # SystemRequirements: mono-runtime 4.x or higher (including System.Data library) on Linux/macOS, .Net Framework (>= 4.5.1) on Microsoft Windows. requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-rawrr >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-rawrr >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-rawrr >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-rawrr >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base test: commands: diff --git a/recipes/bioconductor-msbackendsql/meta.yaml b/recipes/bioconductor-msbackendsql/meta.yaml index 42926a7a93c1d..ebd150923cd74 100644 --- a/recipes/bioconductor-msbackendsql/meta.yaml +++ b/recipes/bioconductor-msbackendsql/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "MsBackendSql" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 750baf1c6b633a31eb5e8ed0ccb74887 + md5: c5d7c6ce9c877e7c0bbbc1b63a71eb70 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msbackendsql", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, msdata, rmarkdown, microbenchmark, mzR requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base - r-data.table - r-dbi - r-progress run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base - r-data.table - r-dbi diff --git a/recipes/bioconductor-mscoreutils/meta.yaml b/recipes/bioconductor-mscoreutils/meta.yaml index e47c8407560ae..abc01147f991f 100644 --- a/recipes/bioconductor-mscoreutils/meta.yaml +++ b/recipes/bioconductor-mscoreutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.1" %} {% set name = "MsCoreUtils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e1a918ab120b13cee142f6ae08898d0a + md5: 163cc129bc77ed033c124fed5bf7d9ca build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD, impute, norm, norm2, pcaMethods, vsn, Matrix, preprocessCore, missForest + run_exports: '{{ pin_subpackage("bioconductor-mscoreutils", max_pin="x.x") }}' +# Suggests: testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD, impute, norm, pcaMethods, vsn, Matrix, preprocessCore, missForest requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-clue - r-mass @@ -28,7 +29,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-clue - r-mass diff --git a/recipes/bioconductor-msd16s/meta.yaml b/recipes/bioconductor-msd16s/meta.yaml index fa6623c0cc230..093763b193ce2 100644 --- a/recipes/bioconductor-msd16s/meta.yaml +++ b/recipes/bioconductor-msd16s/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "msd16s" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 48cc66a74ec0aeff91a4c5217f69c57d + md5: fddb80467192bbe28bb92599941be5d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msd16s", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-msd16s/post-link.sh b/recipes/bioconductor-msd16s/post-link.sh index eb39e5c656947..62fa20ab286f1 100644 --- a/recipes/bioconductor-msd16s/post-link.sh +++ b/recipes/bioconductor-msd16s/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "msd16s-1.20.0" +installBiocDataPackage.sh "msd16s-1.22.0" diff --git a/recipes/bioconductor-msdata/meta.yaml b/recipes/bioconductor-msdata/meta.yaml index 3524f3b40f8d2..a93c158772cf0 100644 --- a/recipes/bioconductor-msdata/meta.yaml +++ b/recipes/bioconductor-msdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.40.0" %} +{% set version = "0.42.0" %} {% set name = "msdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dc6c949e6d593b4220d08511155b9316 + md5: 3ef7fea0866799a767fb8ac2d1da0a16 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msdata", max_pin="x.x") }}' noarch: generic # Suggests: xcms, mzR, MSnbase requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-msdata/post-link.sh b/recipes/bioconductor-msdata/post-link.sh index 183325d55e1d2..d125e3b63b591 100644 --- a/recipes/bioconductor-msdata/post-link.sh +++ b/recipes/bioconductor-msdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "msdata-0.40.0" +installBiocDataPackage.sh "msdata-0.42.0" diff --git a/recipes/bioconductor-msdatahub/meta.yaml b/recipes/bioconductor-msdatahub/meta.yaml index 461800d7ef3c1..2e0d17ac40a1a 100644 --- a/recipes/bioconductor-msdatahub/meta.yaml +++ b/recipes/bioconductor-msdatahub/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "MsDataHub" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c683540dc7f74f68fbd233970fda9a51 + md5: f355465b6b3994491364cbe994e4488d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msdatahub", max_pin="x.x") }}' noarch: generic # Suggests: ExperimentHubData, DT, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), Spectra, mzR, PSMatch, QFeatures requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base test: commands: diff --git a/recipes/bioconductor-msexperiment/meta.yaml b/recipes/bioconductor-msexperiment/meta.yaml index 23cb602f88adb..13793f29ea8ce 100644 --- a/recipes/bioconductor-msexperiment/meta.yaml +++ b/recipes/bioconductor-msexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "MsExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ef4ff755bcf01849577c7ab9393eb49 + md5: b248141f2ad9d5421d067b7f90a4c87e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msexperiment", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown, rpx, mzR, msdata requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-msfeatures/meta.yaml b/recipes/bioconductor-msfeatures/meta.yaml index 805d24a097fad..f2f78d9cab20a 100644 --- a/recipes/bioconductor-msfeatures/meta.yaml +++ b/recipes/bioconductor-msfeatures/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MsFeatures" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3100535245dfbd18aacb93a38a7db53c + md5: 326a08270ef7c22e636f1fed4cf569b6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msfeatures", max_pin="x.x") }}' noarch: generic # Suggests: testthat, roxygen2, BiocStyle, pheatmap, knitr, rmarkdown requirements: host: - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-msgbsr/meta.yaml b/recipes/bioconductor-msgbsr/meta.yaml index 51513290152d2..945baebb54043 100644 --- a/recipes/bioconductor-msgbsr/meta.yaml +++ b/recipes/bioconductor-msgbsr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "msgbsR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 091994f16f89c9151c5f5625d3fcbf23 + md5: 41ae41a9216ffbe0ee9c51a91f89112c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msgbsr", max_pin="x.x") }}' noarch: generic # Suggests: roxygen2, BSgenome.Rnorvegicus.UCSC.rn6 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-easyrnaseq >=2.36.0,<2.37.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-easyrnaseq >=2.38.0,<2.39.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-plyr - r-r.utils run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-easyrnaseq >=2.36.0,<2.37.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-easyrnaseq >=2.38.0,<2.39.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-plyr diff --git a/recipes/bioconductor-msigdb/meta.yaml b/recipes/bioconductor-msigdb/meta.yaml index 51c8be04e8ebd..04f7f6cf90356 100644 --- a/recipes/bioconductor-msigdb/meta.yaml +++ b/recipes/bioconductor-msigdb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "msigdb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1468865f501a46ee6410f5fac54d9441 + md5: eb5822dab5f9ad68cc5a46beaf626de0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msigdb", max_pin="x.x") }}' noarch: generic # Suggests: singscore, vissE, knitr, prettydoc, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocFileCache, GO.db, stringr, limma requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-msigdb/post-link.sh b/recipes/bioconductor-msigdb/post-link.sh index 2b9b4297b4376..62fbfe5ec1ef4 100644 --- a/recipes/bioconductor-msigdb/post-link.sh +++ b/recipes/bioconductor-msigdb/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "msigdb-1.8.0" +installBiocDataPackage.sh "msigdb-1.10.0" diff --git a/recipes/bioconductor-msimpute/meta.yaml b/recipes/bioconductor-msimpute/meta.yaml index 6a1a8598b3119..3da17fd266353 100644 --- a/recipes/bioconductor-msimpute/meta.yaml +++ b/recipes/bioconductor-msimpute/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "msImpute" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 66df74b17cee32a58263c3f8ff86ab65 + md5: 493d744acd5f63e07590f22b2ce0eea2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msimpute", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD # SystemRequirements: python requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' - r-base - r-data.table - r-dplyr @@ -35,8 +36,8 @@ requirements: - r-softimpute - r-tidyr run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-mslp/meta.yaml b/recipes/bioconductor-mslp/meta.yaml index b701deb301f74..cffb95da2b231 100644 --- a/recipes/bioconductor-mslp/meta.yaml +++ b/recipes/bioconductor-mslp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "mslp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1ce8ff13dcb84461ad3044da4fa1d95d + md5: 8d78607401143e315c9ad75923a0c9c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mslp", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, doFuture, future, knitr, rmarkdown, roxygen2, tinytest requirements: host: - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rankprod >=3.26.0,<3.27.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rankprod >=3.28.0,<3.29.0' - r-base - 'r-data.table >=1.13.0' - r-dorng @@ -32,8 +33,8 @@ requirements: - r-proc - r-randomforest run: - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rankprod >=3.26.0,<3.27.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rankprod >=3.28.0,<3.29.0' - r-base - 'r-data.table >=1.13.0' - r-dorng diff --git a/recipes/bioconductor-msmb/meta.yaml b/recipes/bioconductor-msmb/meta.yaml index c0651e7ad2023..75d847b490453 100644 --- a/recipes/bioconductor-msmb/meta.yaml +++ b/recipes/bioconductor-msmb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "MSMB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d9b11ea89215a562d46146b97e3208e + md5: bc2942708f54a40d59ce7e41daff7df0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msmb", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle requirements: @@ -27,7 +28,7 @@ requirements: - r-base - r-tibble - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-msmb/post-link.sh b/recipes/bioconductor-msmb/post-link.sh index 06758ac01f71c..3244b61f86248 100644 --- a/recipes/bioconductor-msmb/post-link.sh +++ b/recipes/bioconductor-msmb/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "msmb-1.18.0" +installBiocDataPackage.sh "msmb-1.20.0" diff --git a/recipes/bioconductor-msmseda/meta.yaml b/recipes/bioconductor-msmseda/meta.yaml index abd89b96a49e9..71435d318c253 100644 --- a/recipes/bioconductor-msmseda/meta.yaml +++ b/recipes/bioconductor-msmseda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "msmsEDA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2cc93eaf5f937a738bcde6c7827142b7 + md5: d2350677044dfea55c25faa434894cb2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msmseda", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - r-gplots - r-mass - r-rcolorbrewer run: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - r-gplots - r-mass diff --git a/recipes/bioconductor-msmstests/meta.yaml b/recipes/bioconductor-msmstests/meta.yaml index cf1e2f7ba84e2..f842cafcbe067 100644 --- a/recipes/bioconductor-msmstests/meta.yaml +++ b/recipes/bioconductor-msmstests/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "msmsTests" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14ec34cafa4bce236590d54cd072aca8 + md5: 90c08df612ce3e4608ab3b9fa048764a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msmstests", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-msmseda >=1.38.0,<1.39.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-msmseda >=1.40.0,<1.41.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-msmseda >=1.38.0,<1.39.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-msmseda >=1.40.0,<1.41.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base test: commands: diff --git a/recipes/bioconductor-msnbase/meta.yaml b/recipes/bioconductor-msnbase/meta.yaml index 03c1307ba1595..a3dd29afe1be0 100644 --- a/recipes/bioconductor-msnbase/meta.yaml +++ b/recipes/bioconductor-msnbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.1" %} {% set name = "MSnbase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f68f7e648144f82ce9926ca58b575a23 + md5: 4d3cbd696e9ca193ec9bdc4722f2ac49 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msnbase", max_pin="x.x") }}' # Suggests: testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.7.1), msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny, magrittr, SummarizedExperiment requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-mzid >=1.38.0,<1.39.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-mzid >=1.40.0,<1.41.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-digest - r-ggplot2 @@ -46,19 +47,19 @@ requirements: - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-mzid >=1.38.0,<1.39.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-mzid >=1.40.0,<1.41.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-digest - r-ggplot2 diff --git a/recipes/bioconductor-msnid/meta.yaml b/recipes/bioconductor-msnid/meta.yaml index e5617ace168c0..2c78af9e2fe61 100644 --- a/recipes/bioconductor-msnid/meta.yaml +++ b/recipes/bioconductor-msnid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "MSnID" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: be86f620a2146c8c3d84cf9b095b1898 + md5: e0491fe4f99deb1c0128ab4dcde8f3f3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msnid", max_pin="x.x") }}' requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msmstests >=1.38.0,<1.39.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzid >=1.38.0,<1.39.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msmstests >=1.40.0,<1.41.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzid >=1.40.0,<1.41.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - r-base - r-data.table - r-doparallel @@ -49,17 +50,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msmstests >=1.38.0,<1.39.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzid >=1.38.0,<1.39.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msmstests >=1.40.0,<1.41.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzid >=1.40.0,<1.41.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-msprep/meta.yaml b/recipes/bioconductor-msprep/meta.yaml index 438b4348fd63e..a6f5d896e023c 100644 --- a/recipes/bioconductor-msprep/meta.yaml +++ b/recipes/bioconductor-msprep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MSPrep" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f1732ab760da9c7217119d26609efc56 + md5: 65036a0ebe0b1280a2c4666c263a6e5f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msprep", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 1.0.2) requirements: host: - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-crmn - 'r-dplyr >=0.7' @@ -37,11 +38,11 @@ requirements: - r-tidyr - r-vim run: - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-crmn - 'r-dplyr >=0.7' diff --git a/recipes/bioconductor-mspurity/meta.yaml b/recipes/bioconductor-mspurity/meta.yaml index c35428558a1b7..3dcb43f28b697 100644 --- a/recipes/bioconductor-mspurity/meta.yaml +++ b/recipes/bioconductor-mspurity/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "msPurity" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0bef4ca96c52c5c6ee0ba8b4a454ec8c + md5: 0a29b8f3eacf707bf9791d50df53083a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mspurity", max_pin="x.x") }}' # Suggests: MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA, RPostgres, RMySQL requirements: host: - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-base - r-dbi - r-dbplyr @@ -38,7 +39,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-base - r-dbi - r-dbplyr diff --git a/recipes/bioconductor-mspuritydata/meta.yaml b/recipes/bioconductor-mspuritydata/meta.yaml index 93d318ef1d154..52332729fbed8 100644 --- a/recipes/bioconductor-mspuritydata/meta.yaml +++ b/recipes/bioconductor-mspuritydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "msPurityData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 758e960ac371d347930ab01398f27127 + md5: 6c86343515cbb9f81131baa3f25659f0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mspuritydata", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mspuritydata/post-link.sh b/recipes/bioconductor-mspuritydata/post-link.sh index c975c68fe6f81..7b9e5d412b057 100644 --- a/recipes/bioconductor-mspuritydata/post-link.sh +++ b/recipes/bioconductor-mspuritydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mspuritydata-1.28.0" +installBiocDataPackage.sh "mspuritydata-1.30.0" diff --git a/recipes/bioconductor-msqc1/meta.yaml b/recipes/bioconductor-msqc1/meta.yaml index 1ace9e6f47bf7..b1e92a856601d 100644 --- a/recipes/bioconductor-msqc1/meta.yaml +++ b/recipes/bioconductor-msqc1/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "msqc1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eec753dc0f640e28b06685127ac3794e + md5: a95a760a0c0ef5e8053acee1d59170a4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msqc1", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, specL (>= 1.2) requirements: @@ -27,7 +28,7 @@ requirements: - r-base - r-lattice - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-msqc1/post-link.sh b/recipes/bioconductor-msqc1/post-link.sh index 61a449edfbb82..7c052c8f8c306 100644 --- a/recipes/bioconductor-msqc1/post-link.sh +++ b/recipes/bioconductor-msqc1/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "msqc1-1.28.0" +installBiocDataPackage.sh "msqc1-1.30.0" diff --git a/recipes/bioconductor-msqrob2/meta.yaml b/recipes/bioconductor-msqrob2/meta.yaml index 533a90b1cd280..5084c4368d7b3 100644 --- a/recipes/bioconductor-msqrob2/meta.yaml +++ b/recipes/bioconductor-msqrob2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "msqrob2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 47e977ca03352478eee88298fb305024 + md5: b2c0046b0c67c24dd7d94eeb22fea3a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msqrob2", max_pin="x.x") }}' noarch: generic # Suggests: multcomp, gridExtra, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown, testthat, tidyverse, plotly, msdata, MSnbase, matrixStats, MsCoreUtils, covr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-codetools - r-lme4 @@ -33,11 +34,11 @@ requirements: - r-matrix - r-purrr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-codetools - r-lme4 diff --git a/recipes/bioconductor-msquality/meta.yaml b/recipes/bioconductor-msquality/meta.yaml index 1db6c970dcc1b..541bf61068252 100644 --- a/recipes/bioconductor-msquality/meta.yaml +++ b/recipes/bioconductor-msquality/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "MsQuality" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,43 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9c0813d8ece6db8cec01df6ea741da18 + md5: 1d8e2101f472e8fc93bfa275db511982 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msquality", max_pin="x.x") }}' noarch: generic -# Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), dplyr (>= 1.0.5), knitr (>= 1.11), msdata (>= 0.32.0), mzR (>= 2.32.0), rmarkdown (>= 2.7), S4Vectors (>= 0.29.17), testthat (>= 2.2.1) +# Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), dplyr (>= 1.0.5), knitr (>= 1.11), mzR (>= 2.32.0), rmarkdown (>= 2.7), S4Vectors (>= 0.29.17), testthat (>= 2.2.1) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-msexperiment >=1.2.0,<1.3.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-msdata >=0.42.0,<0.43.0' + - 'bioconductor-msexperiment >=1.4.0,<1.5.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base - 'r-ggplot2 >=3.3.5' - 'r-htmlwidgets >=1.5.3' - 'r-plotly >=4.9.4.1' + - 'r-rmzqc >=0.5.0' - 'r-shiny >=1.6.0' - 'r-shinydashboard >=0.7.1' - 'r-stringr >=1.4.0' - 'r-tibble >=3.1.4' - 'r-tidyr >=1.1.3' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-msexperiment >=1.2.0,<1.3.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-msdata >=0.42.0,<0.43.0' + - 'bioconductor-msexperiment >=1.4.0,<1.5.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base - 'r-ggplot2 >=3.3.5' - 'r-htmlwidgets >=1.5.3' - 'r-plotly >=4.9.4.1' + - 'r-rmzqc >=0.5.0' - 'r-shiny >=1.6.0' - 'r-shinydashboard >=0.7.1' - 'r-stringr >=1.4.0' diff --git a/recipes/bioconductor-msstats/meta.yaml b/recipes/bioconductor-msstats/meta.yaml index 56e1895593f48..e17bbdfaade32 100644 --- a/recipes/bioconductor-msstats/meta.yaml +++ b/recipes/bioconductor-msstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.8.3" %} +{% set version = "4.10.0" %} {% set name = "MSstats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 06dfde9c4e7960e84e1bb35698986b45 + md5: fac3a495f2e627a75b10a9b941d3674d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstats", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, tinytest, covr, markdown requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-checkmate - r-data.table @@ -39,10 +40,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-checkmate - r-data.table diff --git a/recipes/bioconductor-msstatsbig/build.sh b/recipes/bioconductor-msstatsbig/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-msstatsbig/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msstatsbig/meta.yaml b/recipes/bioconductor-msstatsbig/meta.yaml new file mode 100644 index 0000000000000..18aabd0559ba2 --- /dev/null +++ b/recipes/bioconductor-msstatsbig/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.0.0" %} +{% set name = "MSstatsBig" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a53de589b47964296160c6fb8aaeb3b4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstatsbig", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - r-arrow + - r-base + - r-dbi + - r-dplyr + - r-readr + - r-sparklyr + run: + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - r-arrow + - r-base + - r-dbi + - r-dplyr + - r-readr + - r-sparklyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'MSstats Preprocessing for Larger than Memory Data' + description: 'MSstats package provide tools for preprocessing, summarization and differential analysis of mass spectrometry (MS) proteomics data. Recently, some MS protocols enable acquisition of data sets that result in larger than memory quantitative data. MSstats functions are not able to process such data. MSstatsBig package provides additional converter functions that enable processing larger than memory data sets.' + diff --git a/recipes/bioconductor-msstatsconvert/meta.yaml b/recipes/bioconductor-msstatsconvert/meta.yaml index f8af78a8eb74d..f5eb9823683aa 100644 --- a/recipes/bioconductor-msstatsconvert/meta.yaml +++ b/recipes/bioconductor-msstatsconvert/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.3" %} +{% set version = "1.12.0" %} {% set name = "MSstatsConvert" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c32e16a748d6a0f6fa9d733c3586524 + md5: 1a8b79ba830db5296c2d3f589b398b7f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstatsconvert", max_pin="x.x") }}' noarch: generic # Suggests: tinytest, covr, knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-msstatslip/meta.yaml b/recipes/bioconductor-msstatslip/meta.yaml index 717f277859654..9f580d896931f 100644 --- a/recipes/bioconductor-msstatslip/meta.yaml +++ b/recipes/bioconductor-msstatslip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.1" %} {% set name = "MSstatsLiP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b374b82219e6c374a9d8697cf04151ad + md5: 677e775b1c84f40715703064cd74faff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstatslip", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' - - 'bioconductor-msstatsptm >=2.2.0,<2.3.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - 'bioconductor-msstatsptm >=2.4.0,<2.5.0' - r-base - r-checkmate - r-data.table @@ -42,10 +43,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' - - 'bioconductor-msstatsptm >=2.2.0,<2.3.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - 'bioconductor-msstatsptm >=2.4.0,<2.5.0' - r-base - r-checkmate - r-data.table diff --git a/recipes/bioconductor-msstatslobd/meta.yaml b/recipes/bioconductor-msstatslobd/meta.yaml index bb59795e8d38a..a464e413da1ea 100644 --- a/recipes/bioconductor-msstatslobd/meta.yaml +++ b/recipes/bioconductor-msstatslobd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MSstatsLOBD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 463905ce41e90270bdf7b7fa3c1098d8 + md5: 1d67c5813cb057b72100d71487c26f64 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstatslobd", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr requirements: host: diff --git a/recipes/bioconductor-msstatsptm/meta.yaml b/recipes/bioconductor-msstatsptm/meta.yaml index d36bbbe5aa754..6ce348235cd97 100644 --- a/recipes/bioconductor-msstatsptm/meta.yaml +++ b/recipes/bioconductor-msstatsptm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.4" %} +{% set version = "2.4.1" %} {% set name = "MSstatsPTM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 145549a30b3191f757ab605d629686bb + md5: 73b092b7145deaaa579c525e7d243a1e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstatsptm", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, tinytest, covr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' - - 'bioconductor-msstatstmt >=2.8.0,<2.9.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - 'bioconductor-msstatstmt >=2.10.0,<2.11.0' - r-base - r-checkmate - r-data.table @@ -37,10 +38,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' - - 'bioconductor-msstatstmt >=2.8.0,<2.9.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - 'bioconductor-msstatstmt >=2.10.0,<2.11.0' - r-base - r-checkmate - r-data.table diff --git a/recipes/bioconductor-msstatsqc/meta.yaml b/recipes/bioconductor-msstatsqc/meta.yaml index 86717ae213a79..fd453766efc47 100644 --- a/recipes/bioconductor-msstatsqc/meta.yaml +++ b/recipes/bioconductor-msstatsqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "MSstatsQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e4777a03d82bbf62a75d8731f5131347 + md5: 9328babd37ae774a13dff37e38088339 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstatsqc", max_pin="x.x") }}' noarch: generic # Suggests: knitr,rmarkdown, testthat, RforProteomics requirements: host: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-qcmetrics >=1.38.0,<1.39.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-qcmetrics >=1.40.0,<1.41.0' - r-base - r-dplyr - r-ggextra - r-ggplot2 - r-plotly run: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-qcmetrics >=1.38.0,<1.39.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-qcmetrics >=1.40.0,<1.41.0' - r-base - r-dplyr - r-ggextra diff --git a/recipes/bioconductor-msstatsqcgui/meta.yaml b/recipes/bioconductor-msstatsqcgui/meta.yaml index 5f7e42ec22a95..acb4bf4a02184 100644 --- a/recipes/bioconductor-msstatsqcgui/meta.yaml +++ b/recipes/bioconductor-msstatsqcgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MSstatsQCgui" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a9fb31259f2479840addd189193dd56 + md5: 1e648f2226907f737e1d7e71a375f01c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstatsqcgui", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-msstatsqc >=2.18.0,<2.19.0' + - 'bioconductor-msstatsqc >=2.20.0,<2.21.0' - r-base - r-dplyr - r-ggextra @@ -29,7 +30,7 @@ requirements: - r-plotly - r-shiny run: - - 'bioconductor-msstatsqc >=2.18.0,<2.19.0' + - 'bioconductor-msstatsqc >=2.20.0,<2.21.0' - r-base - r-dplyr - r-ggextra diff --git a/recipes/bioconductor-msstatsshiny/meta.yaml b/recipes/bioconductor-msstatsshiny/meta.yaml index c3a7952dbc3d4..0b5bc563d63a4 100644 --- a/recipes/bioconductor-msstatsshiny/meta.yaml +++ b/recipes/bioconductor-msstatsshiny/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.3" %} +{% set version = "1.4.1" %} {% set name = "MSstatsShiny" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dd8ced0fd30746c179d8b8fe12f29b0b + md5: 4eb74ec920d96afc15079226261224f9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstatsshiny", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, tinytest, sessioninfo, knitr, testthat (>= 3.0.0), shinytest2, mockery requirements: host: - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' - - 'bioconductor-msstatsptm >=2.2.0,<2.3.0' - - 'bioconductor-msstatstmt >=2.8.0,<2.9.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - 'bioconductor-msstatsptm >=2.4.0,<2.5.0' + - 'bioconductor-msstatstmt >=2.10.0,<2.11.0' - r-base - r-data.table - r-dplyr @@ -43,11 +44,11 @@ requirements: - r-tidyr - r-uuid run: - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' - - 'bioconductor-msstatsptm >=2.2.0,<2.3.0' - - 'bioconductor-msstatstmt >=2.8.0,<2.9.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - 'bioconductor-msstatsptm >=2.4.0,<2.5.0' + - 'bioconductor-msstatstmt >=2.10.0,<2.11.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-msstatstmt/meta.yaml b/recipes/bioconductor-msstatstmt/meta.yaml index 1959649a11e22..5ea13afd7ae7c 100644 --- a/recipes/bioconductor-msstatstmt/meta.yaml +++ b/recipes/bioconductor-msstatstmt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "MSstatsTMT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d471cc96d18a6910e6ffd312f1b8700 + md5: 73166086fd3882b4771350fde01f37fb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstatstmt", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' - r-base - r-checkmate - r-data.table @@ -31,9 +32,9 @@ requirements: - r-lme4 - r-lmertest run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' - r-base - r-checkmate - r-data.table diff --git a/recipes/bioconductor-mta10probeset.db/meta.yaml b/recipes/bioconductor-mta10probeset.db/meta.yaml index 0c22dc74a8d66..6e88a7ceb061d 100644 --- a/recipes/bioconductor-mta10probeset.db/meta.yaml +++ b/recipes/bioconductor-mta10probeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mta10probeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 84517c6b354690cd72ccefbe3b39d8e1 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mta10probeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml b/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml index cf5b6d76c6d2c..9a39f45852b4d 100644 --- a/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mta10transcriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bfd13b16b71ac2cfc82f40f2d102892b build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mta10transcriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mtbls2/meta.yaml b/recipes/bioconductor-mtbls2/meta.yaml index 7787f4fb6f5e9..fb928253ee251 100644 --- a/recipes/bioconductor-mtbls2/meta.yaml +++ b/recipes/bioconductor-mtbls2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "mtbls2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9f3494d399dd599b5e462dba8bd126bb + md5: 820109836c79f398ea5b82f5887b7fea build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mtbls2", max_pin="x.x") }}' noarch: generic # Suggests: xcms (>= 3.13.8), CAMERA, Risa (>= 1.0.0), knitr, Heatplus, pcaMethods, sp, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mtbls2/post-link.sh b/recipes/bioconductor-mtbls2/post-link.sh index a631a19cb959c..0ef2e910328f4 100644 --- a/recipes/bioconductor-mtbls2/post-link.sh +++ b/recipes/bioconductor-mtbls2/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mtbls2-1.30.0" +installBiocDataPackage.sh "mtbls2-1.32.0" diff --git a/recipes/bioconductor-mu11ksuba.db/meta.yaml b/recipes/bioconductor-mu11ksuba.db/meta.yaml index dd83c8e9876a7..b55de485fc588 100644 --- a/recipes/bioconductor-mu11ksuba.db/meta.yaml +++ b/recipes/bioconductor-mu11ksuba.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mu11ksuba.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 73d80611d1eaf8ee1eb37ebc469d97e9 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu11ksuba.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu11ksubacdf/meta.yaml b/recipes/bioconductor-mu11ksubacdf/meta.yaml index e838910a4056a..b59ac2145b73a 100644 --- a/recipes/bioconductor-mu11ksubacdf/meta.yaml +++ b/recipes/bioconductor-mu11ksubacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu11ksubacdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 52fb8ac56435775022fb62f40efafd22 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu11ksubacdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu11ksubaprobe/meta.yaml b/recipes/bioconductor-mu11ksubaprobe/meta.yaml index 3e8c94ad02544..dcedba4948626 100644 --- a/recipes/bioconductor-mu11ksubaprobe/meta.yaml +++ b/recipes/bioconductor-mu11ksubaprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu11ksubaprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 813cd0750cca6ff0cfb696b83286177e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu11ksubaprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu11ksubb.db/meta.yaml b/recipes/bioconductor-mu11ksubb.db/meta.yaml index ba344620c6ebd..63bb7d8ea3a05 100644 --- a/recipes/bioconductor-mu11ksubb.db/meta.yaml +++ b/recipes/bioconductor-mu11ksubb.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mu11ksubb.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2b61d911c3595843e80041949cb79b41 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu11ksubb.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu11ksubbcdf/meta.yaml b/recipes/bioconductor-mu11ksubbcdf/meta.yaml index 6c076b4d23b69..c998c26278a66 100644 --- a/recipes/bioconductor-mu11ksubbcdf/meta.yaml +++ b/recipes/bioconductor-mu11ksubbcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu11ksubbcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f9691ea74e19dfe57bf6cca6ed396947 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu11ksubbcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu11ksubbprobe/meta.yaml b/recipes/bioconductor-mu11ksubbprobe/meta.yaml index 5c19b7e0d066a..8b5ab818deb4d 100644 --- a/recipes/bioconductor-mu11ksubbprobe/meta.yaml +++ b/recipes/bioconductor-mu11ksubbprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu11ksubbprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 28d162e18e4e16e3c6db47195d2ea0ac build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu11ksubbprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu15v1.db/meta.yaml b/recipes/bioconductor-mu15v1.db/meta.yaml index 9e51592eede5f..74f2380efbe7e 100644 --- a/recipes/bioconductor-mu15v1.db/meta.yaml +++ b/recipes/bioconductor-mu15v1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "Mu15v1.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e9297b5fe223b046bc65dc6ea0b4376d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu15v1.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu19ksuba.db/meta.yaml b/recipes/bioconductor-mu19ksuba.db/meta.yaml index a87af58bf9b82..35416f946ef4e 100644 --- a/recipes/bioconductor-mu19ksuba.db/meta.yaml +++ b/recipes/bioconductor-mu19ksuba.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mu19ksuba.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c057d8793f2db914a93d2e1f5a3af178 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu19ksuba.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu19ksubacdf/meta.yaml b/recipes/bioconductor-mu19ksubacdf/meta.yaml index 9c33eba108be9..795c51c9e9101 100644 --- a/recipes/bioconductor-mu19ksubacdf/meta.yaml +++ b/recipes/bioconductor-mu19ksubacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu19ksubacdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 83a9e7a3bac665b655786e66dbd77848 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu19ksubacdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu19ksubb.db/meta.yaml b/recipes/bioconductor-mu19ksubb.db/meta.yaml index 30815c0163287..0dcbb94ef24d0 100644 --- a/recipes/bioconductor-mu19ksubb.db/meta.yaml +++ b/recipes/bioconductor-mu19ksubb.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mu19ksubb.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1b177a3b5626c825c91e7c25e0acd897 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu19ksubb.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu19ksubbcdf/meta.yaml b/recipes/bioconductor-mu19ksubbcdf/meta.yaml index c8bc3b4ce3fce..f36b278a44c54 100644 --- a/recipes/bioconductor-mu19ksubbcdf/meta.yaml +++ b/recipes/bioconductor-mu19ksubbcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu19ksubbcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 35e5ebcb4cb51950a85c1e3622bb39f0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu19ksubbcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu19ksubc.db/meta.yaml b/recipes/bioconductor-mu19ksubc.db/meta.yaml index dcddf61bea78a..2a6ec8567e56b 100644 --- a/recipes/bioconductor-mu19ksubc.db/meta.yaml +++ b/recipes/bioconductor-mu19ksubc.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mu19ksubc.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bef37c9cd01032e9f1fb177a1af8cba4 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu19ksubc.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu19ksubccdf/meta.yaml b/recipes/bioconductor-mu19ksubccdf/meta.yaml index 8e59b4a88c832..a36c87e66abc3 100644 --- a/recipes/bioconductor-mu19ksubccdf/meta.yaml +++ b/recipes/bioconductor-mu19ksubccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu19ksubccdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e53ef2716f88022e5e41e2cd857fc2a3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu19ksubccdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu22v3.db/meta.yaml b/recipes/bioconductor-mu22v3.db/meta.yaml index be15e8d840786..2f51fdab19768 100644 --- a/recipes/bioconductor-mu22v3.db/meta.yaml +++ b/recipes/bioconductor-mu22v3.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "Mu22v3.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 44aaebe909be9b0108256194c55cf6fb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu22v3.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu6500subacdf/meta.yaml b/recipes/bioconductor-mu6500subacdf/meta.yaml index 0da1ec948f8c1..70ad8c1a4d40a 100644 --- a/recipes/bioconductor-mu6500subacdf/meta.yaml +++ b/recipes/bioconductor-mu6500subacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu6500subacdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e72152fc4bae307e3858160e018b7f92 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu6500subacdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu6500subbcdf/meta.yaml b/recipes/bioconductor-mu6500subbcdf/meta.yaml index 5d675542693ec..3d1466e9f7e83 100644 --- a/recipes/bioconductor-mu6500subbcdf/meta.yaml +++ b/recipes/bioconductor-mu6500subbcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu6500subbcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5000bea2a018b4b6ec05cda111438bc1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu6500subbcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu6500subccdf/meta.yaml b/recipes/bioconductor-mu6500subccdf/meta.yaml index 4e28b798416fe..7d7b7e16103de 100644 --- a/recipes/bioconductor-mu6500subccdf/meta.yaml +++ b/recipes/bioconductor-mu6500subccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu6500subccdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c7cbbe6c70a0a3ae11600ad6c0e540c1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu6500subccdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu6500subdcdf/meta.yaml b/recipes/bioconductor-mu6500subdcdf/meta.yaml index 548d24141b096..33e237d79d7f6 100644 --- a/recipes/bioconductor-mu6500subdcdf/meta.yaml +++ b/recipes/bioconductor-mu6500subdcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu6500subdcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a614674e8bc60fefd8520dd25d45f8d0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu6500subdcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mudata/meta.yaml b/recipes/bioconductor-mudata/meta.yaml index b766c63a41b66..bf39d295640fb 100644 --- a/recipes/bioconductor-mudata/meta.yaml +++ b/recipes/bioconductor-mudata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "MuData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 389ee9f10c659c43649c72093a748e4a + md5: 10ef702e87a5f0517e59c1ccb96b08dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mudata", max_pin="x.x") }}' noarch: generic # Suggests: HDF5Array, rmarkdown, knitr, fs, testthat, BiocStyle, covr, SingleCellMultiModal, CiteFuse, scater requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-mugaexampledata/meta.yaml b/recipes/bioconductor-mugaexampledata/meta.yaml index 3e27f5daa3a80..4141815c412fb 100644 --- a/recipes/bioconductor-mugaexampledata/meta.yaml +++ b/recipes/bioconductor-mugaexampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MUGAExampleData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e9d37ebfc20b7c46c5e0d98528dc188 + md5: b7fe2c7ad41486695fb78263a8c9a854 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mugaexampledata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mugaexampledata/post-link.sh b/recipes/bioconductor-mugaexampledata/post-link.sh index db9219ea03f72..36035835faa9e 100644 --- a/recipes/bioconductor-mugaexampledata/post-link.sh +++ b/recipes/bioconductor-mugaexampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mugaexampledata-1.20.0" +installBiocDataPackage.sh "mugaexampledata-1.22.0" diff --git a/recipes/bioconductor-mulcom/meta.yaml b/recipes/bioconductor-mulcom/meta.yaml index 8b1f30c26397a..87516158ebe13 100644 --- a/recipes/bioconductor-mulcom/meta.yaml +++ b/recipes/bioconductor-mulcom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "Mulcom" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 959bad703faed95503f5eca2cf9d5152 + md5: 87375077f62104b18567db2e68a07488 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mulcom", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-fields - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-fields build: diff --git a/recipes/bioconductor-multiassayexperiment/meta.yaml b/recipes/bioconductor-multiassayexperiment/meta.yaml index 8be82a3ce2582..d65438bca2711 100644 --- a/recipes/bioconductor-multiassayexperiment/meta.yaml +++ b/recipes/bioconductor-multiassayexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "MultiAssayExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 62505a73913bf3c40c77e5c33e779c03 + md5: 01844376cd208e33797b236e2e65fd77 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multiassayexperiment", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, HDF5Array (>= 1.19.17), knitr, maftools (>= 2.7.10), rmarkdown, R.rsp, RaggedExperiment, UpSetR, survival, survminer, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-tidyr test: diff --git a/recipes/bioconductor-multibac/meta.yaml b/recipes/bioconductor-multibac/meta.yaml index c0d4f723b91c1..56235ddd1ac34 100644 --- a/recipes/bioconductor-multibac/meta.yaml +++ b/recipes/bioconductor-multibac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MultiBaC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4469b7a12aea60b8882fb3bccc5fb9e8 + md5: 5585e9f823074db09f44221063a3e64b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multibac", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, devtools requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' - r-base - r-ggplot2 - r-matrix - r-plotrix run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' - r-base - r-ggplot2 - r-matrix diff --git a/recipes/bioconductor-multiclust/meta.yaml b/recipes/bioconductor-multiclust/meta.yaml index 5cf90fae7abc1..93e1c54ad3fec 100644 --- a/recipes/bioconductor-multiclust/meta.yaml +++ b/recipes/bioconductor-multiclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "multiClust" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 88d9663dab3cbdc5ce296edde7632508 + md5: 86c305cad6c68f0a1850f056dad9615e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multiclust", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery requirements: host: - - 'bioconductor-ctc >=1.74.0,<1.75.0' + - 'bioconductor-ctc >=1.76.0,<1.77.0' - r-amap - r-base - r-cluster @@ -29,7 +30,7 @@ requirements: - r-mclust - r-survival run: - - 'bioconductor-ctc >=1.74.0,<1.75.0' + - 'bioconductor-ctc >=1.76.0,<1.77.0' - r-amap - r-base - r-cluster diff --git a/recipes/bioconductor-multicrispr/meta.yaml b/recipes/bioconductor-multicrispr/meta.yaml index dbcfa4f9022e0..fe725d944bd47 100644 --- a/recipes/bioconductor-multicrispr/meta.yaml +++ b/recipes/bioconductor-multicrispr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.3" %} {% set name = "multicrispr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b9bfeb36b38297c0c222e36950b2423a + md5: d0bbc847e39772348376d944c884290a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multicrispr", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer1, ensembldb, IRanges, knitr, magick, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprseek >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-karyoploter >=1.26.0,<1.27.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-rbowtie >=1.40.0,<1.41.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - r-assertive + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprseek >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-karyoploter >=1.28.0,<1.29.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rbowtie >=1.42.0,<1.43.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - r-assertive.base + - r-assertive.files + - r-assertive.numbers + - r-assertive.reflection + - r-assertive.sets - r-base - r-data.table - r-ggplot2 @@ -42,18 +47,22 @@ requirements: - r-tidyr - r-tidyselect run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprseek >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-karyoploter >=1.26.0,<1.27.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-rbowtie >=1.40.0,<1.41.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - r-assertive + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprseek >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-karyoploter >=1.28.0,<1.29.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rbowtie >=1.42.0,<1.43.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - r-assertive.base + - r-assertive.files + - r-assertive.numbers + - r-assertive.reflection + - r-assertive.sets - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-multidataset/meta.yaml b/recipes/bioconductor-multidataset/meta.yaml index 5766230883d6e..8cbbdbf9d333b 100644 --- a/recipes/bioconductor-multidataset/meta.yaml +++ b/recipes/bioconductor-multidataset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "MultiDataSet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 40343f355c0b2c4824b8dbae2d99a46e + md5: 304e6d8ccbb54c446f43f2df5e13f530 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multidataset", max_pin="x.x") }}' noarch: generic # Suggests: brgedata, minfi, minfiData, knitr, rmarkdown, testthat, omicade4, iClusterPlus, GEOquery, MultiAssayExperiment, BiocStyle, RaggedExperiment requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggrepel - r-qqman run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-multigsea/meta.yaml b/recipes/bioconductor-multigsea/meta.yaml index aaf5ffda635e0..52e09755c08a2 100644 --- a/recipes/bioconductor-multigsea/meta.yaml +++ b/recipes/bioconductor-multigsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "multiGSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 402790b4fd5fe02d3cf9f8c0aec866f3 + md5: 4f22605155c363e634e9a2ca6afae5c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multigsea", max_pin="x.x") }}' noarch: generic # Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Ss.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Xl.eg.db, org.Cf.eg.db, knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' - 'bioconductor-metaboliteidmapping >=1.0.0,<1.1.0' - r-base - r-dplyr @@ -32,9 +33,9 @@ requirements: - r-rappdirs - r-rlang run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' - 'bioconductor-metaboliteidmapping >=1.0.0,<1.1.0' - r-base - r-dplyr diff --git a/recipes/bioconductor-multihiccompare/meta.yaml b/recipes/bioconductor-multihiccompare/meta.yaml index d6e500783897c..d25d76d5d4fc4 100644 --- a/recipes/bioconductor-multihiccompare/meta.yaml +++ b/recipes/bioconductor-multihiccompare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "multiHiCcompare" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d18f5b456ea8b27f8f3646821c85e204 + md5: 04512b7be1f12fa8bfb32a13dbbb408f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multihiccompare", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hiccompare >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hiccompare >=1.24.0,<1.25.0' - r-aggregation - r-base - r-data.table @@ -35,12 +36,12 @@ requirements: - r-pheatmap - r-qqman run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hiccompare >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hiccompare >=1.24.0,<1.25.0' - r-aggregation - r-base - r-data.table diff --git a/recipes/bioconductor-multimed/meta.yaml b/recipes/bioconductor-multimed/meta.yaml index e566afa49af3f..0efc3b4e5acb4 100644 --- a/recipes/bioconductor-multimed/meta.yaml +++ b/recipes/bioconductor-multimed/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "MultiMed" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 25b04f108f1617d3db68d9aacb8d7451 + md5: 019bc5d7be15d1688b3b5df7b87246f7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multimed", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: diff --git a/recipes/bioconductor-multimir/meta.yaml b/recipes/bioconductor-multimir/meta.yaml index e34af927faac8..f62e261c71752 100644 --- a/recipes/bioconductor-multimir/meta.yaml +++ b/recipes/bioconductor-multimir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "multiMiR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9f6fbcf9e864eee972e452fe334fedb1 + md5: 7102f312557b010d184bac5dea6e5009 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multimir", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dplyr - 'r-purrr >=0.2.2' @@ -30,8 +31,8 @@ requirements: - 'r-tibble >=1.2' - r-xml run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dplyr - 'r-purrr >=0.2.2' diff --git a/recipes/bioconductor-multimodalexperiment/meta.yaml b/recipes/bioconductor-multimodalexperiment/meta.yaml index b71a72ef509ec..4e86eba270849 100644 --- a/recipes/bioconductor-multimodalexperiment/meta.yaml +++ b/recipes/bioconductor-multimodalexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "MultimodalExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3edef95bdd0fd57c9c2e7b077aeac135 + md5: 376186ba5972df1b6d4be9dc69253a61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multimodalexperiment", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-multirnaflow/build.sh b/recipes/bioconductor-multirnaflow/build.sh new file mode 100644 index 0000000000000..497f7b5bdb678 --- /dev/null +++ b/recipes/bioconductor-multirnaflow/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +export LD_LIBRARY_PATH=${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-multirnaflow/build_failure.linux-64.yaml b/recipes/bioconductor-multirnaflow/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..8506b569378e7 --- /dev/null +++ b/recipes/bioconductor-multirnaflow/build_failure.linux-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: bb62d3b200f33f1ffccfa82f8214efabe8d38de5aa2a4135bccc1e17878148d7 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + package r-plot3drgl-1.0.4-r43h6115d3f_0 is excluded by strict repo priority +category: |- + dependency issue diff --git a/recipes/bioconductor-multirnaflow/meta.yaml b/recipes/bioconductor-multirnaflow/meta.yaml new file mode 100644 index 0000000000000..46b7f0655ed98 --- /dev/null +++ b/recipes/bioconductor-multirnaflow/meta.yaml @@ -0,0 +1,89 @@ +{% set version = "1.0.0" %} +{% set name = "MultiRNAflow" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cefc109896f4cb34b4ee6a09ae966f42 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multirnaflow", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocGenerics (>= 0.40.0), BiocStyle, e1071 (>= 1.7.12), knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-mfuzz >=2.62.0,<2.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - 'r-factoextra >=1.0.7' + - 'r-factominer >=2.6' + - 'r-ggalluvial >=0.12.3' + - 'r-ggplot2 >=3.4.0' + - 'r-ggrepel >=0.9.2' + - 'r-ggsci >=2.9' + - 'r-gprofiler2 >=0.2.1' + - 'r-plot3d >=1.4' + - 'r-plot3drgl >=1.0.3' + - 'r-plyr >=1.8.8' + - 'r-rcolorbrewer >=1.1.3' + - 'r-reshape2 >=1.4.4' + - 'r-rlang >=1.1.1' + - 'r-scales >=1.2.1' + - 'r-upsetr >=1.4.0' + run: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-mfuzz >=2.62.0,<2.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - 'r-factoextra >=1.0.7' + - 'r-factominer >=2.6' + - 'r-ggalluvial >=0.12.3' + - 'r-ggplot2 >=3.4.0' + - 'r-ggrepel >=0.9.2' + - 'r-ggsci >=2.9' + - 'r-gprofiler2 >=0.2.1' + - 'r-plot3d >=1.4' + - 'r-plot3drgl >=1.0.3' + - 'r-plyr >=1.8.8' + - 'r-rcolorbrewer >=1.1.3' + - 'r-reshape2 >=1.4.4' + - 'r-rlang >=1.1.1' + - 'r-scales >=1.2.1' + - 'r-upsetr >=1.4.0' + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] +test: + commands: + - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 | file LICENSE' + summary: 'An R package for analysing RNA-seq raw counts with several biological conditions and different time points' + description: 'Our R package MultiRNAflow provides an easy to use unified framework allowing to automatically make both unsupervised and supervised (DE) analysis for datasets with an arbitrary number of biological conditions and time points. In particular, our code makes a deep downstream analysis of DE information, e.g. identifying temporal patterns across biological conditions and DE genes which are specific to a biological condition for each time.' + license_file: LICENSE +extra: + container: + extended-base: true + diff --git a/recipes/bioconductor-multiscan/meta.yaml b/recipes/bioconductor-multiscan/meta.yaml index 9354f244130e1..703917f5a7eb5 100644 --- a/recipes/bioconductor-multiscan/meta.yaml +++ b/recipes/bioconductor-multiscan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "multiscan" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d181a09f635a8d5f7cca61849e4ac8a2 + md5: 58243690ff05bdbd30da46ea01e409a3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multiscan", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-multiwgcna/build.sh b/recipes/bioconductor-multiwgcna/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-multiwgcna/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-multiwgcna/meta.yaml b/recipes/bioconductor-multiwgcna/meta.yaml new file mode 100644 index 0000000000000..b40ef3418752f --- /dev/null +++ b/recipes/bioconductor-multiwgcna/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.0.0" %} +{% set name = "multiWGCNA" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b8f70e9496cf73238aa3ba3c08cb81fa +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multiwgcna", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, doParallel, ExperimentHub, knitr, markdown, rmarkdown, testthat (>= 3.0.0), vegan +requirements: + host: + - 'bioconductor-dcanr >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-cowplot + - r-data.table + - r-dplyr + - r-flashclust + - r-ggalluvial + - r-ggplot2 + - r-ggrepel + - r-igraph + - r-patchwork + - r-readr + - r-reshape2 + - r-scales + - r-stringr + - r-wgcna + run: + - 'bioconductor-dcanr >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-cowplot + - r-data.table + - r-dplyr + - r-flashclust + - r-ggalluvial + - r-ggplot2 + - r-ggrepel + - r-igraph + - r-patchwork + - r-readr + - r-reshape2 + - r-scales + - r-stringr + - r-wgcna +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: multiWGCNA + description: 'An R package for deeping mining gene co-expression networks in multi-trait expression data. Provides functions for analyzing, comparing, and visualizing WGCNA networks across conditions. multiWGCNA was designed to handle the common case where there are multiple biologically meaningful sample traits, such as disease vs wildtype across development or anatomical region.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-multtest/meta.yaml b/recipes/bioconductor-multtest/meta.yaml index 97a738c9090aa..2921e8d93355a 100644 --- a/recipes/bioconductor-multtest/meta.yaml +++ b/recipes/bioconductor-multtest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.56.0" %} +{% set version = "2.58.0" %} {% set name = "multtest" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2c19179f77fab3d8d805e284334c8a2c + md5: 7d81a8460781f4a86f01a9df5fcf50d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multtest", max_pin="x.x") }}' # Suggests: snow requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-mass - r-survival - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-mass - r-survival diff --git a/recipes/bioconductor-mumosa/meta.yaml b/recipes/bioconductor-mumosa/meta.yaml index 773d5fad68828..8030f8a98140c 100644 --- a/recipes/bioconductor-mumosa/meta.yaml +++ b/recipes/bioconductor-mumosa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "mumosa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,53 +11,54 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 029ee75ea5b608ec5c691437e20a9df8 + md5: 634ea9c4fce9573e5da8297886d4b699 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mumosa", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle, rmarkdown, scater, bluster, DropletUtils, scRNAseq requirements: host: - - 'bioconductor-batchelor >=1.16.0,<1.17.0' - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-metapod >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scaledmatrix >=1.8.0,<1.9.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-batchelor >=1.18.0,<1.19.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-metapod >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-matrix - r-uwot run: - - 'bioconductor-batchelor >=1.16.0,<1.17.0' - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-metapod >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scaledmatrix >=1.8.0,<1.9.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-batchelor >=1.18.0,<1.19.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-metapod >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-matrix diff --git a/recipes/bioconductor-mungesumstats/meta.yaml b/recipes/bioconductor-mungesumstats/meta.yaml index 5b60a43283b23..b1efda96dcf54 100644 --- a/recipes/bioconductor-mungesumstats/meta.yaml +++ b/recipes/bioconductor-mungesumstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.1" %} {% set name = "MungeSumstats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 38021189f212fdcf82d1a314142ec7bf + md5: 9164f3e5c8e7612c387b35bff82dc4cc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mungesumstats", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr, Rsamtools, MatrixGenerics, badger, BiocParallel, GenomicFiles requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-dplyr @@ -39,13 +40,13 @@ requirements: - r-rcurl - r-stringr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-mus.musculus/meta.yaml b/recipes/bioconductor-mus.musculus/meta.yaml index 9797f1ad64b34..59c522bbcc842 100644 --- a/recipes/bioconductor-mus.musculus/meta.yaml +++ b/recipes/bioconductor-mus.musculus/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1" %} {% set name = "Mus.musculus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1b8defe64c2dd308a88d1ac7a4ce04b9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mus.musculus", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-muscat/meta.yaml b/recipes/bioconductor-muscat/meta.yaml index 08c28a46c8fc8..9dbac95cfe90b 100644 --- a/recipes/bioconductor-muscat/meta.yaml +++ b/recipes/bioconductor-muscat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "muscat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c076dd82606240da8ce32441aba3a2fa + md5: ee69286717f8d129ce59fb554c1c0994 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-muscat", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, countsimQC, cowplot, ExperimentHub, iCOBRA, knitr, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, testthat, UpSetR requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variancepartition >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variancepartition >=1.32.0,<1.33.0' - r-base - r-blme - r-data.table @@ -48,17 +49,17 @@ requirements: - r-sctransform - r-viridis run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variancepartition >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variancepartition >=1.32.0,<1.33.0' - r-base - r-blme - r-data.table diff --git a/recipes/bioconductor-muscdata/meta.yaml b/recipes/bioconductor-muscdata/meta.yaml index f552a704d78c1..9db11d8026d1c 100644 --- a/recipes/bioconductor-muscdata/meta.yaml +++ b/recipes/bioconductor-muscdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "muscData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d39accb42da56f5ca951a6f735f1586a + md5: f34c376f88f97c98d4aac5490b45bc24 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-muscdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, dplyr, DropletUtils, knitr, GEOquery, Matrix, matrixStats, methods, muscat, rmarkdown, R.utils, readxl, scater, scds, Seurat requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-muscdata/post-link.sh b/recipes/bioconductor-muscdata/post-link.sh index 1a1accd88b16f..87addac2bf682 100644 --- a/recipes/bioconductor-muscdata/post-link.sh +++ b/recipes/bioconductor-muscdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "muscdata-1.14.0" +installBiocDataPackage.sh "muscdata-1.16.0" diff --git a/recipes/bioconductor-muscle/meta.yaml b/recipes/bioconductor-muscle/meta.yaml index 3f98fbc555ae4..c75199b874840 100644 --- a/recipes/bioconductor-muscle/meta.yaml +++ b/recipes/bioconductor-muscle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.42.0" %} +{% set version = "3.44.0" %} {% set name = "muscle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5f8ece986a6adf5824aa35a420e351f9 + md5: 159745260e624c7aeb3d2e0deeef99ab build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-muscle", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-musicatk/build_failure.linux-64.yaml b/recipes/bioconductor-musicatk/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..424fa8f85cd80 --- /dev/null +++ b/recipes/bioconductor-musicatk/build_failure.linux-64.yaml @@ -0,0 +1,101 @@ +recipe_sha: add20fc7cb5cb40c6bb4cc7b7f4ec8df2354e950eedc2efb6d70c37d5fb83448 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + ERRO Task processing failed: API error (500): {"message":"write /usr/local/lib/libgoogle_cloud_cpp_dialogflow_cx.so.2.12.0: no space left on device"} +category: |- + compiler error +log: |- + .07:05:52 BIOCONDA INFO (ERR) [Dec 15 07:05:52] SERR [Dec 15 07:05:52] ERRO Task processing failed: API error (500): {"message":"write /usr/local/lib/libgoogle_cloud_cpp_dialogflow_cx.so.2.12.0: no space left on device"} + 07:05:52 BIOCONDA INFO (ERR) [Dec 15 07:05:52] SERR + 07:05:52 BIOCONDA INFO (ERR) [Dec 15 07:05:52] ERRO Task processing failed: Unexpected exit code [1] of container [c84c2e941721 step-698cd8abd9], container preserved + .07:06:42 BIOCONDA INFO (OUT) ........ + 07:06:42 BIOCONDA INFO (ERR) Traceback (most recent call last): + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/bin/mulled-build", line 10, in + 07:06:42 BIOCONDA INFO (ERR) sys.exit(main()) + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/galaxy/tools/deps/mulled/mulled_build.py", line 414, in main + 07:06:42 BIOCONDA INFO (ERR) sys.exit(mull_targets(targets, **args_to_mull_targets_kwds(args))) + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/galaxy/tools/deps/mulled/mulled_build.py", line 243, in mull_targets + 07:06:42 BIOCONDA INFO (ERR) ret = involucro_context.exec_command(involucro_args) + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/galaxy/tools/deps/mulled/mulled_build.py", line 287, in exec_command + 07:06:42 BIOCONDA INFO (ERR) shutil.rmtree('./build') + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 718, in rmtree + 07:06:42 BIOCONDA INFO (ERR) _rmtree_safe_fd(fd, path, onerror) + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd + 07:06:42 BIOCONDA INFO (ERR) _rmtree_safe_fd(dirfd, fullname, onerror) + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd + 07:06:42 BIOCONDA INFO (ERR) _rmtree_safe_fd(dirfd, fullname, onerror) + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd + 07:06:42 BIOCONDA INFO (ERR) _rmtree_safe_fd(dirfd, fullname, onerror) + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 675, in _rmtree_safe_fd + 07:06:42 BIOCONDA INFO (ERR) onerror(os.unlink, fullname, sys.exc_info()) + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 673, in _rmtree_safe_fd + 07:06:42 BIOCONDA INFO (ERR) os.unlink(entry.name, dir_fd=topfd) + 07:06:42 BIOCONDA INFO (ERR) PermissionError: [Errno 13] Permission denied: 'pcre2_set_callout.3' + 07:06:42 BIOCONDA ERROR COMMAND FAILED (exited with 1): mulled-build build-and-test bioconductor-musicatk=1.12.0--r43hdfd78af_0 -n biocontainers --test bash -c '/usr/local/env-execute true && . /usr/local/env-activate.sh && Rscript -e "library('"'"'musicatk'"'"')"' --channels conda-forge,file:///opt/mambaforge/envs/bioconda/conda-bld,bioconda,defaults --involucro-path /opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/involucro + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/pkg_test.py", line 180, in test_package + p = utils.run(cmd, env=env, cwd=d, mask=False, live=live_logs) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/utils.py", line 697, in run + raise sp.CalledProcessError(returncode, masked_cmds, output=output) + subprocess.CalledProcessError: Command '['mulled-build', 'build-and-test', 'bioconductor-musicatk=1.12.0--r43hdfd78af_0', '-n', 'biocontainers', '--test', 'bash -c \'/usr/local/env-execute true && . /usr/local/env-activate.sh && Rscript -e "library(\'"\'"\'musicatk\'"\'"\')"\'', '--channels', 'conda-forge,file:///opt/mambaforge/envs/bioconda/conda-bld,bioconda,defaults', '--involucro-path', '/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/involucro']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 673, in _rmtree_safe_fd + os.unlink(entry.name, dir_fd=topfd) + PermissionError: [Errno 13] Permission denied: 'pcre2_set_callout.3' + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/bioconda-utils", line 8, in + sys.exit(main()) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/cli.py", line 1114, in main + argh.dispatch_commands([ + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/argh/dispatching.py", line 328, in dispatch_commands + dispatch(parser, *args, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/argh/dispatching.py", line 174, in dispatch + for line in lines: + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/argh/dispatching.py", line 277, in _execute_command + for line in result: + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/argh/dispatching.py", line 260, in _call + result = function(*positional, **keywords) + File "", line 2, in build + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/cli.py", line 137, in wrapper + func(*args, **kwargs) + File "", line 2, in build + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/cli.py", line 66, in wrapper + func(*args, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/cli.py", line 492, in build + success = build_recipes(recipe_folder, config, recipes, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/build.py", line 421, in build_recipes + res = build(recipe=recipe, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/build.py", line 185, in build + pkg_test.test_package(pkg_path, base_image=base_image, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/pkg_test.py", line 180, in test_package + p = utils.run(cmd, env=env, cwd=d, mask=False, live=live_logs) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/tempfile.py", line 827, in __exit__ + self.cleanup() + File "/opt/mambaforge/envs/bioconda/lib/python3.8/tempfile.py", line 831, in cleanup + self._rmtree(self.name) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/tempfile.py", line 813, in _rmtree + _shutil.rmtree(name, onerror=onerror) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 718, in rmtree + _rmtree_safe_fd(fd, path, onerror) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd + _rmtree_safe_fd(dirfd, fullname, onerror) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd + _rmtree_safe_fd(dirfd, fullname, onerror) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd + _rmtree_safe_fd(dirfd, fullname, onerror) + [Previous line repeated 1 more time] + File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 675, in _rmtree_safe_fd + onerror(os.unlink, fullname, sys.exc_info()) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/tempfile.py", line 798, in onerror + resetperms(_os.path.dirname(path)) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/tempfile.py", line 794, in resetperms + _os.chmod(path, 0o700) + PermissionError: [Errno 1] Operation not permitted: '/tmp/tmpeaviicao/build/dist/man/man3' + Error: Process completed with exit code 1. diff --git a/recipes/bioconductor-musicatk/meta.yaml b/recipes/bioconductor-musicatk/meta.yaml index 384cee72811a5..3bbcc539d032f 100644 --- a/recipes/bioconductor-musicatk/meta.yaml +++ b/recipes/bioconductor-musicatk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "musicatk" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 23833374b24d85aa3fb37d69c818ad9d + md5: 50869915aff9dd79823e05b4ae163bc6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-musicatk", max_pin="x.x") }}' noarch: generic # Suggests: TCGAbiolinks, shinyBS, shinyalert, shinybusy, shinydashboard, shinyjs, shinyjqui, sortable, testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr, shinyWidgets, cowplot, withr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-decomptumor2sig >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-maftools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-decomptumor2sig >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-maftools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-cluster - r-data.table @@ -67,24 +68,24 @@ requirements: - r-topicmodels - r-uwot run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-decomptumor2sig >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-maftools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-decomptumor2sig >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-maftools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-cluster - r-data.table diff --git a/recipes/bioconductor-mutationalpatterns/meta.yaml b/recipes/bioconductor-mutationalpatterns/meta.yaml index d3cfa91018d80..78b54176ec5de 100644 --- a/recipes/bioconductor-mutationalpatterns/meta.yaml +++ b/recipes/bioconductor-mutationalpatterns/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.10.0" %} +{% set version = "3.12.0" %} {% set name = "MutationalPatterns" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1e8261046a65aa290c5026e6ab0bfef9 + md5: 6c800e4f89957108a1b4ab1d3a2b4cb6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mutationalpatterns", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BiocStyle (>= 2.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), biomaRt (>= 2.28.0), gridExtra (>= 2.2.1), rtracklayer (>= 1.32.2), ccfindR (>= 1.6.0), GenomicFeatures, AnnotationDbi, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-cowplot >=0.9.2' - 'r-dplyr >=0.8.3' @@ -44,14 +45,14 @@ requirements: - 'r-tibble >=2.1.3' - 'r-tidyr >=1.0.0' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-cowplot >=0.9.2' - 'r-dplyr >=0.8.3' diff --git a/recipes/bioconductor-mvcclass/meta.yaml b/recipes/bioconductor-mvcclass/meta.yaml index 7ea5d2273d088..dc8edbb507c49 100644 --- a/recipes/bioconductor-mvcclass/meta.yaml +++ b/recipes/bioconductor-mvcclass/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "MVCClass" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 624849899bde24809fa8df9780da0eb3 + md5: 2ef3331b86ae7981a2ab3323386caf61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mvcclass", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-mvoutdata/meta.yaml b/recipes/bioconductor-mvoutdata/meta.yaml index 9f192cbe3b987..a0a5517d19240 100644 --- a/recipes/bioconductor-mvoutdata/meta.yaml +++ b/recipes/bioconductor-mvoutdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "mvoutData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c4a2c65e797ec8403b7657afc81c2714 + md5: abca7ca8ae7729ed8f146d0083aa9757 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mvoutdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mvoutdata/post-link.sh b/recipes/bioconductor-mvoutdata/post-link.sh index c8bac146b0676..c258bd7e17567 100644 --- a/recipes/bioconductor-mvoutdata/post-link.sh +++ b/recipes/bioconductor-mvoutdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mvoutdata-1.36.0" +installBiocDataPackage.sh "mvoutdata-1.38.0" diff --git a/recipes/bioconductor-mwastools/meta.yaml b/recipes/bioconductor-mwastools/meta.yaml index f512e56ccd79b..75f809f1bc281 100644 --- a/recipes/bioconductor-mwastools/meta.yaml +++ b/recipes/bioconductor-mwastools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "MWASTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b4a49a058ef4c25ba8756e32251ea6c9 + md5: 4af3f3512a794c7944a27bfad640aa81 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mwastools", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-car @@ -36,11 +37,11 @@ requirements: - r-ppcor - r-rcurl run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-car diff --git a/recipes/bioconductor-mwgcod.db/meta.yaml b/recipes/bioconductor-mwgcod.db/meta.yaml index 4f6b7f79bc085..e5a5c3839be7b 100644 --- a/recipes/bioconductor-mwgcod.db/meta.yaml +++ b/recipes/bioconductor-mwgcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "mwgcod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3d6e2af6b05d6e07a212c043dc9d37c4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mwgcod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mygene/meta.yaml b/recipes/bioconductor-mygene/meta.yaml index 80b5f1e3c5d32..a48b4d7634c6f 100644 --- a/recipes/bioconductor-mygene/meta.yaml +++ b/recipes/bioconductor-mygene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "mygene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 13074d33fbfe6415400dab10c372bbac + md5: 01ebbd87d5d6b57ca6987eef9c3ae95a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mygene", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-hmisc - 'r-httr >=0.3' @@ -30,8 +31,8 @@ requirements: - r-plyr - r-sqldf run: - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-hmisc - 'r-httr >=0.3' diff --git a/recipes/bioconductor-myvariant/meta.yaml b/recipes/bioconductor-myvariant/meta.yaml index 2046e5b7d9672..bfcdcd49ceb7b 100644 --- a/recipes/bioconductor-myvariant/meta.yaml +++ b/recipes/bioconductor-myvariant/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "myvariant" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b56b2c182e41681970973e976bb52f7c + md5: 110e5245914806eb225bad404727124f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-myvariant", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-hmisc - r-httr @@ -31,9 +32,9 @@ requirements: - r-magrittr - r-plyr run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-hmisc - r-httr diff --git a/recipes/bioconductor-mzid/meta.yaml b/recipes/bioconductor-mzid/meta.yaml index 27c12cc6d0b75..52a34ad7b0de9 100644 --- a/recipes/bioconductor-mzid/meta.yaml +++ b/recipes/bioconductor-mzid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "mzID" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e92e3ea5ca514f37139a2f9da2ff733 + md5: 8ede9a6260d4b9aa70edd19838e3c80c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mzid", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat requirements: host: - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - r-base - r-doparallel - r-foreach @@ -29,7 +30,7 @@ requirements: - r-plyr - r-xml run: - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-mzr/meta.yaml b/recipes/bioconductor-mzr/meta.yaml index 74feda4882e63..788afdea54a79 100644 --- a/recipes/bioconductor-mzr/meta.yaml +++ b/recipes/bioconductor-mzr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.1" %} +{% set version = "2.36.0" %} {% set name = "mzR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ddbdeebce8ad003ef98a64e98b046dec + md5: aae8b88db5fd49675b653b861702800e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mzr", max_pin="x.x") }}' # Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML, rmarkdown # SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - r-base - r-ncdf4 - 'r-rcpp >=0.10.1' - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - r-base - r-ncdf4 - 'r-rcpp >=0.10.1' diff --git a/recipes/bioconductor-nadfinder/meta.yaml b/recipes/bioconductor-nadfinder/meta.yaml index f2457428ad06a..fef35a4d2ebc1 100644 --- a/recipes/bioconductor-nadfinder/meta.yaml +++ b/recipes/bioconductor-nadfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "NADfinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,50 +11,51 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ed74eabcb223af4a11ffa048cd23d7e + md5: d60f5020a7e46305fafc626c59a11851 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nadfinder", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat, BiocManager, rmarkdown requirements: host: - - 'bioconductor-atacseqqc >=1.24.0,<1.25.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-empiricalbrownsmethod >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trackviewer >=1.36.0,<1.37.0' + - 'bioconductor-atacseqqc >=1.26.0,<1.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-empiricalbrownsmethod >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trackviewer >=1.38.0,<1.39.0' - r-base - r-baseline - r-corrplot - r-metap - r-signal run: - - 'bioconductor-atacseqqc >=1.24.0,<1.25.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-empiricalbrownsmethod >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trackviewer >=1.36.0,<1.37.0' + - 'bioconductor-atacseqqc >=1.26.0,<1.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-empiricalbrownsmethod >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trackviewer >=1.38.0,<1.39.0' - r-base - r-baseline - r-corrplot diff --git a/recipes/bioconductor-nanomethviz/meta.yaml b/recipes/bioconductor-nanomethviz/meta.yaml index abe27f2d8f65c..94a584c8be8d5 100644 --- a/recipes/bioconductor-nanomethviz/meta.yaml +++ b/recipes/bioconductor-nanomethviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.1" %} {% set name = "NanoMethViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 708505992439c9c7f2631c9c5f2f6a89 + md5: 5ddef080c0bf460814f94f28ee5f98d5 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: DSS, Mus.musculus (>= 1.3.1), Homo.sapiens (>= 1.3.1), org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0), covr -# SystemRequirements: C++20 + run_exports: '{{ pin_subpackage("bioconductor-nanomethviz", max_pin="x.x") }}' +# Suggests: BiocStyle, DSS, Mus.musculus (>= 1.3.1), Homo.sapiens (>= 1.3.1), org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm39.refGene, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0), covr +# SystemRequirements: C++17 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-assertthat - r-base + - r-cli - 'r-cpp11 >=0.2.5' - r-data.table + - r-dbscan - r-dplyr - r-e1071 - r-forcats @@ -47,7 +52,6 @@ requirements: - r-rcpp - r-readr - r-rlang - - r-rsqlite - 'r-scales >=1.2.0' - r-scico - r-stringr @@ -57,19 +61,23 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-assertthat - r-base + - r-cli - 'r-cpp11 >=0.2.5' - r-data.table + - r-dbscan - r-dplyr - r-e1071 - r-forcats @@ -83,7 +91,6 @@ requirements: - r-rcpp - r-readr - r-rlang - - r-rsqlite - 'r-scales >=1.2.0' - r-scico - r-stringr diff --git a/recipes/bioconductor-nanoporernaseq/meta.yaml b/recipes/bioconductor-nanoporernaseq/meta.yaml index f5e9e177e2c44..262cf057ce809 100644 --- a/recipes/bioconductor-nanoporernaseq/meta.yaml +++ b/recipes/bioconductor-nanoporernaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "NanoporeRNASeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4efdad7f3e17485998405b6d05612ac2 + md5: eca12ebcd403efd53e1b38d5f03f2027 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nanoporernaseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, bambu, ggbio, BSgenome.Hsapiens.NCBI.GRCh38, circlize, ComplexHeatmap, apeglm, rlang, rmarkdown, GenomicAlignments, Rsamtools requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nanoporernaseq/post-link.sh b/recipes/bioconductor-nanoporernaseq/post-link.sh index 3a381b9a76dd7..cb6624b6a8d06 100644 --- a/recipes/bioconductor-nanoporernaseq/post-link.sh +++ b/recipes/bioconductor-nanoporernaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "nanoporernaseq-1.10.0" +installBiocDataPackage.sh "nanoporernaseq-1.12.0" diff --git a/recipes/bioconductor-nanostringdiff/meta.yaml b/recipes/bioconductor-nanostringdiff/meta.yaml index e3e58c117163c..ed2b6dc1d1f75 100644 --- a/recipes/bioconductor-nanostringdiff/meta.yaml +++ b/recipes/bioconductor-nanostringdiff/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "NanoStringDiff" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9b7337dfd2beccd2c508cd36f6de796d + md5: 3614c5bcf8aeea002875aa005d746092 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nanostringdiff", max_pin="x.x") }}' # Suggests: testthat, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-matrixstats - r-rcpp - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-matrixstats - r-rcpp diff --git a/recipes/bioconductor-nanostringnctools/meta.yaml b/recipes/bioconductor-nanostringnctools/meta.yaml index fee2b2ae279e2..8e2ae08e86524 100644 --- a/recipes/bioconductor-nanostringnctools/meta.yaml +++ b/recipes/bioconductor-nanostringnctools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "NanoStringNCTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 48e7ea143797954a6fdf23341abd5515 + md5: 97985a577c04cc2d7c19d00f2bd8e1d1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nanostringnctools", max_pin="x.x") }}' noarch: generic # Suggests: biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggbeeswarm - r-ggiraph @@ -34,11 +35,11 @@ requirements: - r-pheatmap - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggbeeswarm - r-ggiraph diff --git a/recipes/bioconductor-nanotator/meta.yaml b/recipes/bioconductor-nanotator/meta.yaml index 2d617b65005dc..682082bcff49b 100644 --- a/recipes/bioconductor-nanotator/meta.yaml +++ b/recipes/bioconductor-nanotator/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "nanotatoR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 86bdebac66638200c60dbfe387334f08 + md5: e808c68591d98effbfdba4dbac07ac91 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nanotator", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, yaml requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-curl - r-dplyr @@ -40,9 +41,9 @@ requirements: - r-xml - r-xml2r run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-curl - r-dplyr diff --git a/recipes/bioconductor-nanotube/meta.yaml b/recipes/bioconductor-nanotube/meta.yaml index d93662dcdc24a..9a1e127227387 100644 --- a/recipes/bioconductor-nanotube/meta.yaml +++ b/recipes/bioconductor-nanotube/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "NanoTube" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f94ce1248e7929f4f278f94de9858fe + md5: 524cdc55bcaf670d538be8f6c2f06c11 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nanotube", max_pin="x.x") }}' noarch: generic # Suggests: grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly, rlang, rmarkdown, ruv, RUVSeq, shiny, testthat, xlsx requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-reshape run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-reshape diff --git a/recipes/bioconductor-nanotubes/meta.yaml b/recipes/bioconductor-nanotubes/meta.yaml index de6c307ed2549..3af73d0c984a9 100644 --- a/recipes/bioconductor-nanotubes/meta.yaml +++ b/recipes/bioconductor-nanotubes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "nanotubes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7d068f3a955216378fe66463811e4adf + md5: ff283cb49c319a357c22e17d2df22715 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nanotubes", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer, CAGEfightR requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nanotubes/post-link.sh b/recipes/bioconductor-nanotubes/post-link.sh index 0ad8894e1b628..b2fb9f7b15f26 100644 --- a/recipes/bioconductor-nanotubes/post-link.sh +++ b/recipes/bioconductor-nanotubes/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "nanotubes-1.16.0" +installBiocDataPackage.sh "nanotubes-1.18.0" diff --git a/recipes/bioconductor-nbamseq/meta.yaml b/recipes/bioconductor-nbamseq/meta.yaml index 89f006c1f15bb..4476179efd3cd 100644 --- a/recipes/bioconductor-nbamseq/meta.yaml +++ b/recipes/bioconductor-nbamseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "NBAMSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 44bb5d716c113a4ffe6ab9e069405889 + md5: 45181f95a38937784da7cbad4d416811 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nbamseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, ggplot2 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-mgcv >=1.8-24' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-mgcv >=1.8-24' test: diff --git a/recipes/bioconductor-ncdfflow/meta.yaml b/recipes/bioconductor-ncdfflow/meta.yaml index bb9e9cdff349c..976e9392a7934 100644 --- a/recipes/bioconductor-ncdfflow/meta.yaml +++ b/recipes/bioconductor-ncdfflow/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "ncdfFlow" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 50a5d7442f7508b50359a6570ef591c2 + md5: 974c454443e3ed6c243aed7395f28911 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ncdfflow", max_pin="x.x") }}' # Suggests: testthat,parallel,flowStats,knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bh - r-cpp11 - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bh - r-cpp11 diff --git a/recipes/bioconductor-ncgtw/meta.yaml b/recipes/bioconductor-ncgtw/meta.yaml index 6862f27428261..c74112360f5e6 100644 --- a/recipes/bioconductor-ncgtw/meta.yaml +++ b/recipes/bioconductor-ncgtw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "ncGTW" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0da7500204724de4cd4b4946a37eaec3 + md5: ea33321b03c3751afd04234fd7fbcda3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ncgtw", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-ncigraph/meta.yaml b/recipes/bioconductor-ncigraph/meta.yaml index e250dcc8bb85f..090a8f728c23d 100644 --- a/recipes/bioconductor-ncigraph/meta.yaml +++ b/recipes/bioconductor-ncigraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "NCIgraph" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d49e4ab0775611fdf993b7a0f677bf3e + md5: ed568ded26dce9e64d5f38606e65c13d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ncigraph", max_pin="x.x") }}' noarch: generic # Suggests: Rgraphviz requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - - r-r.methodss3 + - r-r.oo run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - - r-r.methodss3 + - r-r.oo test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ncigraphdata/meta.yaml b/recipes/bioconductor-ncigraphdata/meta.yaml index 2bf79a205576e..91195f389e417 100644 --- a/recipes/bioconductor-ncigraphdata/meta.yaml +++ b/recipes/bioconductor-ncigraphdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "NCIgraphData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: beb23450c51a8f3bcac07438a25d6f9b + md5: f144169473d42fafb1966986dcf15628 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ncigraphdata", max_pin="x.x") }}' noarch: generic # Suggests: Rgraphviz requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ncigraphdata/post-link.sh b/recipes/bioconductor-ncigraphdata/post-link.sh index 3e382feb2fd73..2c15cc4502b3a 100644 --- a/recipes/bioconductor-ncigraphdata/post-link.sh +++ b/recipes/bioconductor-ncigraphdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ncigraphdata-1.36.0" +installBiocDataPackage.sh "ncigraphdata-1.38.0" diff --git a/recipes/bioconductor-ncrnatools/meta.yaml b/recipes/bioconductor-ncrnatools/meta.yaml index 05b5fdb686ad4..0be79f82b0b3b 100644 --- a/recipes/bioconductor-ncrnatools/meta.yaml +++ b/recipes/bioconductor-ncrnatools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ncRNAtools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 29e195e74ec13242c94f3ed0b2b0c6d2 + md5: 4e6f2f3809ca2cfe114ecc2c63f1d3dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ncrnatools", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-httr - r-xml2 run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-httr diff --git a/recipes/bioconductor-ndexr/meta.yaml b/recipes/bioconductor-ndexr/meta.yaml index 149ce9b792e32..e78c598266f08 100644 --- a/recipes/bioconductor-ndexr/meta.yaml +++ b/recipes/bioconductor-ndexr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "ndexr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4101572e631f965b7ae5bc1d51031ba7 + md5: caa87487f3e0c062aa6b56b1dc6f70a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ndexr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-rcx >=1.4.0,<1.5.0' + - 'bioconductor-rcx >=1.6.0,<1.7.0' - r-base - r-httr - r-jsonlite - r-plyr - r-tidyr run: - - 'bioconductor-rcx >=1.4.0,<1.5.0' + - 'bioconductor-rcx >=1.6.0,<1.7.0' - r-base - r-httr - r-jsonlite diff --git a/recipes/bioconductor-nearbynding/meta.yaml b/recipes/bioconductor-nearbynding/meta.yaml index e1e8b53d6a637..5344eaad1760f 100644 --- a/recipes/bioconductor-nearbynding/meta.yaml +++ b/recipes/bioconductor-nearbynding/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "nearBynding" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c0e19b30364b8df75523fe8a8cf6e85e + md5: 2bcc4459fa78c6327ee2708f06da54db build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nearbynding", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown # SystemRequirements: bedtools (>= 2.28.0), Stereogene (>= v2.22), CapR (>= 1.1.1) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-dplyr - r-ggplot2 @@ -41,15 +42,15 @@ requirements: - r-rlang - r-transport run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-nebulosa/meta.yaml b/recipes/bioconductor-nebulosa/meta.yaml index be8b72764b6ab..7ee5a8801e91d 100644 --- a/recipes/bioconductor-nebulosa/meta.yaml +++ b/recipes/bioconductor-nebulosa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "Nebulosa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8aa3fd5e95574c3b0023d243302470d4 + md5: e71c21bbda87365578a49f21dd915fa4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nebulosa", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils, igraph, BiocFileCache, SeuratObject requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ks @@ -30,8 +31,8 @@ requirements: - r-patchwork - r-seurat run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ks diff --git a/recipes/bioconductor-nempi/meta.yaml b/recipes/bioconductor-nempi/meta.yaml index 1cef818a6c9dd..35ac5c2778196 100644 --- a/recipes/bioconductor-nempi/meta.yaml +++ b/recipes/bioconductor-nempi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "nempi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a75421d6b4a639b46ef0ae5ef181abb2 + md5: 1180e323b8f109079a74702ef7159cda build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nempi", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocGenerics, rmarkdown, RUnit, BiocStyle requirements: host: - - 'bioconductor-epinem >=1.24.0,<1.25.0' - - 'bioconductor-mnem >=1.16.0,<1.17.0' + - 'bioconductor-epinem >=1.26.0,<1.27.0' + - 'bioconductor-mnem >=1.18.0,<1.19.0' - r-base - r-e1071 - r-matrixstats @@ -30,8 +31,8 @@ requirements: - r-nnet - r-randomforest run: - - 'bioconductor-epinem >=1.24.0,<1.25.0' - - 'bioconductor-mnem >=1.16.0,<1.17.0' + - 'bioconductor-epinem >=1.26.0,<1.27.0' + - 'bioconductor-mnem >=1.18.0,<1.19.0' - r-base - r-e1071 - r-matrixstats diff --git a/recipes/bioconductor-nestlink/meta.yaml b/recipes/bioconductor-nestlink/meta.yaml index 3dfa79d67adb0..7547790cc430c 100644 --- a/recipes/bioconductor-nestlink/meta.yaml +++ b/recipes/bioconductor-nestlink/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "NestLink" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ae3c598105a6b4fc40e3ce4ad0bf1e99 + md5: 11cd94f5bd8b38cf261ae3346a283e81 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nestlink", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 2.2), DT, ggplot2, knitr, rmarkdown, testthat, specL, lattice, scales requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - 'r-gplots >=3.0' - 'r-protviz >=0.4' run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - 'r-gplots >=3.0' - 'r-protviz >=0.4' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nestlink/post-link.sh b/recipes/bioconductor-nestlink/post-link.sh index 70a917bc106e7..e4c21fc4a1132 100644 --- a/recipes/bioconductor-nestlink/post-link.sh +++ b/recipes/bioconductor-nestlink/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "nestlink-1.16.0" +installBiocDataPackage.sh "nestlink-1.18.0" diff --git a/recipes/bioconductor-netactivity/meta.yaml b/recipes/bioconductor-netactivity/meta.yaml index 451a5f24248ea..78e371d72f461 100644 --- a/recipes/bioconductor-netactivity/meta.yaml +++ b/recipes/bioconductor-netactivity/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "NetActivity" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3937c60ef36d7b14327a8b1c5f803cf + md5: 3493b441d888adf6d3a089936bbeafd6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netactivity", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0), tidyverse requirements: host: - - 'bioconductor-airway >=1.20.0,<1.21.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-netactivitydata >=1.2.0,<1.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-airway >=1.22.0,<1.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-netactivitydata >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-airway >=1.20.0,<1.21.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-netactivitydata >=1.2.0,<1.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-airway >=1.22.0,<1.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-netactivitydata >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-netactivitydata/meta.yaml b/recipes/bioconductor-netactivitydata/meta.yaml index 99d3fc99db88e..eb4cf6502a8c5 100644 --- a/recipes/bioconductor-netactivitydata/meta.yaml +++ b/recipes/bioconductor-netactivitydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "NetActivityData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43f1651effd619c45926094b7f6df44b + md5: a3805046d14d13afc30a0f082952f200 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netactivitydata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-netactivitydata/post-link.sh b/recipes/bioconductor-netactivitydata/post-link.sh index 0092bdf08ff5e..945e66b43cd20 100644 --- a/recipes/bioconductor-netactivitydata/post-link.sh +++ b/recipes/bioconductor-netactivitydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "netactivitydata-1.2.0" +installBiocDataPackage.sh "netactivitydata-1.4.0" diff --git a/recipes/bioconductor-netboost/meta.yaml b/recipes/bioconductor-netboost/meta.yaml index f7474534850b3..827401588e5f8 100644 --- a/recipes/bioconductor-netboost/meta.yaml +++ b/recipes/bioconductor-netboost/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "netboost" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 290c4fcdcc62163c74e30ff61011cba2 + md5: d21f645a3fe85c35ff9b9127bce1fbca build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: knitr, markdown, rmarkdown + run_exports: '{{ pin_subpackage("bioconductor-netboost", max_pin="x.x") }}' +# Suggests: knitr, rmarkdown # SystemRequirements: GNU make, Bash, Perl, Gzip requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-base - r-colorspace - r-dynamictreecut @@ -33,8 +34,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-base - r-colorspace - r-dynamictreecut diff --git a/recipes/bioconductor-netdx/meta.yaml b/recipes/bioconductor-netdx/meta.yaml index 5ccaf70bd86f4..4c60cf23c5c53 100644 --- a/recipes/bioconductor-netdx/meta.yaml +++ b/recipes/bioconductor-netdx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "netDx" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ce730cb8934c6792d800eb5f32559f9 + md5: 6fdc48ce518c74e0261acee84948ce26 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netdx", max_pin="x.x") }}' noarch: generic # Suggests: curatedTCGAData, rmarkdown, testthat, knitr, BiocStyle, RCy3, clusterExperiment, netSmooth, scater requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bigmemory - r-combinat @@ -44,12 +45,12 @@ requirements: - r-rocr - r-rtsne run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bigmemory - r-combinat diff --git a/recipes/bioconductor-nethet/meta.yaml b/recipes/bioconductor-nethet/meta.yaml index a3a9f0c858646..fa9f00d135eb1 100644 --- a/recipes/bioconductor-nethet/meta.yaml +++ b/recipes/bioconductor-nethet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "nethet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e0364a3984a014bf2108f461a2021433 + md5: 35bc35cf08904b721563aa54e486cc95 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nethet", max_pin="x.x") }}' # Suggests: knitr, xtable, BiocStyle, testthat requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-compquadform - r-genenet @@ -38,8 +39,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-compquadform - r-genenet diff --git a/recipes/bioconductor-netomics/meta.yaml b/recipes/bioconductor-netomics/meta.yaml index a27e24166b1ef..b64d798252c5b 100644 --- a/recipes/bioconductor-netomics/meta.yaml +++ b/recipes/bioconductor-netomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "netOmics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37282b31aeb12e9b3af18911b8dd523d + md5: 8ab3cf60546da2beea2e9c3630340c12 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netomics", max_pin="x.x") }}' noarch: generic # Suggests: mixOmics, timeOmics, tidyverse, BiocStyle, testthat, covr, rmarkdown, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-randomwalkrestartmh >=1.20.0,<1.21.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-randomwalkrestartmh >=1.22.0,<1.23.0' - r-base - r-dplyr - r-ggplot2 @@ -35,10 +36,10 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-randomwalkrestartmh >=1.20.0,<1.21.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-randomwalkrestartmh >=1.22.0,<1.23.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-netpathminer/meta.yaml b/recipes/bioconductor-netpathminer/meta.yaml index 5828131271fee..50aca74364875 100644 --- a/recipes/bioconductor-netpathminer/meta.yaml +++ b/recipes/bioconductor-netpathminer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "NetPathMiner" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 76776ce19013b746222cfb08237367b2 + md5: 91cc0601961f682fcf1a2bed61eb6438 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netpathminer", max_pin="x.x") }}' # Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle # SystemRequirements: libxml2, libSBML (>= 5.5) requirements: host: - r-base - - r-igraph + - 'r-igraph >=1.0' - libblas - liblapack - libxml2 run: - r-base - - r-igraph + - 'r-igraph >=1.0' - libxml2 build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-netprior/meta.yaml b/recipes/bioconductor-netprior/meta.yaml index dd14ef112ba9b..146dd2bda1f80 100644 --- a/recipes/bioconductor-netprior/meta.yaml +++ b/recipes/bioconductor-netprior/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "netprioR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 582d959f00a6f534f0cf141a80168936 + md5: 7e4023edbe230057c85ae74d90f59fd1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netprior", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, pander requirements: diff --git a/recipes/bioconductor-netresponse/meta.yaml b/recipes/bioconductor-netresponse/meta.yaml index 12cd8aed603e9..c0beb901e67b0 100644 --- a/recipes/bioconductor-netresponse/meta.yaml +++ b/recipes/bioconductor-netresponse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "netresponse" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 16f0c62907c79eb5d346ae329345310f + md5: 990c864cea311427d5af5f854edf4041 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netresponse", max_pin="x.x") }}' # Suggests: knitr requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-ggplot2 - r-igraph @@ -36,11 +37,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-ggplot2 - r-igraph diff --git a/recipes/bioconductor-netsam/meta.yaml b/recipes/bioconductor-netsam/meta.yaml index 4e91e0438b0a1..7bdf23012be6b 100644 --- a/recipes/bioconductor-netsam/meta.yaml +++ b/recipes/bioconductor-netsam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "NetSAM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd6a61494b69858daa7ea594754eff4a + md5: 8248bae56028b8d8ee872cb007cbd7f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netsam", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, org.Sc.sgd.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dr.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.At.tair.db, rmarkdown, knitr, markdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - 'r-dbi >=0.5-1' - 'r-doparallel >=1.0.10' @@ -34,9 +35,9 @@ requirements: - 'r-survival >=2.37-7' - 'r-wgcna >=1.34.0' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - 'r-dbi >=0.5-1' - 'r-doparallel >=1.0.10' diff --git a/recipes/bioconductor-netsmooth/meta.yaml b/recipes/bioconductor-netsmooth/meta.yaml index eaf08ae7dc387..8ba8209e5b286 100644 --- a/recipes/bioconductor-netsmooth/meta.yaml +++ b/recipes/bioconductor-netsmooth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "netSmooth" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 515bd1a10da3b5db97cce11ba66d0171 + md5: 074a02c5cf8d32c2111268513d8404c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netsmooth", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot requirements: host: - - 'bioconductor-clusterexperiment >=2.20.0,<2.21.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-clusterexperiment >=2.22.0,<2.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-data.table - r-entropy - r-matrix run: - - 'bioconductor-clusterexperiment >=2.20.0,<2.21.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-clusterexperiment >=2.22.0,<2.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-data.table diff --git a/recipes/bioconductor-netzoor/meta.yaml b/recipes/bioconductor-netzoor/meta.yaml index c94a5fb6ffe30..6091f5648d7f6 100644 --- a/recipes/bioconductor-netzoor/meta.yaml +++ b/recipes/bioconductor-netzoor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "netZooR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ab5dcac5e4394525a93ba72131f0f222 + md5: 2f4adb3763df2df201212073e34bab10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netzoor", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), knitr, rmarkdown, pkgdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-pandar >=1.32.0,<1.33.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' - - 'bioconductor-yarn >=1.26.0,<1.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-pandar >=1.34.0,<1.35.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' + - 'bioconductor-yarn >=1.28.0,<1.29.0' - r-assertthat - r-base - r-data.table @@ -53,15 +54,15 @@ requirements: - r-vegan - r-viridislite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-pandar >=1.32.0,<1.33.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' - - 'bioconductor-yarn >=1.26.0,<1.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-pandar >=1.34.0,<1.35.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' + - 'bioconductor-yarn >=1.28.0,<1.29.0' - r-assertthat - r-base - r-data.table diff --git a/recipes/bioconductor-neve2006/meta.yaml b/recipes/bioconductor-neve2006/meta.yaml index 0103cfa7e4a8c..42228ba33d521 100644 --- a/recipes/bioconductor-neve2006/meta.yaml +++ b/recipes/bioconductor-neve2006/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "Neve2006" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 77132d53a223319770a7abcf21d8e202 + md5: 1feec2f09bac8c69ba9df5ea29e7e08c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-neve2006", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - r-base run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-neve2006/post-link.sh b/recipes/bioconductor-neve2006/post-link.sh index 427f48443403c..24e05c66b69e3 100644 --- a/recipes/bioconductor-neve2006/post-link.sh +++ b/recipes/bioconductor-neve2006/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "neve2006-0.38.0" +installBiocDataPackage.sh "neve2006-0.40.0" diff --git a/recipes/bioconductor-newwave/build.sh b/recipes/bioconductor-newwave/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-newwave/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-newwave/meta.yaml b/recipes/bioconductor-newwave/meta.yaml new file mode 100644 index 0000000000000..72507f5c6eb2b --- /dev/null +++ b/recipes/bioconductor-newwave/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.12.0" %} +{% set name = "NewWave" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ed222f643c357c84a7eb8534aa7b3a91 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-newwave", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr +requirements: + host: + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-sharedobject >=1.16.0,<1.17.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-irlba + - r-matrix + run: + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-sharedobject >=1.16.0,<1.17.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-irlba + - r-matrix +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Negative binomial model for scRNA-seq' + description: 'A model designed for dimensionality reduction and batch effect removal for scRNA-seq data. It is designed to be massively parallelizable using shared objects that prevent memory duplication, and it can be used with different mini-batch approaches in order to reduce time consumption. It assumes a negative binomial distribution for the data with a dispersion parameter that can be both commonwise across gene both genewise.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-ngscopydata/meta.yaml b/recipes/bioconductor-ngscopydata/meta.yaml index 9646ebf7b1a92..68de821e7a0fb 100644 --- a/recipes/bioconductor-ngscopydata/meta.yaml +++ b/recipes/bioconductor-ngscopydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "NGScopyData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e2d29d8d5f08328e350974da855da611 + md5: 0ba77cf672a331e4c9dd90b26f41b5c6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ngscopydata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ngscopydata/post-link.sh b/recipes/bioconductor-ngscopydata/post-link.sh index 192efa48a1bee..362855219f4b3 100644 --- a/recipes/bioconductor-ngscopydata/post-link.sh +++ b/recipes/bioconductor-ngscopydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ngscopydata-1.20.0" +installBiocDataPackage.sh "ngscopydata-1.22.0" diff --git a/recipes/bioconductor-ngsreports/meta.yaml b/recipes/bioconductor-ngsreports/meta.yaml index ea350d3c66571..185ed58b5bdcb 100644 --- a/recipes/bioconductor-ngsreports/meta.yaml +++ b/recipes/bioconductor-ngsreports/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.4" %} +{% set version = "2.4.0" %} {% set name = "ngsReports" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3fa618125cffae2c7a1059bc9caacf86 + md5: c2d8c1f7a1869275420e05125fb1b420 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ngsreports", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, Cairo, knitr, testthat, truncnorm requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-checkmate - 'r-dplyr >=1.1.0' @@ -47,8 +48,8 @@ requirements: - 'r-tidyselect >=0.2.3' - r-zoo run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-checkmate - 'r-dplyr >=1.1.0' diff --git a/recipes/bioconductor-nipalsmcia/build.sh b/recipes/bioconductor-nipalsmcia/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-nipalsmcia/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-nipalsmcia/meta.yaml b/recipes/bioconductor-nipalsmcia/meta.yaml new file mode 100644 index 0000000000000..bfba119094b74 --- /dev/null +++ b/recipes/bioconductor-nipalsmcia/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.0.0" %} +{% set name = "nipalsMCIA" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0558d05ea61523c6fcaed9d8ed9b0ded +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nipalsmcia", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, circlize, ggpubr, KernSmooth, knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>= 4.0.0), spatstat.explore, stringr, survival, tidyverse, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-dplyr + - 'r-ggplot2 >=3.0.0' + - r-pracma + - r-rlang + - r-rspectra + - r-scales + run: + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-dplyr + - 'r-ggplot2 >=3.0.0' + - r-pracma + - r-rlang + - r-rspectra + - r-scales +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Multiple Co-Inertia Analysis via the NIPALS Method' + description: 'Computes Multiple Co-Inertia Analysis (MCIA), a dimensionality reduction (jDR) algorithm, for a multi-block dataset using a modification to the Nonlinear Iterative Partial Least Squares method (NIPALS) proposed in (Hanafi et. al, 2010). Allows multiple options for row- and table-level preprocessing, and speeds up computation of variance explained. Vignettes detail application to bulk- and single cell- multi-omics studies.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-nnnorm/meta.yaml b/recipes/bioconductor-nnnorm/meta.yaml index 5f6340ae54b8f..ed154d75e8173 100644 --- a/recipes/bioconductor-nnnorm/meta.yaml +++ b/recipes/bioconductor-nnnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.64.0" %} +{% set version = "2.66.0" %} {% set name = "nnNorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 32948108dfc1ce0d1a90c589af10149a + md5: f6e41106fc2afb44568c00dce1a36670 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nnnorm", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-nnet run: - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-nnet test: diff --git a/recipes/bioconductor-nnsvg/meta.yaml b/recipes/bioconductor-nnsvg/meta.yaml index 7720cd36de4a1..b04d39476984c 100644 --- a/recipes/bioconductor-nnsvg/meta.yaml +++ b/recipes/bioconductor-nnsvg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "nnSVG" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 226c134290d6643df454277b54b5d067 + md5: 4af169b12d944eff8ee9d9e3063ff5ea build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nnsvg", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, STexampleData, WeberDivechaLCdata, scran, ggplot2, testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-brisc - r-matrix - r-matrixstats run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-brisc - r-matrix diff --git a/recipes/bioconductor-noiseq/meta.yaml b/recipes/bioconductor-noiseq/meta.yaml index 6dae72b652d48..675fe63b421b6 100644 --- a/recipes/bioconductor-noiseq/meta.yaml +++ b/recipes/bioconductor-noiseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.44.0" %} +{% set version = "2.46.0" %} {% set name = "NOISeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 546e44e3bd29e9fe3a4d2d35d7eb04c1 + md5: e7ea859871f96aa68269efa3a1e7dd46 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-noiseq", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - 'r-matrix >=1.2' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - 'r-matrix >=1.2' test: diff --git a/recipes/bioconductor-nondetects/meta.yaml b/recipes/bioconductor-nondetects/meta.yaml index 7c27d12de272e..05ea32239f1d2 100644 --- a/recipes/bioconductor-nondetects/meta.yaml +++ b/recipes/bioconductor-nondetects/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "nondetects" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9b56e99e728154927bb62fb6c6120d0c + md5: 6507efbde0bbb76f863c731bcc8464bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nondetects", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle (>= 1.0.0), RUnit, BiocGenerics (>= 0.8.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-htqpcr >=1.54.0,<1.55.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-htqpcr >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-arm - r-base - r-mvtnorm run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-htqpcr >=1.54.0,<1.55.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-htqpcr >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-arm - r-base - r-mvtnorm diff --git a/recipes/bioconductor-norce/meta.yaml b/recipes/bioconductor-norce/meta.yaml index cbd2329e19012..8aea0cd7dd50e 100644 --- a/recipes/bioconductor-norce/meta.yaml +++ b/recipes/bioconductor-norce/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "NoRCE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eda53dbedd3a44f4b5416f2f3d2f77f0 + md5: 8e3a1a53f9c68bc68ab881bd49e28ecb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-norce", max_pin="x.x") }}' noarch: generic # Suggests: knitr, TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene, testthat,TxDb.Celegans.UCSC.ce11.refGene,rmarkdown, TxDb.Rnorvegicus.UCSC.rn6.refGene,TxDb.Hsapiens.UCSC.hg19.knownGene, org.Mm.eg.db, org.Rn.eg.db,org.Hs.eg.db,org.Dr.eg.db,BiocGenerics, org.Sc.sgd.db, org.Ce.eg.db,org.Dm.eg.db, methods,markdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-rwikipathways >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-rwikipathways >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-dbi - r-dbplyr @@ -49,20 +50,20 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-rwikipathways >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-rwikipathways >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-dbi - r-dbplyr diff --git a/recipes/bioconductor-normalize450k/meta.yaml b/recipes/bioconductor-normalize450k/meta.yaml index d362f6a7ca9da..d3980f100fdc2 100644 --- a/recipes/bioconductor-normalize450k/meta.yaml +++ b/recipes/bioconductor-normalize450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "normalize450K" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09d6b4499a0f70e1071d1ddd963cc7f4 + md5: f5ea0fdcbdd43103b5ee941c96fe43fa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-normalize450k", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - r-base - r-quadprog run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - r-base - r-quadprog test: diff --git a/recipes/bioconductor-normalyzerde/meta.yaml b/recipes/bioconductor-normalyzerde/meta.yaml index b7b48ad46e2ee..73ac8ed4eadf9 100644 --- a/recipes/bioconductor-normalyzerde/meta.yaml +++ b/recipes/bioconductor-normalyzerde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "NormalyzerDE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef1878f963a1376db00cfcdb34c8f6f9 + md5: e55d57346b59dbd8b317a263e4b413b0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-normalyzerde", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-ape - r-base - r-car @@ -33,14 +34,12 @@ requirements: - r-ggplot2 - r-mass - r-matrixstats - - r-raster - - r-rcmdrmisc run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-ape - r-base - r-car @@ -48,8 +47,6 @@ requirements: - r-ggplot2 - r-mass - r-matrixstats - - r-raster - - r-rcmdrmisc test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-normqpcr/meta.yaml b/recipes/bioconductor-normqpcr/meta.yaml index 78f8d1ce11160..79afa3c7882ff 100644 --- a/recipes/bioconductor-normqpcr/meta.yaml +++ b/recipes/bioconductor-normqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "NormqPCR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 26722c237731e8a7ed2dcb5f6babb676 + md5: 379e7395ad03c0d57dffa7331748e253 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-normqpcr", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-readqpcr >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-readqpcr >=1.48.0,<1.49.0' - r-base - r-qpcr - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-readqpcr >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-readqpcr >=1.48.0,<1.49.0' - r-base - r-qpcr - r-rcolorbrewer diff --git a/recipes/bioconductor-normr/meta.yaml b/recipes/bioconductor-normr/meta.yaml index 36cea3b30c3a2..7e2b0dacc4662 100644 --- a/recipes/bioconductor-normr/meta.yaml +++ b/recipes/bioconductor-normr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "normr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3d9b6c8514fcac077afbb985ba09d65b + md5: 06d294d5935656789cc44341eca46620 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-normr", max_pin="x.x") }}' # Suggests: BiocStyle, testthat (>= 1.0), knitr, rmarkdown # SystemRequirements: C++11 requirements: host: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - 'r-rcpp >=0.11' - libblas - liblapack run: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - 'r-rcpp >=0.11' build: diff --git a/recipes/bioconductor-norway981.db/meta.yaml b/recipes/bioconductor-norway981.db/meta.yaml index fc706e5452c15..71d94b527398a 100644 --- a/recipes/bioconductor-norway981.db/meta.yaml +++ b/recipes/bioconductor-norway981.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "Norway981.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 85367390919bba9018438585e59fbb87 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-norway981.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nparc/meta.yaml b/recipes/bioconductor-nparc/meta.yaml index 77f43f2b02960..0c5bebf6db5c1 100644 --- a/recipes/bioconductor-nparc/meta.yaml +++ b/recipes/bioconductor-nparc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "NPARC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d5e6e63e7bc6f5681ae1e3e763b7aaa + md5: b49f408fb60e58d3c62cfd2d5d4809cb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nparc", max_pin="x.x") }}' noarch: generic # Suggests: testthat, devtools, knitr, rprojroot, rmarkdown, ggplot2, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-broom - r-dplyr @@ -30,7 +31,7 @@ requirements: - r-rlang - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-broom - r-dplyr diff --git a/recipes/bioconductor-npgsea/meta.yaml b/recipes/bioconductor-npgsea/meta.yaml index e539c18eeb5e9..908e3b860253b 100644 --- a/recipes/bioconductor-npgsea/meta.yaml +++ b/recipes/bioconductor-npgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "npGSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: be25afa3330016c8a304b773601defd1 + md5: 82d2208fe4478a1d5423940daa7128be build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-npgsea", max_pin="x.x") }}' noarch: generic # Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base test: commands: diff --git a/recipes/bioconductor-ntw/meta.yaml b/recipes/bioconductor-ntw/meta.yaml index 2b28a78d7b9b5..61ef8840dc598 100644 --- a/recipes/bioconductor-ntw/meta.yaml +++ b/recipes/bioconductor-ntw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "NTW" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9a724372ec6201f37b22c2c5cc507483 + md5: c64df447dfa43cbb3bf97922655ff516 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ntw", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-nucleosim/meta.yaml b/recipes/bioconductor-nucleosim/meta.yaml index a7e44a2b153f8..3bfd2f9382492 100644 --- a/recipes/bioconductor-nucleosim/meta.yaml +++ b/recipes/bioconductor-nucleosim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "nucleoSim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54387b881dbc7f4ed750081a7d444f1f + md5: b1b994c654ce500e414a8a7caea5162f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nucleosim", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-nucler/meta.yaml b/recipes/bioconductor-nucler/meta.yaml index 2be954587e6bf..340e91083a435 100644 --- a/recipes/bioconductor-nucler/meta.yaml +++ b/recipes/bioconductor-nucler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "nucleR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 033fb6cde8087be9add9a70235e27fb0 + md5: 854586c378515ad6e2eefe2e1a09f394 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nucler", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-dplyr - r-ggplot2 - r-magrittr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-nucpos/meta.yaml b/recipes/bioconductor-nucpos/meta.yaml index 0f6d76078c045..4bc66b50e3842 100644 --- a/recipes/bioconductor-nucpos/meta.yaml +++ b/recipes/bioconductor-nucpos/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "nuCpos" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d825e3c5513f7be0367edf8e72f114d9 + md5: b029b2678c784645c2198f00093bd923 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nucpos", max_pin="x.x") }}' noarch: generic # Suggests: NuPoP, Biostrings, testthat requirements: diff --git a/recipes/bioconductor-nugohs1a520180.db/meta.yaml b/recipes/bioconductor-nugohs1a520180.db/meta.yaml index 2e57f0de3efb1..b418a0f7208e0 100644 --- a/recipes/bioconductor-nugohs1a520180.db/meta.yaml +++ b/recipes/bioconductor-nugohs1a520180.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "nugohs1a520180.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f83701b35b07e69e1ad503b546bb5eaf build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nugohs1a520180.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nugohs1a520180cdf/meta.yaml b/recipes/bioconductor-nugohs1a520180cdf/meta.yaml index f624518fc2b88..f90749d9e7a72 100644 --- a/recipes/bioconductor-nugohs1a520180cdf/meta.yaml +++ b/recipes/bioconductor-nugohs1a520180cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "nugohs1a520180cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: aa152658a4a801cc0edb552a98aee841 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nugohs1a520180cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nugohs1a520180probe/meta.yaml b/recipes/bioconductor-nugohs1a520180probe/meta.yaml index 8134389eb12fd..f0bd987761f56 100644 --- a/recipes/bioconductor-nugohs1a520180probe/meta.yaml +++ b/recipes/bioconductor-nugohs1a520180probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "nugohs1a520180probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6acf20ac4a799eaae97d0a64426d6ac3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nugohs1a520180probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nugomm1a520177.db/meta.yaml b/recipes/bioconductor-nugomm1a520177.db/meta.yaml index ca4aef5adf082..7be86d928b24d 100644 --- a/recipes/bioconductor-nugomm1a520177.db/meta.yaml +++ b/recipes/bioconductor-nugomm1a520177.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "nugomm1a520177.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 99f69ea2cbb80a79bedee99e3d726e50 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nugomm1a520177.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nugomm1a520177cdf/meta.yaml b/recipes/bioconductor-nugomm1a520177cdf/meta.yaml index 749c80d468182..6e57813681d86 100644 --- a/recipes/bioconductor-nugomm1a520177cdf/meta.yaml +++ b/recipes/bioconductor-nugomm1a520177cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "nugomm1a520177cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fc60c2018580decaea30f09de55142fb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nugomm1a520177cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nugomm1a520177probe/meta.yaml b/recipes/bioconductor-nugomm1a520177probe/meta.yaml index 7bf4085f23db2..1d994b823856e 100644 --- a/recipes/bioconductor-nugomm1a520177probe/meta.yaml +++ b/recipes/bioconductor-nugomm1a520177probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "nugomm1a520177probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7fa974389ad2be6ebda8810496221a9b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nugomm1a520177probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nullranges/meta.yaml b/recipes/bioconductor-nullranges/meta.yaml index be1686768f962..61ea19b4a06cf 100644 --- a/recipes/bioconductor-nullranges/meta.yaml +++ b/recipes/bioconductor-nullranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.2" %} +{% set version = "1.8.0" %} {% set name = "nullranges" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 57d37d766de72195faa55f893e79debc + md5: 6ee32a46c332cfeefa89ebc2b32608bf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nullranges", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, ks, DNAcopy, RcppHMM, AnnotationHub, ExperimentHub, nullrangesData, excluderanges, ensembldb, EnsDb.Hsapiens.v86, BSgenome.Hsapiens.UCSC.hg38, patchwork, plotgardener, dplyr, purrr, magrittr, tidyr, cobalt, DiagrammeR, tidySummarizedExperiment requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-ggplot2 @@ -35,12 +36,12 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-nullrangesdata/meta.yaml b/recipes/bioconductor-nullrangesdata/meta.yaml index 9d383cbff145a..357383664f328 100644 --- a/recipes/bioconductor-nullrangesdata/meta.yaml +++ b/recipes/bioconductor-nullrangesdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "nullrangesData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54631ad9bc1a63e3c981cb9df919a1a4 + md5: c8b4cf63d70a2577251c03c093c014b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nullrangesdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nullrangesdata/post-link.sh b/recipes/bioconductor-nullrangesdata/post-link.sh index caa8f21cc6151..56c49a53ff303 100644 --- a/recipes/bioconductor-nullrangesdata/post-link.sh +++ b/recipes/bioconductor-nullrangesdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "nullrangesdata-1.6.0" +installBiocDataPackage.sh "nullrangesdata-1.8.0" diff --git a/recipes/bioconductor-nupop/meta.yaml b/recipes/bioconductor-nupop/meta.yaml index 34a784ea5862f..95a7ccb26204e 100644 --- a/recipes/bioconductor-nupop/meta.yaml +++ b/recipes/bioconductor-nupop/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.1" %} +{% set version = "2.10.0" %} {% set name = "NuPoP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f8fd1ab74555d543f34738389d28587 + md5: 65372d828848fa588584e42324762643 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nupop", max_pin="x.x") }}' # Suggests: knitr, rmarkdown requirements: host: diff --git a/recipes/bioconductor-nxtirfdata/meta.yaml b/recipes/bioconductor-nxtirfdata/meta.yaml index d90d0eb06de8b..60c0e2b69d5f7 100644 --- a/recipes/bioconductor-nxtirfdata/meta.yaml +++ b/recipes/bioconductor-nxtirfdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "NxtIRFdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 49c677044a8e671562fec6f64533b284 + md5: 3d9c35f12650fe6e2eb413224b3590dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nxtirfdata", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-r.utils run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-r.utils - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nxtirfdata/post-link.sh b/recipes/bioconductor-nxtirfdata/post-link.sh index 839225414a35a..bc8f830b35b74 100644 --- a/recipes/bioconductor-nxtirfdata/post-link.sh +++ b/recipes/bioconductor-nxtirfdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "nxtirfdata-1.6.0" +installBiocDataPackage.sh "nxtirfdata-1.8.0" diff --git a/recipes/bioconductor-obmiti/meta.yaml b/recipes/bioconductor-obmiti/meta.yaml index 0cfaa078750e0..a995f44ec42d3 100644 --- a/recipes/bioconductor-obmiti/meta.yaml +++ b/recipes/bioconductor-obmiti/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ObMiTi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 679880ec1082c72dc04b91c7c43b86d1 + md5: 0510665a5231cd3109d19478e4aadbd9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-obmiti", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocManager, GenomicFeatures, S4Vectors, devtools, testthat requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-obmiti/post-link.sh b/recipes/bioconductor-obmiti/post-link.sh index 739594a5416ea..03b4d1416cd34 100644 --- a/recipes/bioconductor-obmiti/post-link.sh +++ b/recipes/bioconductor-obmiti/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "obmiti-1.8.0" +installBiocDataPackage.sh "obmiti-1.10.0" diff --git a/recipes/bioconductor-occugene/meta.yaml b/recipes/bioconductor-occugene/meta.yaml index 18d0068dc24ec..f5f74d87be869 100644 --- a/recipes/bioconductor-occugene/meta.yaml +++ b/recipes/bioconductor-occugene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "occugene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c3bc7c5109e680763202f69c7a35abce + md5: 264da1422714d735ac474b414e57a2a9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-occugene", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-ocplus/meta.yaml b/recipes/bioconductor-ocplus/meta.yaml index 2edb915b101ae..5dd736c909f68 100644 --- a/recipes/bioconductor-ocplus/meta.yaml +++ b/recipes/bioconductor-ocplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "OCplus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f1c461ba3d6b8e3310af4f823f80061c + md5: 8093ec3c635bc4ba57d27f42c6c85c48 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ocplus", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-interp run: - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-interp test: diff --git a/recipes/bioconductor-oct4/meta.yaml b/recipes/bioconductor-oct4/meta.yaml index d331169780dbd..14a38304a08b0 100644 --- a/recipes/bioconductor-oct4/meta.yaml +++ b/recipes/bioconductor-oct4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "oct4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 733c8377b6b7065265506a938f1c7c09 + md5: 1b6bbc6300c74c038689c7fb5b7d5eb2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oct4", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-oct4/post-link.sh b/recipes/bioconductor-oct4/post-link.sh index c58332df2a32d..b3235662475f3 100644 --- a/recipes/bioconductor-oct4/post-link.sh +++ b/recipes/bioconductor-oct4/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "oct4-1.16.0" +installBiocDataPackage.sh "oct4-1.18.0" diff --git a/recipes/bioconductor-octad.db/meta.yaml b/recipes/bioconductor-octad.db/meta.yaml index e249cf73495ec..a4fa56d807f6c 100644 --- a/recipes/bioconductor-octad.db/meta.yaml +++ b/recipes/bioconductor-octad.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "octad.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 242e1f3e5df68b1ccbc324eaf3924797 + md5: ef8723031fea32015ee26dbf30d2c8ba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-octad.db", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-octad.db/post-link.sh b/recipes/bioconductor-octad.db/post-link.sh index c9d4883ad95ce..2b1a3295db9c8 100644 --- a/recipes/bioconductor-octad.db/post-link.sh +++ b/recipes/bioconductor-octad.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "octad.db-1.2.0" +installBiocDataPackage.sh "octad.db-1.4.0" diff --git a/recipes/bioconductor-octad/meta.yaml b/recipes/bioconductor-octad/meta.yaml index 4b05424e89677..5247c0dddb66c 100644 --- a/recipes/bioconductor-octad/meta.yaml +++ b/recipes/bioconductor-octad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "octad" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 16534514ddcf3ab39f87e15eb20527dd + md5: 65dcd54e4646d61afcfb9afc90108ba4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-octad", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-octad.db >=1.2.0,<1.3.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-octad.db >=1.4.0,<1.5.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr @@ -45,18 +46,18 @@ requirements: - r-reshape2 - r-rfast run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-octad.db >=1.2.0,<1.3.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-octad.db >=1.4.0,<1.5.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-odseq/meta.yaml b/recipes/bioconductor-odseq/meta.yaml index 80bde4e87ab53..15f186744d094 100644 --- a/recipes/bioconductor-odseq/meta.yaml +++ b/recipes/bioconductor-odseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "odseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 28a91ac69eb76e788013a765301cb90d + md5: 5eac4befb045c1d0531b13501f3aa880 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-odseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr(>= 1.11) requirements: host: - - 'bioconductor-kebabs >=1.34.0,<1.35.0' - - 'bioconductor-msa >=1.32.0,<1.33.0' + - 'bioconductor-kebabs >=1.36.0,<1.37.0' + - 'bioconductor-msa >=1.34.0,<1.35.0' - r-base - 'r-mclust >=5.1' run: - - 'bioconductor-kebabs >=1.34.0,<1.35.0' - - 'bioconductor-msa >=1.32.0,<1.33.0' + - 'bioconductor-kebabs >=1.36.0,<1.37.0' + - 'bioconductor-msa >=1.34.0,<1.35.0' - r-base - 'r-mclust >=5.1' test: diff --git a/recipes/bioconductor-ogre/meta.yaml b/recipes/bioconductor-ogre/meta.yaml index d41487802403a..31154fe4bd61b 100644 --- a/recipes/bioconductor-ogre/meta.yaml +++ b/recipes/bioconductor-ogre/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "OGRE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8573ec05b2170c32440425eaa57567a7 + md5: cff18fd2eda3eb1e67e9f7739fb9e773 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ogre", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), knitr (>= 1.36), rmarkdown (>= 2.11) requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - r-data.table @@ -39,13 +40,13 @@ requirements: - r-shinyfiles - r-tidyr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - r-data.table diff --git a/recipes/bioconductor-oligo/meta.yaml b/recipes/bioconductor-oligo/meta.yaml index d9592d51fb19e..b3a0210da009e 100644 --- a/recipes/bioconductor-oligo/meta.yaml +++ b/recipes/bioconductor-oligo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.1" %} +{% set version = "1.66.0" %} {% set name = "oligo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0e40f8ea848ec94333feb3fc9d0cd7ac + md5: 3ba99dedbe0ebca2fcaa81a400777469 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oligo", max_pin="x.x") }}' # Suggests: BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, ACME, RCurl requirements: host: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - 'r-dbi >=0.3.1' - r-ff @@ -35,14 +36,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - 'r-dbi >=0.3.1' - r-ff diff --git a/recipes/bioconductor-oligoclasses/meta.yaml b/recipes/bioconductor-oligoclasses/meta.yaml index da8d8b7d73f58..f580b7d23a33d 100644 --- a/recipes/bioconductor-oligoclasses/meta.yaml +++ b/recipes/bioconductor-oligoclasses/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "oligoClasses" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 81ef026f64df521596ed8f336cf7c139 + md5: 379f1364d7159e2456c9310556e990e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oligoclasses", max_pin="x.x") }}' noarch: generic # Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), RUnit, human370v1cCrlmm, VanillaICE, crlmm requirements: host: - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biocmanager - r-dbi @@ -36,14 +37,14 @@ requirements: - r-foreach - r-rsqlite run: - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biocmanager - r-dbi diff --git a/recipes/bioconductor-oligodata/meta.yaml b/recipes/bioconductor-oligodata/meta.yaml index f462620f0a2bb..3359689fb98fc 100644 --- a/recipes/bioconductor-oligodata/meta.yaml +++ b/recipes/bioconductor-oligodata/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.8.0" %} {% set name = "oligoData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9625cfd4b31bb575c4029a0632a7ee12 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oligodata", max_pin="x.x") }}' noarch: generic # Suggests: pd.hg.u95av2, pd.huex.1.0.st.v2, pd.mapping50k.xba240, pd.hg18.60mer.expr, pd.2006.07.18.hg18.refseq.promoter, pd.hugene.1.0.st.v1 requirements: host: - - 'bioconductor-oligo >=1.64.0,<1.65.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' - r-base run: - - 'bioconductor-oligo >=1.64.0,<1.65.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-olin/meta.yaml b/recipes/bioconductor-olin/meta.yaml index 800c3a8724560..90100d3abd625 100644 --- a/recipes/bioconductor-olin/meta.yaml +++ b/recipes/bioconductor-olin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "OLIN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 78861856588cb82ace6edbe1ab39c8f7 + md5: 3a6ce43e9272204280a346c20012f710 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-olin", max_pin="x.x") }}' noarch: generic # Suggests: convert requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-locfit run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-locfit test: diff --git a/recipes/bioconductor-olingui/meta.yaml b/recipes/bioconductor-olingui/meta.yaml index dfc53412fb04a..229943f4192e8 100644 --- a/recipes/bioconductor-olingui/meta.yaml +++ b/recipes/bioconductor-olingui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "OLINgui" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8ae51f7c642bee5c4fd8e3734d838a59 + md5: 5f960cc922153099a7b7a6e7ee939d9f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-olingui", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-olin >=1.78.0,<1.79.0' - - 'bioconductor-tkwidgets >=1.78.0,<1.79.0' - - 'bioconductor-widgettools >=1.78.0,<1.79.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-olin >=1.80.0,<1.81.0' + - 'bioconductor-tkwidgets >=1.80.0,<1.81.0' + - 'bioconductor-widgettools >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-olin >=1.78.0,<1.79.0' - - 'bioconductor-tkwidgets >=1.78.0,<1.79.0' - - 'bioconductor-widgettools >=1.78.0,<1.79.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-olin >=1.80.0,<1.81.0' + - 'bioconductor-tkwidgets >=1.80.0,<1.81.0' + - 'bioconductor-widgettools >=1.80.0,<1.81.0' - r-base test: commands: diff --git a/recipes/bioconductor-omada/meta.yaml b/recipes/bioconductor-omada/meta.yaml index e0436b7414617..009cfe955a23d 100644 --- a/recipes/bioconductor-omada/meta.yaml +++ b/recipes/bioconductor-omada/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.1.0" %} +{% set version = "1.4.0" %} {% set name = "omada" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 86be333cce02f3ba85831756d5f599ff + md5: d214fdb20c51cbce86bf1d34c59cb84b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omada", max_pin="x.x") }}' # Suggests: rmarkdown, knitr, testthat requirements: host: - r-base - - 'r-clustercrit >=1.2.8' - 'r-clvalid >=0.7' - 'r-dicer >=0.6.0' - 'r-dplyr >=1.0.7' - 'r-fpc >=2.2-9' + - 'r-genieclust >=1.1.3' - 'r-ggplot2 >=3.3.5' - 'r-glmnet >=4.1.3' - 'r-kernlab >=0.9-29' @@ -36,11 +37,11 @@ requirements: - liblapack run: - r-base - - 'r-clustercrit >=1.2.8' - 'r-clvalid >=0.7' - 'r-dicer >=0.6.0' - 'r-dplyr >=1.0.7' - 'r-fpc >=2.2-9' + - 'r-genieclust >=1.1.3' - 'r-ggplot2 >=3.3.5' - 'r-glmnet >=4.1.3' - 'r-kernlab >=0.9-29' diff --git a/recipes/bioconductor-omadb/meta.yaml b/recipes/bioconductor-omadb/meta.yaml index 9191ab18d378e..2f326296a255a 100644 --- a/recipes/bioconductor-omadb/meta.yaml +++ b/recipes/bioconductor-omadb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "OmaDB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9bd7ca3376459757a00128152fde6617 + md5: 4bfced261f7429c6e881e05dc45ec0d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omadb", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-ape - r-base - 'r-httr >=1.2.1' - r-jsonlite - 'r-plyr >=1.8.4' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-ape - r-base - 'r-httr >=1.2.1' diff --git a/recipes/bioconductor-omicade4/meta.yaml b/recipes/bioconductor-omicade4/meta.yaml index 11202dcd1613b..d1459a945c810 100644 --- a/recipes/bioconductor-omicade4/meta.yaml +++ b/recipes/bioconductor-omicade4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "omicade4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a22d04cdab97b81511ff76f4a8ca34fa + md5: ed6de2f603d54a9ad262ff62784818a2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omicade4", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-made4 >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-made4 >=1.76.0,<1.77.0' - r-ade4 - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-made4 >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-made4 >=1.76.0,<1.77.0' - r-ade4 - r-base test: diff --git a/recipes/bioconductor-omiccircos/meta.yaml b/recipes/bioconductor-omiccircos/meta.yaml index 30c9f1733d7fc..38a85dda1eaff 100644 --- a/recipes/bioconductor-omiccircos/meta.yaml +++ b/recipes/bioconductor-omiccircos/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "OmicCircos" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 82db65a2a816bf1811423176dc23a908 + md5: 7d77b9a00853d3e6fec869012ce33daf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omiccircos", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base test: commands: diff --git a/recipes/bioconductor-omicplotr/meta.yaml b/recipes/bioconductor-omicplotr/meta.yaml index 43d68b9cf96ad..f4321b6264bdd 100644 --- a/recipes/bioconductor-omicplotr/meta.yaml +++ b/recipes/bioconductor-omicplotr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "omicplotR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2399395b2b761fa04cdb0370398db8ee + md5: 1ab1c2e82c98f8086b4dba4f65a613e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omicplotr", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-aldex2 >=1.32.0,<1.33.0' + - 'bioconductor-aldex2 >=1.34.0,<1.35.0' - r-base - r-compositions - r-dt @@ -32,7 +33,7 @@ requirements: - r-vegan - r-zcompositions run: - - 'bioconductor-aldex2 >=1.32.0,<1.33.0' + - 'bioconductor-aldex2 >=1.34.0,<1.35.0' - r-base - r-compositions - r-dt diff --git a/recipes/bioconductor-omicrexposome/meta.yaml b/recipes/bioconductor-omicrexposome/meta.yaml index 1fdf6a1e7b990..b6b78aeaefd18 100644 --- a/recipes/bioconductor-omicrexposome/meta.yaml +++ b/recipes/bioconductor-omicrexposome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.2" %} {% set name = "omicRexposome" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 764e526f71b89b0846d239fc3b963904 + md5: 3b7a896124164c0dd282c91c79d2db00 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omicrexposome", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, snpStats, brgedata requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-omicade4 >=1.40.0,<1.41.0' - - 'bioconductor-rexposome >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-omicade4 >=1.42.0,<1.43.0' + - 'bioconductor-rexposome >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-ggplot2 - r-ggrepel @@ -37,13 +38,13 @@ requirements: - r-smartsva - r-stringr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-omicade4 >=1.40.0,<1.41.0' - - 'bioconductor-rexposome >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-omicade4 >=1.42.0,<1.43.0' + - 'bioconductor-rexposome >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-omicspca/meta.yaml b/recipes/bioconductor-omicspca/meta.yaml index 962db73ce6c27..3dfa436153af2 100644 --- a/recipes/bioconductor-omicspca/meta.yaml +++ b/recipes/bioconductor-omicspca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "OMICsPCA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 72c763d94cf3a24deaa8a3a84913ee53 + md5: d115069df9bde574c2439532f584f19a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omicspca", max_pin="x.x") }}' noarch: generic # Suggests: knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-helloranges >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-omicspcadata >=1.18.0,<1.19.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-helloranges >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-omicspcadata >=1.20.0,<1.21.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-cluster - r-clvalid @@ -48,12 +49,12 @@ requirements: - r-rmarkdown - r-tidyr run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-helloranges >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-omicspcadata >=1.18.0,<1.19.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-helloranges >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-omicspcadata >=1.20.0,<1.21.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-cluster - r-clvalid diff --git a/recipes/bioconductor-omicspcadata/meta.yaml b/recipes/bioconductor-omicspcadata/meta.yaml index ed5731bde2f4d..463dedac14b20 100644 --- a/recipes/bioconductor-omicspcadata/meta.yaml +++ b/recipes/bioconductor-omicspcadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "OMICsPCAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 058c8440badd8afe17e693d3055fbf23 + md5: ba3167fdf846cb80aea07162b88c9b73 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omicspcadata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, kableExtra, rmarkdown requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-omicspcadata/post-link.sh b/recipes/bioconductor-omicspcadata/post-link.sh index 2275b7d5f9fd8..ca5c61ccc8b1f 100644 --- a/recipes/bioconductor-omicspcadata/post-link.sh +++ b/recipes/bioconductor-omicspcadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "omicspcadata-1.18.0" +installBiocDataPackage.sh "omicspcadata-1.20.0" diff --git a/recipes/bioconductor-omicsprint/meta.yaml b/recipes/bioconductor-omicsprint/meta.yaml index 6db33b6e24e67..43008f464b26c 100644 --- a/recipes/bioconductor-omicsprint/meta.yaml +++ b/recipes/bioconductor-omicsprint/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "omicsPrint" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bde78492e675b58b7797c253a972330a + md5: 4e45c908441cedfc0dac097c558e61f1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omicsprint", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-mass - r-matrixstats run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-mass - r-matrixstats diff --git a/recipes/bioconductor-omicsviewer/build_failure.linux-64.yaml b/recipes/bioconductor-omicsviewer/build_failure.linux-64.yaml index 860b1ad27b912..42c095bbef5d2 100644 --- a/recipes/bioconductor-omicsviewer/build_failure.linux-64.yaml +++ b/recipes/bioconductor-omicsviewer/build_failure.linux-64.yaml @@ -1,8 +1,11 @@ -recipe_sha: a7735e832a66d80dfff55fe542bfee9b6a353575cd5dbf9ce52813c0ecb6eeb4 # The commit at which this recipe failed to build. +recipe_sha: 239d6bdc75a778a6447bf4fc3495c2f506b1d9b087b303660bddf9344473faef # The commit at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + r-flatxml 0.1.1 would require r-base >=4.2,<4.3.0a0, which conflicts with any installable versions previously reported; +category: |- + dependency issue log: |- - - Encountered problems while solving: - - - package bioconductor-summarizedexperiment-1.30.2-r43hdfd78af_0 requires bioconductor-genomicranges >=1.52.0,<1.53.0, but none of the providers can be installed + - - package bioconductor-summarizedexperiment-1.32.0-r43hdfd78af_0 requires bioconductor-delayedarray >=0.28.0,<0.29.0, but none of the providers can be installed - Leaving build/test directories: @@ -25,48 +28,49 @@ log: |- File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve raise RuntimeError("Solver could not find solution." error_string) RuntimeError: Solver could not find solution.Mamba failed to solve: - - r-rcolorbrewer - - r-plotly - - bioconductor-biobase >=2.60.0,<2.61.0 - - r-shinythemes - - r-shinyjs - - r-shinycssloaders - r-ggplot2 - - r-shinybusy - r-matrixstats - - r-openxlsx - - r-rsqlite - - r-shiny - - bioconductor-s4vectors >=0.38.0,<0.39.0 - - bioconductor-fgsea >=1.26.0,<1.27.0 + - r-fastmatch - r-psych - - r-flatxml - - r-survminer - - r-base 4.3.* + - r-rsqlite + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 - r-rocr - - r-stringr - - r-survival - - r-fastmatch - - r-beeswarm + - r-survminer - r-matrix - - r-dt - - r-shinywidgets - - r-reshape2 - - r-ggseqlogo - - r-httr - - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - r-shinybusy - r-htmlwidgets + - r-rcolorbrewer + - bioconductor-fgsea >=1.28.0,<1.29.0 - r-networkd3 + - r-dt + - r-shinyjs + - r-plotly + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - r-ggseqlogo - r-curl + - r-flatxml + - r-shinythemes + - r-httr + - r-shinywidgets + - r-reshape2 + - r-shiny + - r-base 4.3.* + - r-openxlsx + - r-stringr + - bioconductor-biobase >=2.62.0,<2.63.0 + - r-shinycssloaders + - r-survival + - r-beeswarm with channels: + - file:///opt/host-conda-bld - conda-forge - bioconda - defaults The reported errors are: - Encountered problems while solving: - - - package bioconductor-summarizedexperiment-1.30.2-r43hdfd78af_0 requires bioconductor-genomicranges >=1.52.0,<1.53.0, but none of the providers can be installed + - - package bioconductor-summarizedexperiment-1.32.0-r43hdfd78af_0 requires bioconductor-delayedarray >=0.28.0,<0.29.0, but none of the providers can be installed - During handling of the above exception, another exception occurred: @@ -100,5 +104,5 @@ log: |- actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-summarizedexperiment==1.30.2=r43hdfd78af_0"), MatchSpec("bioconductor-genomicranges[version='>=1.52.0,<1.53.0']")} + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-summarizedexperiment==1.32.0=r43hdfd78af_0"), MatchSpec("bioconductor-delayedarray[version='>=0.28.0,<0.29.0']")} # Last 100 lines of the build log. diff --git a/recipes/bioconductor-omicsviewer/meta.yaml b/recipes/bioconductor-omicsviewer/meta.yaml index b457e664d14ce..bc96b7d767299 100644 --- a/recipes/bioconductor-omicsviewer/meta.yaml +++ b/recipes/bioconductor-omicsviewer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "omicsViewer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ba3a9dc8fda84db3bbfd024389c9d4e6 + md5: 7d650ff242a133610199a574a29abfde build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omicsviewer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, unittest requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-beeswarm - r-curl @@ -55,10 +56,10 @@ requirements: - r-survival - r-survminer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-beeswarm - r-curl diff --git a/recipes/bioconductor-omixer/meta.yaml b/recipes/bioconductor-omixer/meta.yaml index be9e560a6cb29..5a6e3c4aa6eb1 100644 --- a/recipes/bioconductor-omixer/meta.yaml +++ b/recipes/bioconductor-omixer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "Omixer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71204a8a366fca0179c7c8d8df4e476f + md5: 6360569495c662f2c34c86dbd7387f4a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omixer", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, magick, testthat requirements: diff --git a/recipes/bioconductor-omnipathr/meta.yaml b/recipes/bioconductor-omnipathr/meta.yaml index 20fac42c22e3a..e3b362d4d7544 100644 --- a/recipes/bioconductor-omnipathr/meta.yaml +++ b/recipes/bioconductor-omnipathr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.8.0" %} +{% set version = "3.10.1" %} {% set name = "OmnipathR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,14 +11,15 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5026627a035e201129c1765133a2c3e4 + md5: c51296b40e8d580f14dc3ff6839495f6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omnipathr", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, biomaRt, bookdown, dnet, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, smoof, supraHex, testthat +# Suggests: BiocStyle, biomaRt, bookdown, dnet, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, sigmajs, smoof, supraHex, testthat requirements: host: - r-base @@ -26,12 +27,13 @@ requirements: - r-crayon - r-curl - r-digest - - r-dplyr + - 'r-dplyr >=1.1.0' - r-httr - r-igraph - r-jsonlite - r-later - r-logger + - r-lubridate - r-magrittr - r-progress - r-purrr @@ -41,6 +43,7 @@ requirements: - r-rlang - r-rmarkdown - r-rvest + - r-stringi - r-stringr - r-tibble - r-tidyr @@ -54,12 +57,13 @@ requirements: - r-crayon - r-curl - r-digest - - r-dplyr + - 'r-dplyr >=1.1.0' - r-httr - r-igraph - r-jsonlite - r-later - r-logger + - r-lubridate - r-magrittr - r-progress - r-purrr @@ -69,6 +73,7 @@ requirements: - r-rlang - r-rmarkdown - r-rvest + - r-stringi - r-stringr - r-tibble - r-tidyr diff --git a/recipes/bioconductor-ompbam/meta.yaml b/recipes/bioconductor-ompbam/meta.yaml index 211fce60b8a72..87ebc1481b424 100644 --- a/recipes/bioconductor-ompbam/meta.yaml +++ b/recipes/bioconductor-ompbam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "ompBAM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 118828a1b81d93cb734b85dfa7dea65c + md5: 9e9d31ddcad0b4bb4acb30ad970a0cd5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ompbam", max_pin="x.x") }}' # Suggests: RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis, desc, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-onassisjavalibs/meta.yaml b/recipes/bioconductor-onassisjavalibs/meta.yaml index aa33d15402a43..d2c32d35b58e1 100644 --- a/recipes/bioconductor-onassisjavalibs/meta.yaml +++ b/recipes/bioconductor-onassisjavalibs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "OnassisJavaLibs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 32a85e21248ac13de54dfee722eee3f1 + md5: 88d86bc7e7d339146ba7ea689c2d8080 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-onassisjavalibs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown, knitr # SystemRequirements: Java (>= 1.8) @@ -29,7 +30,7 @@ requirements: - r-base - r-rjava - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' - openjdk test: commands: diff --git a/recipes/bioconductor-onassisjavalibs/post-link.sh b/recipes/bioconductor-onassisjavalibs/post-link.sh index c9c7f57e98503..2e98dfca3f0c9 100644 --- a/recipes/bioconductor-onassisjavalibs/post-link.sh +++ b/recipes/bioconductor-onassisjavalibs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "onassisjavalibs-1.22.0" +installBiocDataPackage.sh "onassisjavalibs-1.24.0" diff --git a/recipes/bioconductor-oncomix/meta.yaml b/recipes/bioconductor-oncomix/meta.yaml index 403e8e73f96ce..e3d50be1cdf3e 100644 --- a/recipes/bioconductor-oncomix/meta.yaml +++ b/recipes/bioconductor-oncomix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "oncomix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 366323b113f34a562f6a3fe523595cb0 + md5: dd6381604152d7cb96f7c592e8f82ab7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oncomix", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, RMySQL requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggrepel - r-mclust - r-rcolorbrewer run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-oncoscanr/meta.yaml b/recipes/bioconductor-oncoscanr/meta.yaml index 3479ba987b17b..84d19dea331fa 100644 --- a/recipes/bioconductor-oncoscanr/meta.yaml +++ b/recipes/bioconductor-oncoscanr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "oncoscanR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80e05d30297850d138e26ad1ccc9f51c + md5: 48aee6850c94c299417e75cf74418b01 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oncoscanr", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-magrittr - r-readr run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-magrittr - r-readr diff --git a/recipes/bioconductor-oncoscore/meta.yaml b/recipes/bioconductor-oncoscore/meta.yaml index b8102697059ad..f85345b846e04 100644 --- a/recipes/bioconductor-oncoscore/meta.yaml +++ b/recipes/bioconductor-oncoscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "OncoScore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 62b68dec725d2a79df4d45eb05fbfe86 + md5: 5b61a8738f91d4c8ff214b38878a8564 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oncoscore", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, knitr, testthat, requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-oncosimulr/build.sh b/recipes/bioconductor-oncosimulr/build.sh index 8723af305997a..ac78ea511ccf4 100644 --- a/recipes/bioconductor-oncosimulr/build.sh +++ b/recipes/bioconductor-oncosimulr/build.sh @@ -11,4 +11,4 @@ CXX14=$CXX" > ~/.R/Makevars if [[ $OSTYPE == "darwin"* ]]; then sed -i.bak "s/OncoSimulR.so/OncoSimulR.dylib/g" src/install.libs.R fi -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-oncosimulr/meta.yaml b/recipes/bioconductor-oncosimulr/meta.yaml index 1a46c55588f7a..daa4bec2d291d 100644 --- a/recipes/bioconductor-oncosimulr/meta.yaml +++ b/recipes/bioconductor-oncosimulr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.2.0" %} +{% set version = "4.4.0" %} {% set name = "OncoSimulR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 741c17927e4a7a2022f6d757602e3c72 + md5: 9b908040a100f075d4f2493ec3c1fa85 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oncosimulr", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-car - r-data.table @@ -37,8 +38,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-car - r-data.table diff --git a/recipes/bioconductor-onlinefdr/meta.yaml b/recipes/bioconductor-onlinefdr/meta.yaml index 2ad6e39347b96..24c6eefdc5faf 100644 --- a/recipes/bioconductor-onlinefdr/meta.yaml +++ b/recipes/bioconductor-onlinefdr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "onlineFDR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9f9a9d661fcecba747e4229d4e6cf920 + md5: 1fcb84d6fd99c3f48d43c07adc29f256 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-onlinefdr", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, covr requirements: host: diff --git a/recipes/bioconductor-ontoproc/meta.yaml b/recipes/bioconductor-ontoproc/meta.yaml index b8b5cfba1fd90..ebdd3376d7bee 100644 --- a/recipes/bioconductor-ontoproc/meta.yaml +++ b/recipes/bioconductor-ontoproc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "ontoProc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9b292bc23074c04cfed8987658c6cafc + md5: 157cb78951de651c6be909aef51480a5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ontoproc", max_pin="x.x") }}' noarch: generic # Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown, AnnotationDbi requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-dt @@ -37,13 +38,13 @@ requirements: - r-ontologyplot - r-shiny run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-dt diff --git a/recipes/bioconductor-ontoprocdata/meta.yaml b/recipes/bioconductor-ontoprocdata/meta.yaml index d71b56dc9f9ba..b0247d4b82b11 100644 --- a/recipes/bioconductor-ontoprocdata/meta.yaml +++ b/recipes/bioconductor-ontoprocdata/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.9901" %} {% set name = "ontoProcData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: d4160c1fc853db468ce73c7fe62ca00f build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ontoprocdata", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), AnnotationHub, utils, knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-opencyto/meta.yaml b/recipes/bioconductor-opencyto/meta.yaml index 2e2d3584c5621..6c2923914d7d3 100644 --- a/recipes/bioconductor-opencyto/meta.yaml +++ b/recipes/bioconductor-opencyto/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "openCyto" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fabe8dc6a63062ffd1b3fefadeb787b5 + md5: 04a62bb1960f008fc218686296a3118d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-opencyto", max_pin="x.x") }}' # Suggests: flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2), MASS requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-ncdfflow >=2.46.0,<2.47.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-bh - r-cpp11 @@ -37,15 +38,15 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-ncdfflow >=2.46.0,<2.47.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-bh - r-cpp11 diff --git a/recipes/bioconductor-openprimer/meta.yaml b/recipes/bioconductor-openprimer/meta.yaml index d0e580bce2926..e7ebaf881fc1c 100644 --- a/recipes/bioconductor-openprimer/meta.yaml +++ b/recipes/bioconductor-openprimer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "openPrimeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 105634c21aebdcf44ef3c0151664e343 + md5: e3fe2285d832b192c7054a36e2aedc6b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-openprimer", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 1.0.2), knitr (>= 1.13), rmarkdown (>= 1.0), devtools (>= 1.12.0), doParallel (>= 1.0.10), pander (>= 0.6.0), learnr (>= 0.9) # SystemRequirements: MAFFT (>= 7.305), OligoArrayAux (>= 3.8), ViennaRNA (>= 2.4.1), MELTING (>= 5.1.1), Pandoc (>= 1.12.3) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'r-ape >=3.5' - r-base - 'r-digest >=0.6.9' @@ -52,12 +53,12 @@ requirements: - 'r-xml >=3.98-1.4' - 'mafft >=7.305' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'r-ape >=3.5' - r-base - 'r-digest >=0.6.9' diff --git a/recipes/bioconductor-openprimerui/meta.yaml b/recipes/bioconductor-openprimerui/meta.yaml index 99cb97ce36f13..c0bfddd6d19af 100644 --- a/recipes/bioconductor-openprimerui/meta.yaml +++ b/recipes/bioconductor-openprimerui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "openPrimeRui" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 365ce6ca2bb48726abf97ca874a6f6da + md5: 11cb9510b6a6ecdbc8df2d5c2497d029 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-openprimerui", max_pin="x.x") }}' noarch: generic # Suggests: knitr (>= 1.13) requirements: host: - - 'bioconductor-openprimer >=1.22.0,<1.23.0' + - 'bioconductor-openprimer >=1.24.0,<1.25.0' - r-base - 'r-dt >=0.2' - 'r-rmarkdown >=1.0' @@ -29,7 +30,7 @@ requirements: - 'r-shinybs >=0.61' - 'r-shinyjs >=0.9' run: - - 'bioconductor-openprimer >=1.22.0,<1.23.0' + - 'bioconductor-openprimer >=1.24.0,<1.25.0' - r-base - 'r-dt >=0.2' - 'r-rmarkdown >=1.0' diff --git a/recipes/bioconductor-openstats/meta.yaml b/recipes/bioconductor-openstats/meta.yaml index 73794c3fe60c9..f78c9bcdf4b49 100644 --- a/recipes/bioconductor-openstats/meta.yaml +++ b/recipes/bioconductor-openstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "OpenStats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7930395c0dc75c56e7f67cfef6526ac1 + md5: 0e8a0fcd25ca1377c5bce5068bfaabff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-openstats", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown requirements: diff --git a/recipes/bioconductor-operonhumanv3.db/meta.yaml b/recipes/bioconductor-operonhumanv3.db/meta.yaml index e859629198e93..c1bf73b30fa4b 100644 --- a/recipes/bioconductor-operonhumanv3.db/meta.yaml +++ b/recipes/bioconductor-operonhumanv3.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "OperonHumanV3.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 648da5d4d63c6c8327f6035ee09f2b65 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-operonhumanv3.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-opossom/meta.yaml b/recipes/bioconductor-opossom/meta.yaml index 368d85fca06ae..131a22582ed1a 100644 --- a/recipes/bioconductor-opossom/meta.yaml +++ b/recipes/bioconductor-opossom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "oposSOM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d0e76bf961fef11d0ae091eec82824b + md5: a5660824c13db2ae8bf7b79aa7c529f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-opossom", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-ape - r-base - r-fastica @@ -38,9 +39,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-ape - r-base - r-fastica diff --git a/recipes/bioconductor-oppar/meta.yaml b/recipes/bioconductor-oppar/meta.yaml index dabd8ae7baf3b..9546c106c3853 100644 --- a/recipes/bioconductor-oppar/meta.yaml +++ b/recipes/bioconductor-oppar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "oppar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aa9223b057764734655c8cdbbe8dc740 + md5: 21adf37b9236cf860009e709f63d5e30 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oppar", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-oppti/meta.yaml b/recipes/bioconductor-oppti/meta.yaml index 8a401c37715a6..ceb9efd135c77 100644 --- a/recipes/bioconductor-oppti/meta.yaml +++ b/recipes/bioconductor-oppti/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "oppti" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ee66d8bc8d637cf14d5724387ffd3894 + md5: 8f995db99b66e966a96b8ce150c956a7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oppti", max_pin="x.x") }}' noarch: generic # Suggests: markdown requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-devtools - r-ggplot2 @@ -31,7 +32,7 @@ requirements: - r-rcolorbrewer - r-reshape run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-devtools - r-ggplot2 diff --git a/recipes/bioconductor-optimalflow/meta.yaml b/recipes/bioconductor-optimalflow/meta.yaml index c7ba7fd84a780..992876df6f621 100644 --- a/recipes/bioconductor-optimalflow/meta.yaml +++ b/recipes/bioconductor-optimalflow/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "optimalFlow" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fff3df9b484a19d62f4c06e763a554ea + md5: c66127dc23a70fdcfd651543ea596329 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-optimalflow", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown, magick requirements: host: - - 'bioconductor-flowmeans >=1.60.0,<1.61.0' - - 'bioconductor-optimalflowdata >=1.12.0,<1.13.0' + - 'bioconductor-flowmeans >=1.62.0,<1.63.0' + - 'bioconductor-optimalflowdata >=1.14.0,<1.15.0' - r-base - r-dbscan - r-doparallel @@ -36,8 +37,8 @@ requirements: - r-robustbase - r-transport run: - - 'bioconductor-flowmeans >=1.60.0,<1.61.0' - - 'bioconductor-optimalflowdata >=1.12.0,<1.13.0' + - 'bioconductor-flowmeans >=1.62.0,<1.63.0' + - 'bioconductor-optimalflowdata >=1.14.0,<1.15.0' - r-base - r-dbscan - r-doparallel diff --git a/recipes/bioconductor-optimalflowdata/meta.yaml b/recipes/bioconductor-optimalflowdata/meta.yaml index 4b1bf0bf2330b..d65bee9574e4b 100644 --- a/recipes/bioconductor-optimalflowdata/meta.yaml +++ b/recipes/bioconductor-optimalflowdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "optimalFlowData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: daba5d6a8b8fdde9d58fed555c569ad5 + md5: 790ea8af88ecf90abafdef9a7c4abb08 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-optimalflowdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown, magick requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-optimalflowdata/post-link.sh b/recipes/bioconductor-optimalflowdata/post-link.sh index a58d0484a9929..0a5ec1a8c8c2a 100644 --- a/recipes/bioconductor-optimalflowdata/post-link.sh +++ b/recipes/bioconductor-optimalflowdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "optimalflowdata-1.12.0" +installBiocDataPackage.sh "optimalflowdata-1.14.0" diff --git a/recipes/bioconductor-opweight/meta.yaml b/recipes/bioconductor-opweight/meta.yaml index 82f1af5964129..cd88a4afed9cd 100644 --- a/recipes/bioconductor-opweight/meta.yaml +++ b/recipes/bioconductor-opweight/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "OPWeight" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a33f46eeb9e69082fdd9a89cb7a5f23c + md5: 83d9a0007e617f317f9424a4c228c50a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-opweight", max_pin="x.x") }}' noarch: generic # Suggests: airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2, gridExtra, knitr, Matrix, rmarkdown, scales, testthat requirements: host: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-mass - r-tibble run: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-mass - r-tibble diff --git a/recipes/bioconductor-orderedlist/meta.yaml b/recipes/bioconductor-orderedlist/meta.yaml index d4fc2fe472c0a..6be59704a0e91 100644 --- a/recipes/bioconductor-orderedlist/meta.yaml +++ b/recipes/bioconductor-orderedlist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "OrderedList" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 352cb6d578f4aa28920229c8844fe469 + md5: d8239906b10a2630dc25ab749903a511 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-orderedlist", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-twilight >=1.76.0,<1.77.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-twilight >=1.78.0,<1.79.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-twilight >=1.76.0,<1.77.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-twilight >=1.78.0,<1.79.0' - r-base test: commands: diff --git a/recipes/bioconductor-orfhunter/meta.yaml b/recipes/bioconductor-orfhunter/meta.yaml index 67b3d4b0cdee9..239909d4356a3 100644 --- a/recipes/bioconductor-orfhunter/meta.yaml +++ b/recipes/bioconductor-orfhunter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ORFhunteR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de379db06acbc82ad053e95517675ebf + md5: c9e57a998b0746df96e6d173d75fd032 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-orfhunter", max_pin="x.x") }}' # Suggests: knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-peptides @@ -33,9 +34,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-peptides diff --git a/recipes/bioconductor-orfik/meta.yaml b/recipes/bioconductor-orfik/meta.yaml index a443240ae3bdb..3a5075e7dd6ce 100644 --- a/recipes/bioconductor-orfik/meta.yaml +++ b/recipes/bioconductor-orfik/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ORFik" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 712d98a9513f8a55085f3269902744f2 + md5: 80a8144faafb88fcd9745dcfce492512 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-orfik", max_pin="x.x") }}' # Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biomartr - 'r-cowplot >=1.0.0' + - r-curl - 'r-data.table >=1.11.8' + - r-downloader - 'r-fst >=0.9.2' - 'r-ggplot2 >=2.2.1' - 'r-gridextra >=2.3' @@ -47,30 +50,35 @@ requirements: - r-jsonlite - r-r.utils - 'r-rcpp >=1.0.0' + - r-rcurl + - r-withr + - r-xml - 'r-xml2 >=1.2.0' - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biomartr - 'r-cowplot >=1.0.0' + - r-curl - 'r-data.table >=1.11.8' + - r-downloader - 'r-fst >=0.9.2' - 'r-ggplot2 >=2.2.1' - 'r-gridextra >=2.3' @@ -78,6 +86,9 @@ requirements: - r-jsonlite - r-r.utils - 'r-rcpp >=1.0.0' + - r-rcurl + - r-withr + - r-xml - 'r-xml2 >=1.2.0' build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-org.ag.eg.db/meta.yaml b/recipes/bioconductor-org.ag.eg.db/meta.yaml index 1051e8dd1d8c4..6a62269c6da3b 100644 --- a/recipes/bioconductor-org.ag.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ag.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Ag.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb3e06ad1afc3c386367a239e559f342 + md5: a67c309f5472338fd47fe43ff20ce2e5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.ag.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.ag.eg.db/post-link.sh b/recipes/bioconductor-org.ag.eg.db/post-link.sh index b668057bfacd7..914a57fe474f6 100644 --- a/recipes/bioconductor-org.ag.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ag.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.ag.eg.db-3.17.0" +installBiocDataPackage.sh "org.ag.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.at.tair.db/meta.yaml b/recipes/bioconductor-org.at.tair.db/meta.yaml index 23f5054e0fde6..6ed40899b87cc 100644 --- a/recipes/bioconductor-org.at.tair.db/meta.yaml +++ b/recipes/bioconductor-org.at.tair.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.At.tair.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 568e09bfbf9b86a9120b52ca6eb47879 + md5: 5d6161b859de99eaeadebc0e03ae9c68 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.at.tair.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.at.tair.db/post-link.sh b/recipes/bioconductor-org.at.tair.db/post-link.sh index 96929528fea52..4fbdf92ea3f91 100644 --- a/recipes/bioconductor-org.at.tair.db/post-link.sh +++ b/recipes/bioconductor-org.at.tair.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.at.tair.db-3.17.0" +installBiocDataPackage.sh "org.at.tair.db-3.18.0" diff --git a/recipes/bioconductor-org.bt.eg.db/meta.yaml b/recipes/bioconductor-org.bt.eg.db/meta.yaml index a83cc489b9227..c0fef6c777d07 100644 --- a/recipes/bioconductor-org.bt.eg.db/meta.yaml +++ b/recipes/bioconductor-org.bt.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Bt.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 13b2350bb7e6219a25caea3a4038f104 + md5: 23fd8017323c86930c50d596204bad54 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.bt.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.bt.eg.db/post-link.sh b/recipes/bioconductor-org.bt.eg.db/post-link.sh index 6b094edee61d3..cd489eb184530 100644 --- a/recipes/bioconductor-org.bt.eg.db/post-link.sh +++ b/recipes/bioconductor-org.bt.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.bt.eg.db-3.17.0" +installBiocDataPackage.sh "org.bt.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.ce.eg.db/meta.yaml b/recipes/bioconductor-org.ce.eg.db/meta.yaml index dc4e0188f33c5..495acc87d6521 100644 --- a/recipes/bioconductor-org.ce.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ce.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Ce.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8884864a691574d7640b2059a8d6613b + md5: 441a5efb4649a1201b5552b14c1f1cef build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.ce.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.ce.eg.db/post-link.sh b/recipes/bioconductor-org.ce.eg.db/post-link.sh index 7f5644e45824a..2bdc66737e6a1 100644 --- a/recipes/bioconductor-org.ce.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ce.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.ce.eg.db-3.17.0" +installBiocDataPackage.sh "org.ce.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.cf.eg.db/meta.yaml b/recipes/bioconductor-org.cf.eg.db/meta.yaml index dc71863d364c4..67f62fb8f70c8 100644 --- a/recipes/bioconductor-org.cf.eg.db/meta.yaml +++ b/recipes/bioconductor-org.cf.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Cf.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 594a306e7ac757df56e9563163168713 + md5: 038d08c046a81218a31ff8db0877dd15 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.cf.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.cf.eg.db/post-link.sh b/recipes/bioconductor-org.cf.eg.db/post-link.sh index 1f27db3f27775..06faa06376c83 100644 --- a/recipes/bioconductor-org.cf.eg.db/post-link.sh +++ b/recipes/bioconductor-org.cf.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.cf.eg.db-3.17.0" +installBiocDataPackage.sh "org.cf.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.dm.eg.db/meta.yaml b/recipes/bioconductor-org.dm.eg.db/meta.yaml index b16f5f34268f6..f5b192c04a705 100644 --- a/recipes/bioconductor-org.dm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.dm.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Dm.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a680c3ea7320013c7ab1181d11e2177 + md5: 92577ed3bc5d76b78905169eebfebe7d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.dm.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.dm.eg.db/post-link.sh b/recipes/bioconductor-org.dm.eg.db/post-link.sh index e5724e3adb8e1..d0c3e58bb8bf4 100644 --- a/recipes/bioconductor-org.dm.eg.db/post-link.sh +++ b/recipes/bioconductor-org.dm.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.dm.eg.db-3.17.0" +installBiocDataPackage.sh "org.dm.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.dr.eg.db/meta.yaml b/recipes/bioconductor-org.dr.eg.db/meta.yaml index 794990e882fae..38cae1002a138 100644 --- a/recipes/bioconductor-org.dr.eg.db/meta.yaml +++ b/recipes/bioconductor-org.dr.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Dr.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 03edb42214f27a93743dfc57200cddbb + md5: cfea28c45f2f34c675975eacbe861a5f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.dr.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.dr.eg.db/post-link.sh b/recipes/bioconductor-org.dr.eg.db/post-link.sh index 565224b42083a..f65f46693b80e 100644 --- a/recipes/bioconductor-org.dr.eg.db/post-link.sh +++ b/recipes/bioconductor-org.dr.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.dr.eg.db-3.17.0" +installBiocDataPackage.sh "org.dr.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.eck12.eg.db/meta.yaml b/recipes/bioconductor-org.eck12.eg.db/meta.yaml index d2bfbf47153ea..496eac6758b52 100644 --- a/recipes/bioconductor-org.eck12.eg.db/meta.yaml +++ b/recipes/bioconductor-org.eck12.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.EcK12.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 676642eb784017bf9f82711274f8987e + md5: 50d3d3ca9efec212eae3a920b00750a3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.eck12.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.eck12.eg.db/post-link.sh b/recipes/bioconductor-org.eck12.eg.db/post-link.sh index 9d039702bf9a3..ebfed362951d8 100644 --- a/recipes/bioconductor-org.eck12.eg.db/post-link.sh +++ b/recipes/bioconductor-org.eck12.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.eck12.eg.db-3.17.0" +installBiocDataPackage.sh "org.eck12.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml b/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml index 40bfe1dfaf5fe..d251c5b30c35e 100644 --- a/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.EcSakai.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 135a50e2604715a7c5f1c2a36bddf691 + md5: 3f26ffa55ce30fc8caa64f826207ac61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.ecsakai.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh b/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh index 1190bbfee42ac..8ec1c9f68fb4b 100644 --- a/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.ecsakai.eg.db-3.17.0" +installBiocDataPackage.sh "org.ecsakai.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.gg.eg.db/meta.yaml b/recipes/bioconductor-org.gg.eg.db/meta.yaml index cbb9dabfd6da5..4e11232145408 100644 --- a/recipes/bioconductor-org.gg.eg.db/meta.yaml +++ b/recipes/bioconductor-org.gg.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Gg.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 292b22ea846c6c184528e92ab4a53247 + md5: 4ebcbfb0baeee3332a2a07aeae2402a9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.gg.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.gg.eg.db/post-link.sh b/recipes/bioconductor-org.gg.eg.db/post-link.sh index 14fb60f9390bb..19ca51f5ad61d 100644 --- a/recipes/bioconductor-org.gg.eg.db/post-link.sh +++ b/recipes/bioconductor-org.gg.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.gg.eg.db-3.17.0" +installBiocDataPackage.sh "org.gg.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.hs.eg.db/meta.yaml b/recipes/bioconductor-org.hs.eg.db/meta.yaml index d2144f7ab5e8c..2aaffdc1eb4a7 100644 --- a/recipes/bioconductor-org.hs.eg.db/meta.yaml +++ b/recipes/bioconductor-org.hs.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Hs.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a1015fd071ab69055865940ef6e205f4 + md5: e1f74b9d0c541b5678a0d88f6a8ec847 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.hs.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.hs.eg.db/post-link.sh b/recipes/bioconductor-org.hs.eg.db/post-link.sh index 3a9f65c1b9409..88931ccb51392 100644 --- a/recipes/bioconductor-org.hs.eg.db/post-link.sh +++ b/recipes/bioconductor-org.hs.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.hs.eg.db-3.17.0" +installBiocDataPackage.sh "org.hs.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.mm.eg.db/meta.yaml b/recipes/bioconductor-org.mm.eg.db/meta.yaml index 62b1b53e60da6..9d5b8774b3b7a 100644 --- a/recipes/bioconductor-org.mm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.mm.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Mm.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7b2124d1ef7c0936bb4ecfcbd2a979b8 + md5: bd95e1ff46f764fff51acc60b249fe95 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.mm.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.mm.eg.db/post-link.sh b/recipes/bioconductor-org.mm.eg.db/post-link.sh index 498545f19ed05..ea3b970a24917 100644 --- a/recipes/bioconductor-org.mm.eg.db/post-link.sh +++ b/recipes/bioconductor-org.mm.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.mm.eg.db-3.17.0" +installBiocDataPackage.sh "org.mm.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.mmu.eg.db/meta.yaml b/recipes/bioconductor-org.mmu.eg.db/meta.yaml index 1af50dabafd7f..408a76b274591 100644 --- a/recipes/bioconductor-org.mmu.eg.db/meta.yaml +++ b/recipes/bioconductor-org.mmu.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Mmu.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d59c3d744ec7def892edacf12c99b869 + md5: 45a35940d0d1ab91b2b262a8666afa53 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.mmu.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.mmu.eg.db/post-link.sh b/recipes/bioconductor-org.mmu.eg.db/post-link.sh index f4810f44dd65f..017b895a9759c 100644 --- a/recipes/bioconductor-org.mmu.eg.db/post-link.sh +++ b/recipes/bioconductor-org.mmu.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.mmu.eg.db-3.17.0" +installBiocDataPackage.sh "org.mmu.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.mxanthus.db/meta.yaml b/recipes/bioconductor-org.mxanthus.db/meta.yaml index f5df60ed94e1b..558a2aefd9d12 100644 --- a/recipes/bioconductor-org.mxanthus.db/meta.yaml +++ b/recipes/bioconductor-org.mxanthus.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.27" %} {% set name = "org.Mxanthus.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,27 +13,28 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e493814c41401de383b4f6e0f3d39619 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.mxanthus.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, RUnit, clusterProfiler, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.pt.eg.db/meta.yaml b/recipes/bioconductor-org.pt.eg.db/meta.yaml index 05faf04d070c0..b98e9dd870761 100644 --- a/recipes/bioconductor-org.pt.eg.db/meta.yaml +++ b/recipes/bioconductor-org.pt.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Pt.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b3c4135532486951e94ed5d182030217 + md5: d6672365e68ece6415e2736f40bf096c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.pt.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.pt.eg.db/post-link.sh b/recipes/bioconductor-org.pt.eg.db/post-link.sh index 03ab6fa472388..9bcd0492d2c7f 100644 --- a/recipes/bioconductor-org.pt.eg.db/post-link.sh +++ b/recipes/bioconductor-org.pt.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.pt.eg.db-3.17.0" +installBiocDataPackage.sh "org.pt.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.rn.eg.db/meta.yaml b/recipes/bioconductor-org.rn.eg.db/meta.yaml index 670d3c8303da1..aa8ee6cf68f8d 100644 --- a/recipes/bioconductor-org.rn.eg.db/meta.yaml +++ b/recipes/bioconductor-org.rn.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Rn.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bf40322d9b95075d75777ec63a797198 + md5: 1ff92cec0fc2cbd5b3055d1153526ce3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.rn.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.rn.eg.db/post-link.sh b/recipes/bioconductor-org.rn.eg.db/post-link.sh index 73d94ea033353..58dd4a7343f2b 100644 --- a/recipes/bioconductor-org.rn.eg.db/post-link.sh +++ b/recipes/bioconductor-org.rn.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.rn.eg.db-3.17.0" +installBiocDataPackage.sh "org.rn.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.sc.sgd.db/meta.yaml b/recipes/bioconductor-org.sc.sgd.db/meta.yaml index f93e10ad3af11..278039220b5c7 100644 --- a/recipes/bioconductor-org.sc.sgd.db/meta.yaml +++ b/recipes/bioconductor-org.sc.sgd.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Sc.sgd.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b0fd2fcd421007a5b9bd7bc2f5874ae3 + md5: cd83de7109be623e7a294a47ca65f160 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.sc.sgd.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.sc.sgd.db/post-link.sh b/recipes/bioconductor-org.sc.sgd.db/post-link.sh index d98eb50cfefb3..ad3c38e6e585e 100644 --- a/recipes/bioconductor-org.sc.sgd.db/post-link.sh +++ b/recipes/bioconductor-org.sc.sgd.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.sc.sgd.db-3.17.0" +installBiocDataPackage.sh "org.sc.sgd.db-3.18.0" diff --git a/recipes/bioconductor-org.ss.eg.db/meta.yaml b/recipes/bioconductor-org.ss.eg.db/meta.yaml index b016e212ce8c3..6e7b63562d155 100644 --- a/recipes/bioconductor-org.ss.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ss.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Ss.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a9f8354c9869e86a610ad30f51eb533b + md5: f9b32c76d23f9195df7a7eb6529f3340 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.ss.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.ss.eg.db/post-link.sh b/recipes/bioconductor-org.ss.eg.db/post-link.sh index b54a6e63afd13..5696d4ac5b715 100644 --- a/recipes/bioconductor-org.ss.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ss.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.ss.eg.db-3.17.0" +installBiocDataPackage.sh "org.ss.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.xl.eg.db/meta.yaml b/recipes/bioconductor-org.xl.eg.db/meta.yaml index 70fb5c04244ff..48b5a78fe55b9 100644 --- a/recipes/bioconductor-org.xl.eg.db/meta.yaml +++ b/recipes/bioconductor-org.xl.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Xl.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ce9e0dc3566a220f5c12b70ffb2538c + md5: bbea76a4373d8b51048029b83c591aca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.xl.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.xl.eg.db/post-link.sh b/recipes/bioconductor-org.xl.eg.db/post-link.sh index f6af33a8d689b..d079ec990a1cf 100644 --- a/recipes/bioconductor-org.xl.eg.db/post-link.sh +++ b/recipes/bioconductor-org.xl.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.xl.eg.db-3.17.0" +installBiocDataPackage.sh "org.xl.eg.db-3.18.0" diff --git a/recipes/bioconductor-organism.dplyr/meta.yaml b/recipes/bioconductor-organism.dplyr/meta.yaml index c3360180e94ae..2ccba681f13c0 100644 --- a/recipes/bioconductor-organism.dplyr/meta.yaml +++ b/recipes/bioconductor-organism.dplyr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.1" %} {% set name = "Organism.dplyr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d89fd354e720e5b09282fa271367efe3 + md5: b16c25c3ee5abafa1007a9c7bd731801 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-organism.dplyr", max_pin="x.x") }}' noarch: generic -# Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, BiocStyle, ggplot2 +# Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, magick, BiocStyle, ggplot2 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-dbplyr @@ -37,14 +38,14 @@ requirements: - r-rsqlite - r-tibble run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-dbplyr diff --git a/recipes/bioconductor-organismdbi/meta.yaml b/recipes/bioconductor-organismdbi/meta.yaml index 7e0477602eab8..3424eb8e53508 100644 --- a/recipes/bioconductor-organismdbi/meta.yaml +++ b/recipes/bioconductor-organismdbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "OrganismDbi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4b63d172cafa48c26622cff0fa0a338a + md5: 3d6c3ba042e4e0b6ecf5fa27fc344a82 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-organismdbi", max_pin="x.x") }}' noarch: generic # Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, rtracklayer, biomaRt, RUnit, RMariaDB, BiocStyle, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-dbi run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-dbi diff --git a/recipes/bioconductor-orthogene/meta.yaml b/recipes/bioconductor-orthogene/meta.yaml index 6856abd424938..5fb52c90803da 100644 --- a/recipes/bioconductor-orthogene/meta.yaml +++ b/recipes/bioconductor-orthogene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "orthogene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e4dcc64a91b436e77b287eb1c94ed801 + md5: f3597fa7ce02e2e32ee6cebb20f67c08 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-orthogene", max_pin="x.x") }}' noarch: generic # Suggests: rworkflows, remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-babelgene - r-base - r-data.table @@ -37,8 +38,8 @@ requirements: - r-patchwork - r-repmis run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-babelgene - r-base - r-data.table diff --git a/recipes/bioconductor-orthology.eg.db/meta.yaml b/recipes/bioconductor-orthology.eg.db/meta.yaml index c01f01405c677..b4bceecfb8d50 100644 --- a/recipes/bioconductor-orthology.eg.db/meta.yaml +++ b/recipes/bioconductor-orthology.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "Orthology.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90c181057a638413afc54bb11071a42e + md5: 1e53a6a144a5074544cbe166ad241012 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-orthology.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-orthology.eg.db/post-link.sh b/recipes/bioconductor-orthology.eg.db/post-link.sh index 9de63532c30a8..62dc891778772 100644 --- a/recipes/bioconductor-orthology.eg.db/post-link.sh +++ b/recipes/bioconductor-orthology.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "orthology.eg.db-3.17.0" +installBiocDataPackage.sh "orthology.eg.db-3.18.0" diff --git a/recipes/bioconductor-orthos/build.sh b/recipes/bioconductor-orthos/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-orthos/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-orthos/meta.yaml b/recipes/bioconductor-orthos/meta.yaml new file mode 100644 index 0000000000000..638a68a53caf2 --- /dev/null +++ b/recipes/bioconductor-orthos/meta.yaml @@ -0,0 +1,81 @@ +{% set version = "1.0.1" %} +{% set name = "orthos" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c35d515c0e956e4207b00db662192707 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-orthos", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-orthosdata >=1.0.0,<1.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-colorspace + - r-cowplot + - r-dplyr + - r-ggplot2 + - r-ggpubr + - r-ggrepel + - r-ggsci + - r-keras + - r-plyr + - r-reticulate + - r-rlang + - r-tensorflow + - r-tidyr + run: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-orthosdata >=1.0.0,<1.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-colorspace + - r-cowplot + - r-dplyr + - r-ggplot2 + - r-ggpubr + - r-ggrepel + - r-ggsci + - r-keras + - r-plyr + - r-reticulate + - r-rlang + - r-tensorflow + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: '`orthos` is an R package for variance decomposition using conditional variational auto-encoders' + description: '`orthos` decomposes RNA-seq contrasts, for example obtained from a gene knock-out or compound treatment experiment, into unspecific and experiment-specific components. Original and decomposed contrasts can be efficiently queried against a large database of contrasts (derived from ARCHS4, https://maayanlab.cloud/archs4/) to identify similar experiments. `orthos` furthermore provides plotting functions to visualize the results of such a search for similar contrasts.' + license_file: LICENSE + diff --git a/recipes/bioconductor-orthosdata/meta.yaml b/recipes/bioconductor-orthosdata/meta.yaml new file mode 100644 index 0000000000000..8aca3fc0ed845 --- /dev/null +++ b/recipes/bioconductor-orthosdata/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.0.0" %} +{% set name = "orthosData" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7970587455fa5197daf1f6b640b7f688 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-orthosdata", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, ggplot2, knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-stringr + run: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-stringr + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Data for the orthos package' + description: '`orthosData` is the companion ExperimentData package to the `orthos` R package for mechanistic studies using differential gene expression experiments. It provides functions for retrieval from ExperimentHub and local caching of the models and datasets used internally in orthos.' + license_file: LICENSE + diff --git a/recipes/bioconductor-orthosdata/post-link.sh b/recipes/bioconductor-orthosdata/post-link.sh new file mode 100644 index 0000000000000..5c3cfd2f32ffc --- /dev/null +++ b/recipes/bioconductor-orthosdata/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "orthosdata-1.0.0" diff --git a/recipes/bioconductor-orthosdata/pre-unlink.sh b/recipes/bioconductor-orthosdata/pre-unlink.sh new file mode 100644 index 0000000000000..78d90840ebfb5 --- /dev/null +++ b/recipes/bioconductor-orthosdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ orthosData diff --git a/recipes/bioconductor-osat/meta.yaml b/recipes/bioconductor-osat/meta.yaml index a41d9a8ef09cc..8b31b07c069f0 100644 --- a/recipes/bioconductor-osat/meta.yaml +++ b/recipes/bioconductor-osat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "OSAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 41b946e0e889d7756364cff5f9a3386e + md5: 64bba183cfa8a211960d891cb5ee3ddb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-osat", max_pin="x.x") }}' noarch: generic # Suggests: xtable, Biobase requirements: diff --git a/recipes/bioconductor-oscope/meta.yaml b/recipes/bioconductor-oscope/meta.yaml index a5f1f62cfab43..d854e94085c0f 100644 --- a/recipes/bioconductor-oscope/meta.yaml +++ b/recipes/bioconductor-oscope/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "Oscope" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1fdee060dfcb4bd73e1e89a377abe73e + md5: 96a8fc6730b6d493d352d74032c4b3d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oscope", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebseq >=1.40.0,<1.41.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' - r-base - r-cluster - r-testthat run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebseq >=1.40.0,<1.41.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' - r-base - r-cluster - r-testthat diff --git a/recipes/bioconductor-otubase/build_failure.linux-64.yaml b/recipes/bioconductor-otubase/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..ffb92d761f8f5 --- /dev/null +++ b/recipes/bioconductor-otubase/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 2466376a66b53bb6cdb3dff2c8ae7300a0ed3b25e36f88bb855a119a89b9d177 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [] 1.2s + conda-forge/linux-64 + conda-forge/noarch + bioconda/linux-64 100% + pkgs/main/linux-64 + pkgs/main/noarch + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gbioconda/linux-64 + [] 1.3s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/linux-64 + pkgs/main/noarch + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.4s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/linux-64 100% + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/linux-64 + [] 1.5s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.6s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/noarch + [] 1.7s + conda-forge/linux-64 + conda-forge/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.8s + conda-forge/linux-64 + conda-forge/noarch 100% + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gconda-forge/noarch + [] 1.9s + conda-forge/linux-64 + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[0Gpkgs/r/noarch + pkgs/r/linux-64 + [] 2.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.9s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.9s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.4s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.5s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.6s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.7s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.8s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.9s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.0s + [2K[1A[2K[0Gconda-forge/linux-64 + [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.6MB/s 0.0s + opt/conda/conda-bld/noarch 922.0 B @ 18.8MB/s 0.0s + [?25hTraceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3089, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2879, in test + environ.create_env(metadata.config.test_prefix, actions, config=metadata.config, + File "/opt/conda/lib/python3.8/site-packages/conda_build/environ.py", line 1052, in create_env + display_actions(actions, index) + File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in display_actions + actions['LINK'] = [index[d] for d in actions['LINK']] + File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in + actions['LINK'] = [index[d] for d in actions['LINK']] + KeyError: Dist(channel='conda-forge', dist_name='python-3.12.1-hab00c5b_0_cpython', name='python', fmt='.conda', version='3.12.1', build_string='hab00c5b_0_cpython', build_number=0, base_url=None, platform=None) +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-otubase/meta.yaml b/recipes/bioconductor-otubase/meta.yaml index d46aa09d35d25..51975ccd38e1e 100644 --- a/recipes/bioconductor-otubase/meta.yaml +++ b/recipes/bioconductor-otubase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "OTUbase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ff077bed280afa9c1460747ad4bb96b + md5: 612c0f07995eb5cc0f753eb6750e5216 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-otubase", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-vegan run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-vegan test: diff --git a/recipes/bioconductor-outrider/meta.yaml b/recipes/bioconductor-outrider/meta.yaml index 1a290b5564a2c..7fb41ce9d207b 100644 --- a/recipes/bioconductor-outrider/meta.yaml +++ b/recipes/bioconductor-outrider/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "OUTRIDER" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e41d4122f3ed2b2b7fbc9e73d0f5341 + md5: 92609d3ce486cdf55004d26887a9494d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-outrider", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bbmisc - r-data.table @@ -48,15 +49,15 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bbmisc - r-data.table diff --git a/recipes/bioconductor-outsplice/meta.yaml b/recipes/bioconductor-outsplice/meta.yaml index b8d74daa973f8..88b5efe5ba59d 100644 --- a/recipes/bioconductor-outsplice/meta.yaml +++ b/recipes/bioconductor-outsplice/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "OutSplice" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 216bb720d2a43d5d264f25733e0dd546 + md5: 7a55735983a79681a2bbcd567c9f0c53 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-outsplice", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-repitools >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-repitools >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-repitools >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-repitools >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base test: commands: diff --git a/recipes/bioconductor-oveseg/meta.yaml b/recipes/bioconductor-oveseg/meta.yaml index 6334a2389e884..9f062d2d0697a 100644 --- a/recipes/bioconductor-oveseg/meta.yaml +++ b/recipes/bioconductor-oveseg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "OVESEG" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3cc11546cd7fdf569be32319bbac34b4 + md5: 2a1ac203dcd19e6c511d4bcefa0cee45 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oveseg", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-fdrtool - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-fdrtool - r-rcpp diff --git a/recipes/bioconductor-paa/meta.yaml b/recipes/bioconductor-paa/meta.yaml index 7c378000470d1..e433b71cba99c 100644 --- a/recipes/bioconductor-paa/meta.yaml +++ b/recipes/bioconductor-paa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "PAA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4be8a4102d0386d6a8ef5e446e538bd7 + md5: 4968ea3bfbaa5edd0e6d00dcbe93a6d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-paa", max_pin="x.x") }}' # Suggests: BiocStyle, RUnit, BiocGenerics, vsn # SystemRequirements: C++ software package Random Jungle requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-e1071 - r-gplots @@ -35,8 +36,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-e1071 - r-gplots diff --git a/recipes/bioconductor-packfinder/meta.yaml b/recipes/bioconductor-packfinder/meta.yaml index e097de4cffde0..f973e5d16efa5 100644 --- a/recipes/bioconductor-packfinder/meta.yaml +++ b/recipes/bioconductor-packfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "packFinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c1b5c25374c50cdd102cea61cf7739ce + md5: 8c2f41158644b4d04136910e0ce39af8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-packfinder", max_pin="x.x") }}' noarch: generic # Suggests: biomartr, knitr, rmarkdown, testthat, dendextend, biocViews, BiocCheck, BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-ape - r-base - r-kmer run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-ape - r-base - r-kmer diff --git a/recipes/bioconductor-padma/meta.yaml b/recipes/bioconductor-padma/meta.yaml index a2324e45cd0db..b61afc3f54526 100644 --- a/recipes/bioconductor-padma/meta.yaml +++ b/recipes/bioconductor-padma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "padma" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f47e277f616547846880f0f924f63e66 + md5: 126a8aec3057f8ccc5a435c5435adfc0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-padma", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA, ggplot2, ggrepel, car, cowplot requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-factominer run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-factominer test: diff --git a/recipes/bioconductor-padog/meta.yaml b/recipes/bioconductor-padog/meta.yaml index 9351472072933..a248a46b7416c 100644 --- a/recipes/bioconductor-padog/meta.yaml +++ b/recipes/bioconductor-padog/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "PADOG" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2791538f9d0ad24c3373a42e750db060 + md5: ca2c1e477f0ef2d2be1eaf52570dd8c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-padog", max_pin="x.x") }}' noarch: generic # Suggests: doParallel, parallel requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-keggdzpathwaysgeo >=1.38.0,<1.39.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-keggdzpathwaysgeo >=1.40.0,<1.41.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-dorng - r-foreach - r-gsa - r-nlme run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-keggdzpathwaysgeo >=1.38.0,<1.39.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-keggdzpathwaysgeo >=1.40.0,<1.41.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-dorng - r-foreach diff --git a/recipes/bioconductor-paeg1acdf/meta.yaml b/recipes/bioconductor-paeg1acdf/meta.yaml index f318eb8326b9d..83f68341ac443 100644 --- a/recipes/bioconductor-paeg1acdf/meta.yaml +++ b/recipes/bioconductor-paeg1acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "paeg1acdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 73af974112051db0f715518393e84726 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-paeg1acdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-paeg1aprobe/meta.yaml b/recipes/bioconductor-paeg1aprobe/meta.yaml index a274b700708aa..52fa2ca8579b2 100644 --- a/recipes/bioconductor-paeg1aprobe/meta.yaml +++ b/recipes/bioconductor-paeg1aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "paeg1aprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 493fa1fc7b92a78c8114b65038113c42 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-paeg1aprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pagerank/meta.yaml b/recipes/bioconductor-pagerank/meta.yaml index 88a28aebda42f..fadcf0f1bd68e 100644 --- a/recipes/bioconductor-pagerank/meta.yaml +++ b/recipes/bioconductor-pagerank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "pageRank" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95bbea12ddfe8b6f3e526c78defd4eaf + md5: 05578860ad3f7021d25c6c07953218ea build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pagerank", max_pin="x.x") }}' noarch: generic # Suggests: bcellViper, BSgenome.Hsapiens.UCSC.hg19, JASPAR2018, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, TFBSTools, GenomicFeatures, annotate requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' - r-base - r-igraph run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' - r-base - r-igraph test: diff --git a/recipes/bioconductor-pairadise/meta.yaml b/recipes/bioconductor-pairadise/meta.yaml index 076065bb143ad..da305a20a0c68 100644 --- a/recipes/bioconductor-pairadise/meta.yaml +++ b/recipes/bioconductor-pairadise/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "PAIRADISE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a974fbe1fda2aafd380d6faac180347a + md5: 2a3889d2380363b7a9b0ee3c75ef0891 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pairadise", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-nloptr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-nloptr diff --git a/recipes/bioconductor-paircompviz/meta.yaml b/recipes/bioconductor-paircompviz/meta.yaml index 242d9a92a6680..1a78dfad94d52 100644 --- a/recipes/bioconductor-paircompviz/meta.yaml +++ b/recipes/bioconductor-paircompviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "paircompviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eca876e3442dd83dc7e355080a6e5af6 + md5: e9c57c7305e15062d9258019fed12f3e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-paircompviz", max_pin="x.x") }}' noarch: generic # Suggests: multcomp, reshape, rpart, plyr, xtable requirements: host: - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base run: - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-pairedgsea/meta.yaml b/recipes/bioconductor-pairedgsea/meta.yaml index 31d687a75a195..f5f6ebb5140ba 100644 --- a/recipes/bioconductor-pairedgsea/meta.yaml +++ b/recipes/bioconductor-pairedgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "pairedGSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f8f47e26a85154c5df37d0729db4c24d + md5: 591cbbc31b4eab5064ef39c4b8133fa5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pairedgsea", max_pin="x.x") }}' noarch: generic # Suggests: writexl, readxl, readr, rhdf5, msigdbr, plotly, testthat (>= 3.0.0), knitr, rmarkdown, covr, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dexseq >=1.46.0,<1.47.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-aggregation - r-base - r-ggplot2 run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dexseq >=1.46.0,<1.47.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-aggregation - r-base - r-ggplot2 diff --git a/recipes/bioconductor-pairkat/meta.yaml b/recipes/bioconductor-pairkat/meta.yaml index 8bdd341e56c06..88e9611ce00c4 100644 --- a/recipes/bioconductor-pairkat/meta.yaml +++ b/recipes/bioconductor-pairkat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "pairkat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 548c23a7fea8eec39dc6fd06b283ec76 + md5: 030b0f4ea6e9f71adf6769ca9b16cae0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pairkat", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, BiocStyle, dplyr requirements: host: - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-compquadform - r-data.table @@ -30,8 +31,8 @@ requirements: - r-magrittr - r-tibble run: - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-compquadform - r-data.table diff --git a/recipes/bioconductor-pandar/meta.yaml b/recipes/bioconductor-pandar/meta.yaml index 66cf2a539d820..b750dee69940d 100644 --- a/recipes/bioconductor-pandar/meta.yaml +++ b/recipes/bioconductor-pandar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "pandaR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eae276fe37e113e2e860952b2004645c + md5: 203422d8a9df096677530f57bffe9e9c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pandar", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-ggplot2 - r-hexbin @@ -32,8 +33,8 @@ requirements: - r-reshape - r-runit run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-ggplot2 - r-hexbin diff --git a/recipes/bioconductor-panelcn.mops/meta.yaml b/recipes/bioconductor-panelcn.mops/meta.yaml index d436c6ae205e2..a1f76cb47c1ad 100644 --- a/recipes/bioconductor-panelcn.mops/meta.yaml +++ b/recipes/bioconductor-panelcn.mops/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "panelcn.mops" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a9626de33823bb9f8a22e83136a5ade8 + md5: c40de00a870c4b693e6312b7d2110b96 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-panelcn.mops", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, RUnit, BiocGenerics requirements: host: - - 'bioconductor-cn.mops >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-cn.mops >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-cn.mops >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-cn.mops >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-panomir/meta.yaml b/recipes/bioconductor-panomir/meta.yaml index ca9c1e393db04..0ded484f43400 100644 --- a/recipes/bioconductor-panomir/meta.yaml +++ b/recipes/bioconductor-panomir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "PanomiR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3aa1e186fd1ce598777d57f08c4e00e9 + md5: a8f96cdc267551107e69e8cb260a05c0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-panomir", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dplyr - r-forcats @@ -36,11 +37,11 @@ requirements: - r-tibble - r-withr run: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dplyr - r-forcats diff --git a/recipes/bioconductor-panp/meta.yaml b/recipes/bioconductor-panp/meta.yaml index cbfbb7effa540..88b59b7b344ae 100644 --- a/recipes/bioconductor-panp/meta.yaml +++ b/recipes/bioconductor-panp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "panp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f0193664c739a413e0bc97960f3e859d + md5: 1cc532873dbc4e2cde6c04ca995545db build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-panp", max_pin="x.x") }}' noarch: generic # Suggests: gcrma requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-panr/meta.yaml b/recipes/bioconductor-panr/meta.yaml index d4f06ff44235b..5a1a71d18d317 100644 --- a/recipes/bioconductor-panr/meta.yaml +++ b/recipes/bioconductor-panr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "PANR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a76063c60e0a92870203aa9b907281e1 + md5: accc5472b6656e95d885960d9f1ecee3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-panr", max_pin="x.x") }}' noarch: generic # Suggests: snow requirements: host: - - 'bioconductor-reder >=2.4.0,<2.5.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' - r-base - r-igraph - r-mass - r-pvclust run: - - 'bioconductor-reder >=2.4.0,<2.5.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' - r-base - r-igraph - r-mass diff --git a/recipes/bioconductor-panther.db/meta.yaml b/recipes/bioconductor-panther.db/meta.yaml index 9d0ca87b10175..9f4277d05f21e 100644 --- a/recipes/bioconductor-panther.db/meta.yaml +++ b/recipes/bioconductor-panther.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.11" %} +{% set version = "1.0.12" %} {% set name = "PANTHER.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 561f6b164b27f6dc4287f0d7fd6bb8b3 + md5: edafd1c94f2f1cf3975f525fae7a9b83 build: - number: 4 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-panther.db", max_pin="x.x") }}' noarch: generic # Suggests: RUnit,knitr,BiocStyle,rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-rsqlite - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-panther.db/post-link.sh b/recipes/bioconductor-panther.db/post-link.sh index b4e3a5abb373c..6801e59a4e786 100644 --- a/recipes/bioconductor-panther.db/post-link.sh +++ b/recipes/bioconductor-panther.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "panther.db-1.0.11" +installBiocDataPackage.sh "panther.db-1.0.12" diff --git a/recipes/bioconductor-panviz/meta.yaml b/recipes/bioconductor-panviz/meta.yaml index 6720e043d4792..96a8028875a67 100644 --- a/recipes/bioconductor-panviz/meta.yaml +++ b/recipes/bioconductor-panviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "PanViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a17196e1176705982077a84a995f6340 + md5: 5d5ced4ee7d68f57367aed30633f29e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-panviz", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, networkD3, requirements: diff --git a/recipes/bioconductor-parathyroidse/meta.yaml b/recipes/bioconductor-parathyroidse/meta.yaml index afd868a5c35f1..a43c027d7671f 100644 --- a/recipes/bioconductor-parathyroidse/meta.yaml +++ b/recipes/bioconductor-parathyroidse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "parathyroidSE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 055bda4d4376fcdec3bce484ec634117 + md5: e4d06f888feb4015273e20b14f8ee37a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-parathyroidse", max_pin="x.x") }}' noarch: generic # Suggests: Rsamtools, GenomicAlignments, GEOquery, SRAdb, GenomicFeatures, BiocStyle requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-parathyroidse/post-link.sh b/recipes/bioconductor-parathyroidse/post-link.sh index 0216c73790017..170c351577c93 100644 --- a/recipes/bioconductor-parathyroidse/post-link.sh +++ b/recipes/bioconductor-parathyroidse/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "parathyroidse-1.38.0" +installBiocDataPackage.sh "parathyroidse-1.40.0" diff --git a/recipes/bioconductor-pareg/build.sh b/recipes/bioconductor-pareg/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pareg/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pareg/meta.yaml b/recipes/bioconductor-pareg/meta.yaml new file mode 100644 index 0000000000000..b98c62126d92e --- /dev/null +++ b/recipes/bioconductor-pareg/meta.yaml @@ -0,0 +1,97 @@ +{% set version = "1.6.0" %} +{% set name = "pareg" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: fef96a7ed5d753b6729186f4870f4283 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pareg", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, plotROC, PRROC, mgsa, topGO, msigdbr, betareg, fgsea, ComplexHeatmap, GGally, ggsignif, circlize, enrichplot, ggnewscale, tidyverse, cowplot, ggfittext, simplifyEnrichment, GSEABenchmarkeR, BiocParallel, ggupset, latex2exp, org.Hs.eg.db, GO.db +requirements: + host: + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - r-base + - r-devtools + - r-dofuture + - r-dorng + - r-dplyr + - r-foreach + - r-future + - r-ggplot2 + - r-ggraph + - r-ggrepel + - r-glue + - r-hms + - r-igraph + - r-keras + - r-logger + - r-magrittr + - r-matrix + - r-nloptr + - r-progress + - r-proxy + - r-purrr + - r-reticulate + - r-rlang + - r-stringr + - 'r-tensorflow >=2.2.0' + - 'r-tfprobability >=0.10.0' + - r-tibble + - r-tidygraph + - r-tidyr + run: + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - r-base + - r-devtools + - r-dofuture + - r-dorng + - r-dplyr + - r-foreach + - r-future + - r-ggplot2 + - r-ggraph + - r-ggrepel + - r-glue + - r-hms + - r-igraph + - r-keras + - r-logger + - r-magrittr + - r-matrix + - r-nloptr + - r-progress + - r-proxy + - r-purrr + - r-reticulate + - r-rlang + - r-stringr + - 'r-tensorflow >=2.2.0' + - 'r-tfprobability >=0.10.0' + - r-tibble + - r-tidygraph + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Pathway enrichment using a regularized regression approach' + description: 'Compute pathway enrichment scores while accounting for term-term relations. This package uses a regularized multiple linear regression to regress differential expression p-values obtained from multi-condition experiments on a pathway membership matrix. By doing so, it is able to incorporate additional biological knowledge into the enrichment analysis and to estimate pathway enrichment scores more robustly.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-parglms/meta.yaml b/recipes/bioconductor-parglms/meta.yaml index 72f49afd8f4d5..ddeebc825c183 100644 --- a/recipes/bioconductor-parglms/meta.yaml +++ b/recipes/bioconductor-parglms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "parglms" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0e74c1ca871ba837fb9329207a55c3e4 + md5: 0d6a2dc756389064b9be38e755e1a24b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-parglms", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges, gwascat, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-batchjobs - r-doparallel - r-foreach run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-batchjobs - r-doparallel diff --git a/recipes/bioconductor-parody/meta.yaml b/recipes/bioconductor-parody/meta.yaml index 87ce03a669d80..c39b7ed701f61 100644 --- a/recipes/bioconductor-parody/meta.yaml +++ b/recipes/bioconductor-parody/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "parody" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e329e9fd1626c3d05bd1f2cf7208f5cf + md5: b466cc7b30f33e1854daac921ec9dc87 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-parody", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, testthat, rmarkdown requirements: diff --git a/recipes/bioconductor-partcnv/build.sh b/recipes/bioconductor-partcnv/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-partcnv/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-partcnv/meta.yaml b/recipes/bioconductor-partcnv/meta.yaml new file mode 100644 index 0000000000000..b464c8fbd145d --- /dev/null +++ b/recipes/bioconductor-partcnv/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.0.0" %} +{% set name = "partCNV" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e004f2129cbb1fe1e84e33cf223c06f6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-partcnv", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, rmarkdown, knitr, IRanges, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - r-base + - r-data.table + - r-depmixs4 + - r-magrittr + - r-seurat + run: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - r-base + - r-data.table + - r-depmixs4 + - r-magrittr + - r-seurat +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Infer locally aneuploid cells using single cell RNA-seq data' + description: 'This package uses a statistical framework for rapid and accurate detection of aneuploid cells with local copy number deletion or amplification. Our method uses an EM algorithm with mixtures of Poisson distributions while incorporating cytogenetics information (e.g., regional deletion or amplification) to guide the classification (partCNV). When applicable, we further improve the accuracy by integrating a Hidden Markov Model for feature selection (partCNVH).' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + diff --git a/recipes/bioconductor-partheenmetadata.db/meta.yaml b/recipes/bioconductor-partheenmetadata.db/meta.yaml index 6da9a7770c14e..174c5d3e8a5fe 100644 --- a/recipes/bioconductor-partheenmetadata.db/meta.yaml +++ b/recipes/bioconductor-partheenmetadata.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "PartheenMetaData.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1c9fd27e13a341b9aba9a235a67ce978 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-partheenmetadata.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pasilla/meta.yaml b/recipes/bioconductor-pasilla/meta.yaml index d1e60b9363b9a..cbe7571ac3d4a 100644 --- a/recipes/bioconductor-pasilla/meta.yaml +++ b/recipes/bioconductor-pasilla/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "pasilla" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a6abc62e6e4ddde42ee0269256ac8342 + md5: e1fbdd57136d8a29edd1e0164dc2412e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pasilla", max_pin="x.x") }}' noarch: generic -# Suggests: rmarkdown, BiocStyle, knitr +# Suggests: rmarkdown, BiocStyle, knitr, roxygen2 requirements: host: - - 'bioconductor-dexseq >=1.46.0,<1.47.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-dexseq >=1.46.0,<1.47.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pasilla/post-link.sh b/recipes/bioconductor-pasilla/post-link.sh index 409a42d31ba3b..d7bfc5e712bc6 100644 --- a/recipes/bioconductor-pasilla/post-link.sh +++ b/recipes/bioconductor-pasilla/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pasilla-1.28.0" +installBiocDataPackage.sh "pasilla-1.30.0" diff --git a/recipes/bioconductor-pasillabamsubset/meta.yaml b/recipes/bioconductor-pasillabamsubset/meta.yaml index 1d6f3c2d878d3..a7095742aa73c 100644 --- a/recipes/bioconductor-pasillabamsubset/meta.yaml +++ b/recipes/bioconductor-pasillabamsubset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "pasillaBamSubset" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c80a6afcfb87c88e88e8c3c69e66e71 + md5: 8fd05eac2d37650e157871908cbaf306 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pasillabamsubset", max_pin="x.x") }}' noarch: generic # Suggests: pasilla requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pasillabamsubset/post-link.sh b/recipes/bioconductor-pasillabamsubset/post-link.sh index 70c9fa4bf3d2e..6e8d22f6eff32 100644 --- a/recipes/bioconductor-pasillabamsubset/post-link.sh +++ b/recipes/bioconductor-pasillabamsubset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pasillabamsubset-0.38.0" +installBiocDataPackage.sh "pasillabamsubset-0.40.0" diff --git a/recipes/bioconductor-pasillatranscriptexpr/meta.yaml b/recipes/bioconductor-pasillatranscriptexpr/meta.yaml index 28e7132908a6c..befc4ad24b21e 100644 --- a/recipes/bioconductor-pasillatranscriptexpr/meta.yaml +++ b/recipes/bioconductor-pasillatranscriptexpr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "PasillaTranscriptExpr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d5e8ec6f9ba14ca8da1565b8a2b0bac + md5: 7d1d8c852fff7d80c11e8ab79dae7487 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pasillatranscriptexpr", max_pin="x.x") }}' noarch: generic # Suggests: rtracklayer, BiocStyle, knitr, testthat requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pasillatranscriptexpr/post-link.sh b/recipes/bioconductor-pasillatranscriptexpr/post-link.sh index 8d9070d95d4c1..4bb80603c4361 100644 --- a/recipes/bioconductor-pasillatranscriptexpr/post-link.sh +++ b/recipes/bioconductor-pasillatranscriptexpr/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pasillatranscriptexpr-1.28.0" +installBiocDataPackage.sh "pasillatranscriptexpr-1.30.0" diff --git a/recipes/bioconductor-past/meta.yaml b/recipes/bioconductor-past/meta.yaml index 519ae97444a6b..a2f50e875b09f 100644 --- a/recipes/bioconductor-past/meta.yaml +++ b/recipes/bioconductor-past/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "PAST" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 56e17729beeb8a5cbbed7c1a4bdce03a + md5: 9af26fa0c8f74a586f23905b9b2408c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-past", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-dplyr @@ -33,10 +34,10 @@ requirements: - r-iterators - r-rlang run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-dplyr diff --git a/recipes/bioconductor-path2ppi/meta.yaml b/recipes/bioconductor-path2ppi/meta.yaml index 165179a2c5498..0153df53f02fd 100644 --- a/recipes/bioconductor-path2ppi/meta.yaml +++ b/recipes/bioconductor-path2ppi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "Path2PPI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98206bf5ffb337ead19023c0370d1abd + md5: 4fcd4d73b05e2167ecdfb79aadfe8722 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-path2ppi", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle requirements: diff --git a/recipes/bioconductor-pathifier/meta.yaml b/recipes/bioconductor-pathifier/meta.yaml index 6d2ce71cd171d..818306e1cb392 100644 --- a/recipes/bioconductor-pathifier/meta.yaml +++ b/recipes/bioconductor-pathifier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "pathifier" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ec39c0e53442653e330922de4718ebde + md5: 344576d367c4da46c28918be3de3f65e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pathifier", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-pathnet/meta.yaml b/recipes/bioconductor-pathnet/meta.yaml index cfc4a76e93bd0..a65c695e30d6d 100644 --- a/recipes/bioconductor-pathnet/meta.yaml +++ b/recipes/bioconductor-pathnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "PathNet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 34979e84ad0538dcde4f4651440e271c + md5: 13ca247b602840ebfaea9f1e9a5839aa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pathnet", max_pin="x.x") }}' noarch: generic # Suggests: PathNetData, RUnit, BiocGenerics requirements: diff --git a/recipes/bioconductor-pathnetdata/meta.yaml b/recipes/bioconductor-pathnetdata/meta.yaml index e043fc729b5d1..cea53f8bb3615 100644 --- a/recipes/bioconductor-pathnetdata/meta.yaml +++ b/recipes/bioconductor-pathnetdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "PathNetData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20449e0dcf262e4f6c1f7e2521a00370 + md5: d72e955b33c92f1703ae072ec788c1d9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pathnetdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pathnetdata/post-link.sh b/recipes/bioconductor-pathnetdata/post-link.sh index fb162ea9a115b..c51f9a25a4d1a 100644 --- a/recipes/bioconductor-pathnetdata/post-link.sh +++ b/recipes/bioconductor-pathnetdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pathnetdata-1.36.0" +installBiocDataPackage.sh "pathnetdata-1.38.0" diff --git a/recipes/bioconductor-pathostat/meta.yaml b/recipes/bioconductor-pathostat/meta.yaml index 091743b6f0830..adc375d616f15 100644 --- a/recipes/bioconductor-pathostat/meta.yaml +++ b/recipes/bioconductor-pathostat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "PathoStat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2ea0b93420abe012159eb546e13e1c6b + md5: fd391aaf46df86a1608019bd2454d67f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pathostat", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, testthat requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-ape - r-base - r-corpcor @@ -52,12 +53,12 @@ requirements: - r-webshot - r-xml run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-ape - r-base - r-corpcor diff --git a/recipes/bioconductor-pathrender/meta.yaml b/recipes/bioconductor-pathrender/meta.yaml index be81c5a910394..8f6884f8bfe86 100644 --- a/recipes/bioconductor-pathrender/meta.yaml +++ b/recipes/bioconductor-pathrender/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.0" %} {% set name = "pathRender" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 16706f4d1fe0a7f576b59b689c67d608 + md5: 0796d30e763067880a67ed2435d2ac26 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pathrender", max_pin="x.x") }}' noarch: generic # Suggests: ALL, hgu95av2.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - 'bioconductor-cmap >=1.15.0,<1.16.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - 'bioconductor-cmap >=1.15.0,<1.16.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-rcolorbrewer test: diff --git a/recipes/bioconductor-pathview/meta.yaml b/recipes/bioconductor-pathview/meta.yaml index fe5c87f5c51fc..939a3d3b6bded 100644 --- a/recipes/bioconductor-pathview/meta.yaml +++ b/recipes/bioconductor-pathview/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "pathview" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d7f0911b44b34964b38a1e16e2dc7f90 + md5: 5e17ceee29bb13083a2b11be28edacb0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pathview", max_pin="x.x") }}' noarch: generic # Suggests: gage, org.Mm.eg.db, RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-png - r-xml run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-png - r-xml diff --git a/recipes/bioconductor-pathwaypca/meta.yaml b/recipes/bioconductor-pathwaypca/meta.yaml index becc41189d541..caaad95452bb9 100644 --- a/recipes/bioconductor-pathwaypca/meta.yaml +++ b/recipes/bioconductor-pathwaypca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "pathwayPCA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a75a06c3b8dd34524470a4bc72221e9 + md5: 100ae90b68c015f8e344da1d3a2a4863 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pathwaypca", max_pin="x.x") }}' noarch: generic # Suggests: airway, circlize, grDevices, knitr, RCurl, reshape2, rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse requirements: diff --git a/recipes/bioconductor-paxtoolsr/meta.yaml b/recipes/bioconductor-paxtoolsr/meta.yaml index 6b4a2e63d594a..230c75036cd40 100644 --- a/recipes/bioconductor-paxtoolsr/meta.yaml +++ b/recipes/bioconductor-paxtoolsr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "paxtoolsr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9c281fec96db1800644742f7e19d1c17 + md5: 2ed785fb7d7859ff53d143baba8ff73d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-paxtoolsr", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle, formatR, rmarkdown, RColorBrewer, foreach, doSNOW, parallel, org.Hs.eg.db, clusterProfiler # SystemRequirements: Java (>= 1.6) diff --git a/recipes/bioconductor-pcaexplorer/meta.yaml b/recipes/bioconductor-pcaexplorer/meta.yaml index 1c2db1a771ac3..9c16c5e3fce55 100644 --- a/recipes/bioconductor-pcaexplorer/meta.yaml +++ b/recipes/bioconductor-pcaexplorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.26.1" %} +{% set version = "2.28.0" %} {% set name = "pcaExplorer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fd855f02c1ab744f8e2ab682bae0df19 + md5: 622f43cef60e783c51d59ed8624019d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pcaexplorer", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, htmltools requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-base64enc - r-dt @@ -53,18 +54,18 @@ requirements: - r-threejs - r-tidyr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-base64enc - r-dt diff --git a/recipes/bioconductor-pcamethods/meta.yaml b/recipes/bioconductor-pcamethods/meta.yaml index 38c796c6de0cb..daa71eb6ce889 100644 --- a/recipes/bioconductor-pcamethods/meta.yaml +++ b/recipes/bioconductor-pcamethods/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.92.0" %} +{% set version = "1.94.0" %} {% set name = "pcaMethods" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 265adae0e55769ebc4294914cb26b6db + md5: a989ad925a9852f55eb5e4d16d1529d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pcamethods", max_pin="x.x") }}' # Suggests: matrixStats, lattice, ggplot2 # SystemRequirements: Rcpp requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-mass - 'r-rcpp >=0.11.3' - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-mass - 'r-rcpp >=0.11.3' diff --git a/recipes/bioconductor-pcan/meta.yaml b/recipes/bioconductor-pcan/meta.yaml index d9970c2c400cd..47cee63d9eee6 100644 --- a/recipes/bioconductor-pcan/meta.yaml +++ b/recipes/bioconductor-pcan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "PCAN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 33693be38c25d3ebb5ebb1bc7069a724 + md5: 94596d43854d98aee2e6da198147772b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pcan", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base test: commands: diff --git a/recipes/bioconductor-pcatools/meta.yaml b/recipes/bioconductor-pcatools/meta.yaml index 1e4eac16f8ce3..eabd07294dc9a 100644 --- a/recipes/bioconductor-pcatools/meta.yaml +++ b/recipes/bioconductor-pcatools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "PCAtools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f6cda4da875b51f599a56738386685b + md5: 316c693617402890169745a37dfaead6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pcatools", max_pin="x.x") }}' # Suggests: testthat, scran, BiocGenerics, knitr, Biobase, GEOquery, hgu133a.db, ggplotify, beachmat, RMTstat, ggalt, DESeq2, airway, org.Hs.eg.db, magrittr, rmarkdown # SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - r-base - r-bh - r-cowplot @@ -39,11 +40,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - r-base - r-bh - r-cowplot diff --git a/recipes/bioconductor-pchicdata/meta.yaml b/recipes/bioconductor-pchicdata/meta.yaml index 983a1d3ca9aff..ab00c43103068 100644 --- a/recipes/bioconductor-pchicdata/meta.yaml +++ b/recipes/bioconductor-pchicdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "PCHiCdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7048c278620231f478014314a1a16e74 + md5: 8791902075a44ae03c0366150aa3f61e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pchicdata", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr requirements: host: - - 'bioconductor-chicago >=1.28.0,<1.29.0' + - 'bioconductor-chicago >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-chicago >=1.28.0,<1.29.0' + - 'bioconductor-chicago >=1.30.0,<1.31.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pchicdata/post-link.sh b/recipes/bioconductor-pchicdata/post-link.sh index 03b0822345427..3ab10ccd183c5 100644 --- a/recipes/bioconductor-pchicdata/post-link.sh +++ b/recipes/bioconductor-pchicdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pchicdata-1.28.0" +installBiocDataPackage.sh "pchicdata-1.30.0" diff --git a/recipes/bioconductor-pcxn/meta.yaml b/recipes/bioconductor-pcxn/meta.yaml index 1d620be98fc79..ae4e85ca7141e 100644 --- a/recipes/bioconductor-pcxn/meta.yaml +++ b/recipes/bioconductor-pcxn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "pcxn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e984b3bb93ac67438338e968c76556fe + md5: bc66fe53111b80e8978344ddc59eff6f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pcxn", max_pin="x.x") }}' noarch: generic # Suggests: igraph, annotate, org.Hs.eg.db requirements: host: - - 'bioconductor-pcxndata >=2.22.0,<2.23.0' + - 'bioconductor-pcxndata >=2.24.0,<2.25.0' - r-base - r-pheatmap run: - - 'bioconductor-pcxndata >=2.22.0,<2.23.0' + - 'bioconductor-pcxndata >=2.24.0,<2.25.0' - r-base - r-pheatmap test: diff --git a/recipes/bioconductor-pcxndata/meta.yaml b/recipes/bioconductor-pcxndata/meta.yaml index a2411936baeab..edbfeb11dbe00 100644 --- a/recipes/bioconductor-pcxndata/meta.yaml +++ b/recipes/bioconductor-pcxndata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "pcxnData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0d340cd964638e91faf2181216c06159 + md5: 7814b1a6f5dbd08e71df1e92ea4328f6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pcxndata", max_pin="x.x") }}' noarch: generic # Suggests: pcxn requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pcxndata/post-link.sh b/recipes/bioconductor-pcxndata/post-link.sh index fba32530b08c6..2ff975463bbe2 100644 --- a/recipes/bioconductor-pcxndata/post-link.sh +++ b/recipes/bioconductor-pcxndata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pcxndata-2.22.0" +installBiocDataPackage.sh "pcxndata-2.24.0" diff --git a/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml b/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml index 7d05a2bb3b616..d5211fafad4a4 100644 --- a/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml +++ b/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.4" %} {% set name = "pd.081229.hg18.promoter.medip.hx1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f3c240fa0d4503e94047be5ee323856b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.081229.hg18.promoter.medip.hx1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml b/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml index bf32a1b76db93..608d949b2763d 100644 --- a/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml +++ b/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.8.1" %} {% set name = "pd.2006.07.18.hg18.refseq.promoter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 00838332d75b82d212078a9957f495df build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.2006.07.18.hg18.refseq.promoter", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.11.1' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.11.1' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml b/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml index 4d04d0a6c9cc7..fa0edeb2bdc22 100644 --- a/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml +++ b/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.3" %} {% set name = "pd.2006.07.18.mm8.refseq.promoter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 084b0a6759fd96d1bc775dd4c66c42b0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.2006.07.18.mm8.refseq.promoter", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml b/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml index 2f905ead37d08..fc6ff228ae8d5 100644 --- a/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml +++ b/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.3" %} {% set name = "pd.2006.10.31.rn34.refseq.promoter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ab5bb767ad29b213e5a969a5fc51ee7d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.2006.10.31.rn34.refseq.promoter", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ag/meta.yaml b/recipes/bioconductor-pd.ag/meta.yaml index 40eb2c4d96f2c..28b10f01dcf8b 100644 --- a/recipes/bioconductor-pd.ag/meta.yaml +++ b/recipes/bioconductor-pd.ag/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ag" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 21fb288536568ff010ad4847b671f9d6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ag", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml b/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml index a57f85a752c91..626b8d0f92db1 100644 --- a/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.aragene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ff87a0793fd4b713c4a45b6c1d4a4977 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.aragene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml b/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml index 56468db0c0fb1..5393c826fa919 100644 --- a/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.aragene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 828ad790eb2495e396d7fcd9bcbf9133 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.aragene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.atdschip.tiling/meta.yaml b/recipes/bioconductor-pd.atdschip.tiling/meta.yaml index 033ae995d48ad..998de9d485df6 100644 --- a/recipes/bioconductor-pd.atdschip.tiling/meta.yaml +++ b/recipes/bioconductor-pd.atdschip.tiling/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "pd.atdschip.tiling" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a38ac90ece38e2e9f980966194865fe0 + md5: a81ffdc7dfb8eb04e09ec133db77d0d4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.atdschip.tiling", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - 'r-rsqlite >=0.10.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - 'r-rsqlite >=0.10.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.atdschip.tiling/post-link.sh b/recipes/bioconductor-pd.atdschip.tiling/post-link.sh index 7f8b5f2fb87ff..3b973708641a2 100644 --- a/recipes/bioconductor-pd.atdschip.tiling/post-link.sh +++ b/recipes/bioconductor-pd.atdschip.tiling/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pd.atdschip.tiling-0.38.0" +installBiocDataPackage.sh "pd.atdschip.tiling-0.40.0" diff --git a/recipes/bioconductor-pd.ath1.121501/meta.yaml b/recipes/bioconductor-pd.ath1.121501/meta.yaml index 3b73d0a793e9b..994ab7c1fec7b 100644 --- a/recipes/bioconductor-pd.ath1.121501/meta.yaml +++ b/recipes/bioconductor-pd.ath1.121501/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ath1.121501" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d7ed8640f0deac552e0083a091e72a72 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ath1.121501", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.barley1/meta.yaml b/recipes/bioconductor-pd.barley1/meta.yaml index fa7241a0434e7..de7dce84ec276 100644 --- a/recipes/bioconductor-pd.barley1/meta.yaml +++ b/recipes/bioconductor-pd.barley1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.barley1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b8d11f5ad42e75f7a91931b46d449c1a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.barley1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml index 6b8ebc175bfd3..4d35be7142cfe 100644 --- a/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.bovgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6e9747d13aee7825722562ccc49ad35f build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.bovgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml index cfc6be91851e0..8ff60cbe49df0 100644 --- a/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.bovgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 342246c0a76755fcca458cd723b3e98e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.bovgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.bovine/meta.yaml b/recipes/bioconductor-pd.bovine/meta.yaml index 3aad529bd54ad..74ee2b7d78929 100644 --- a/recipes/bioconductor-pd.bovine/meta.yaml +++ b/recipes/bioconductor-pd.bovine/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.bovine" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6c7026dba53b54b547b1f1e135d043b3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.bovine", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.bsubtilis/meta.yaml b/recipes/bioconductor-pd.bsubtilis/meta.yaml index cb55649e8b54a..a22e19c9d4fdf 100644 --- a/recipes/bioconductor-pd.bsubtilis/meta.yaml +++ b/recipes/bioconductor-pd.bsubtilis/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.bsubtilis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2261d8b0ec178beb432d71eafd90ec9a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.bsubtilis", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml b/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml index 2d25076d471e1..be8e5256dd995 100644 --- a/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cangene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0a39d6378193e3f7d31a7210f6766eaf build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.cangene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml b/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml index 99d7bd3b258ba..a37c378d3bfbc 100644 --- a/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cangene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 946074601e7bee72f3b3dd6ae6b3bc33 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.cangene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.canine.2/meta.yaml b/recipes/bioconductor-pd.canine.2/meta.yaml index 34721787008bd..41ddf9797e74f 100644 --- a/recipes/bioconductor-pd.canine.2/meta.yaml +++ b/recipes/bioconductor-pd.canine.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.canine.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bc918d1953a3c7ac7168b60a53405a93 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.canine.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.canine/meta.yaml b/recipes/bioconductor-pd.canine/meta.yaml index 888a7d729b6b8..e825b40089dc5 100644 --- a/recipes/bioconductor-pd.canine/meta.yaml +++ b/recipes/bioconductor-pd.canine/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.canine" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5b40fe9e40d0b7f36d338e413d121ba7 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.canine", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.celegans/meta.yaml b/recipes/bioconductor-pd.celegans/meta.yaml index cdd01dc0395d6..c905fedbbd292 100644 --- a/recipes/bioconductor-pd.celegans/meta.yaml +++ b/recipes/bioconductor-pd.celegans/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.celegans" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b90ea2e071522bb340c103a1c8270205 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.celegans", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.charm.hg18.example/meta.yaml b/recipes/bioconductor-pd.charm.hg18.example/meta.yaml index eb3462223a211..86ae0af9f5bd9 100644 --- a/recipes/bioconductor-pd.charm.hg18.example/meta.yaml +++ b/recipes/bioconductor-pd.charm.hg18.example/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.4" %} {% set name = "pd.charm.hg18.example" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e201d4281a23c202f57bae1135e226b4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.charm.hg18.example", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.chicken/meta.yaml b/recipes/bioconductor-pd.chicken/meta.yaml index ad15c7b0268ee..8a7c80e514a6c 100644 --- a/recipes/bioconductor-pd.chicken/meta.yaml +++ b/recipes/bioconductor-pd.chicken/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.chicken" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: af79b6d0910621910e72ea374499e5eb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.chicken", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml b/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml index 9f9eb85707463..566afb7f346b2 100644 --- a/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.chigene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e37cb047678fabb1801109d4efd16773 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.chigene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml b/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml index ad75c72b6f078..8db3bb63df879 100644 --- a/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.chigene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bec602b45961607f5a4571977d54e015 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.chigene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml b/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml index 03db8e8c462f9..839f379c0b0a9 100644 --- a/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml +++ b/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.chogene.2.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 641718e3d172838185a200bac3d32433 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.chogene.2.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml b/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml index ae06030e3c7d1..5a6d320121240 100644 --- a/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml +++ b/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.chogene.2.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ed25825e58a514cdde70b961bce9b4d7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.chogene.2.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.citrus/meta.yaml b/recipes/bioconductor-pd.citrus/meta.yaml index 3252ab6e7afaa..ff50b6ed856a3 100644 --- a/recipes/bioconductor-pd.citrus/meta.yaml +++ b/recipes/bioconductor-pd.citrus/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.citrus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dee9b3298b84e7dd5152f48ad449b15a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.citrus", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.d.human/meta.yaml b/recipes/bioconductor-pd.clariom.d.human/meta.yaml index a81580f52c92e..69c689cf4964b 100644 --- a/recipes/bioconductor-pd.clariom.d.human/meta.yaml +++ b/recipes/bioconductor-pd.clariom.d.human/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.d.human" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9d3505af53cc7c99980f29c527f0f37d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.d.human", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml b/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml index 5379cb80b4589..aa251a19d8271 100644 --- a/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.human.ht" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 90f910bea1b1aeb550a3f1bdd91d1a06 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.s.human.ht", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.s.human/meta.yaml b/recipes/bioconductor-pd.clariom.s.human/meta.yaml index 9513c52802345..883abafec76d4 100644 --- a/recipes/bioconductor-pd.clariom.s.human/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.human/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.human" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 797afe8a6a8041453a34ced3cce34884 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.s.human", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml b/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml index f2d3116b4cf5f..01a66173dfb16 100644 --- a/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.mouse.ht" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9cb6f77cf9666a0d54e1eacb904fd57c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.s.mouse.ht", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml b/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml index 6ec762255afa7..6339960068e70 100644 --- a/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.mouse" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e3e4ce2b22a78faf525dd6c0c0b2a42d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.s.mouse", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml b/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml index c24c95ff7c0bc..057c509ee1c90 100644 --- a/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.rat.ht" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: be901eb9e8830f3e5bedf154189a3743 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.s.rat.ht", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.s.rat/meta.yaml b/recipes/bioconductor-pd.clariom.s.rat/meta.yaml index 36fe6e688e28b..92289bca2dfa0 100644 --- a/recipes/bioconductor-pd.clariom.s.rat/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.rat/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.rat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: be464b3eaea8eb8bdbcca6047fce4dea build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.s.rat", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cotton/meta.yaml b/recipes/bioconductor-pd.cotton/meta.yaml index a8d90c4caaaa5..b086689a2b42f 100644 --- a/recipes/bioconductor-pd.cotton/meta.yaml +++ b/recipes/bioconductor-pd.cotton/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cotton" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 78c408902bcefb8c695119767534b393 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.cotton", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml b/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml index 3669b80f76118..63fe0e2e116cf 100644 --- a/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cyngene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 784fac6cc92a0fe46dae32c9b737812a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.cyngene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml b/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml index 55402f20e119c..ee76fadc3b263 100644 --- a/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cyngene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a6217267e3e08a15f70c600918c7d4f6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.cyngene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml index 0a8b22e70c70b..9862258a4d044 100644 --- a/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cyrgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 63228c07d3d16d6c62e9c0e83f10a855 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.cyrgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml index 38e8eeda3855f..e0cf4deb6049c 100644 --- a/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cyrgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dbe3bb580b96aaddcc597de45159320d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.cyrgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cytogenetics.array/meta.yaml b/recipes/bioconductor-pd.cytogenetics.array/meta.yaml index 4b79cff1b026a..cc6d19032f9c6 100644 --- a/recipes/bioconductor-pd.cytogenetics.array/meta.yaml +++ b/recipes/bioconductor-pd.cytogenetics.array/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cytogenetics.array" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8c359ff56a9a558d370dc9a6a54218e0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.cytogenetics.array", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml b/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml index 39c4aa15c6cd8..00cff01593c5b 100644 --- a/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.drogene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 67f92a97a5b78a95693edfdd32b67e93 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.drogene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml b/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml index 24c8e44762b4f..3f2c2a0e4aea8 100644 --- a/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.drogene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5c63236ea91390d49dbabea63a48f0a2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.drogene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.drosgenome1/meta.yaml b/recipes/bioconductor-pd.drosgenome1/meta.yaml index f642da5de5c9d..e6a9cb0bbd747 100644 --- a/recipes/bioconductor-pd.drosgenome1/meta.yaml +++ b/recipes/bioconductor-pd.drosgenome1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.drosgenome1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 59c1a37a7d6a43fc70ff8756bf1195ef build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.drosgenome1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.drosophila.2/meta.yaml b/recipes/bioconductor-pd.drosophila.2/meta.yaml index da85a23a63ad9..ce040c054161a 100644 --- a/recipes/bioconductor-pd.drosophila.2/meta.yaml +++ b/recipes/bioconductor-pd.drosophila.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.drosophila.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ddb821e35e722af8dcf0807c6da4fac1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.drosophila.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.e.coli.2/meta.yaml b/recipes/bioconductor-pd.e.coli.2/meta.yaml index b6c8de0807693..65befa3aa9ca4 100644 --- a/recipes/bioconductor-pd.e.coli.2/meta.yaml +++ b/recipes/bioconductor-pd.e.coli.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.e.coli.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9176faa60a0c252a815b2a74d2f63dd4 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.e.coli.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ecoli.asv2/meta.yaml b/recipes/bioconductor-pd.ecoli.asv2/meta.yaml index 77f423303b8d9..9bff540ced298 100644 --- a/recipes/bioconductor-pd.ecoli.asv2/meta.yaml +++ b/recipes/bioconductor-pd.ecoli.asv2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ecoli.asv2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d789ddf5a178a9a50c5587ee3ab294a4 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ecoli.asv2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ecoli/meta.yaml b/recipes/bioconductor-pd.ecoli/meta.yaml index 735960ab3f2ee..faee4d2687af3 100644 --- a/recipes/bioconductor-pd.ecoli/meta.yaml +++ b/recipes/bioconductor-pd.ecoli/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ecoli" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 077e91b2567a32780305f0fb6b126fe9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ecoli", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml b/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml index 01ce29cf5e66c..dea66c5327058 100644 --- a/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.elegene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b6110c58d5964703c7117e5e0668c901 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.elegene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml b/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml index b0c35c061c975..cf32b4ff695a2 100644 --- a/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.elegene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1dbe166ea347a5a7e240db925d2081c7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.elegene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml index 0d4b8edc223b8..2ec09700424d3 100644 --- a/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.equgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3448f36fdb899f04702be37ffab4c4c7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.equgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml index 1fa43fce2724e..f5976ac239916 100644 --- a/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.equgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bed32525513ce25f14d433ce805e7d6c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.equgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml b/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml index 28de8519985b6..fcc901394bc1c 100644 --- a/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml +++ b/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.3" %} {% set name = "pd.feinberg.hg18.me.hx1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b6eeaf79671bab6f597965009516ce57 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.feinberg.hg18.me.hx1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml b/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml index 53ddd0a4744fd..941ef51cff169 100644 --- a/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml +++ b/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.3" %} {% set name = "pd.feinberg.mm8.me.hx1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7332102b69fc9ee087f52d3cdc311d00 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.feinberg.mm8.me.hx1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml index 4b73bb1bf19c8..96ca01bb821b7 100644 --- a/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.felgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b7ac0a5cbde5f248aac5d0a7422bd88d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.felgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml index cd2d1ae2be574..aa2ec52c8c490 100644 --- a/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.felgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 734807a7f3608f6c44c76df7eee04c99 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.felgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml b/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml index 400177cbda04e..aac9805b9a463 100644 --- a/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.fingene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b79e4f8a52cad3b62e32401bbe74603d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.fingene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml b/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml index 9d7da08a16f50..543282bb74fc8 100644 --- a/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.fingene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 29030b14a0e8f8073874fb694a8c0c09 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.fingene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml b/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml index 3822c217acbf6..a9f3b15e3ee6d 100644 --- a/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml +++ b/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.genomewidesnp.5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d02255c861e82fca6a7445ada0c69e5d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.genomewidesnp.5", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml b/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml index 7f1c3bc2d2fbd..b6b0437fd72fd 100644 --- a/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml +++ b/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.genomewidesnp.6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6e5369234e251c763f4f6c0220fbcb0c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.genomewidesnp.6", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml b/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml index c4286326c613f..d1840016e0d28 100644 --- a/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.guigene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 29fe31499931836af72ddd0c7d06acfa build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.guigene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml b/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml index 189178fecf6df..6c1aedcc5bf9d 100644 --- a/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.guigene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: aa3e0389c596a3676322104de5ad2358 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.guigene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hc.g110/meta.yaml b/recipes/bioconductor-pd.hc.g110/meta.yaml index 930ada7cf2017..dce97b5d9dd19 100644 --- a/recipes/bioconductor-pd.hc.g110/meta.yaml +++ b/recipes/bioconductor-pd.hc.g110/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hc.g110" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5c5418c588ed28e2fa088c7952c48b91 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hc.g110", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.focus/meta.yaml b/recipes/bioconductor-pd.hg.focus/meta.yaml index d8c330ad4bc2e..07333501d804f 100644 --- a/recipes/bioconductor-pd.hg.focus/meta.yaml +++ b/recipes/bioconductor-pd.hg.focus/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.focus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a89f344ae7ff8061a8e7968f155f4bcf build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.focus", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml b/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml index 3f747cf51c252..7c7d03a5cbfbd 100644 --- a/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133.plus.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8a87aa63c04e84266962bdde5226c06c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u133.plus.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u133a.2/meta.yaml b/recipes/bioconductor-pd.hg.u133a.2/meta.yaml index 506d65b0d49ac..aa934add79651 100644 --- a/recipes/bioconductor-pd.hg.u133a.2/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133a.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133a.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a7941473bf081831fad4f4412023d9ee build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u133a.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml b/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml index 9d54bcf7d86db..966e51ee906c8 100644 --- a/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133a.tag" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e090383098d6e1062b290889fba065d5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u133a.tag", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u133a/meta.yaml b/recipes/bioconductor-pd.hg.u133a/meta.yaml index 92258642e435e..fd20c37e93ead 100644 --- a/recipes/bioconductor-pd.hg.u133a/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 05b4521f65ab294a5040a0c60198d22c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u133a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u133b/meta.yaml b/recipes/bioconductor-pd.hg.u133b/meta.yaml index 792faa79356bb..4bfe9bab4a6e3 100644 --- a/recipes/bioconductor-pd.hg.u133b/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133b/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133b" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c5eac82ad7480571b9f2b442b4a8faa6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u133b", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u219/meta.yaml b/recipes/bioconductor-pd.hg.u219/meta.yaml index 03cab68e7f700..f55dc3f703be2 100644 --- a/recipes/bioconductor-pd.hg.u219/meta.yaml +++ b/recipes/bioconductor-pd.hg.u219/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u219" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dab073d315af47ff3001c72a6d1e7972 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u219", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u95a/meta.yaml b/recipes/bioconductor-pd.hg.u95a/meta.yaml index 0942bd87f9d52..e66160602d507 100644 --- a/recipes/bioconductor-pd.hg.u95a/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a9ad7d6a085e0e3ed7623902e7810da0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u95a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u95av2/meta.yaml b/recipes/bioconductor-pd.hg.u95av2/meta.yaml index 67a80141c2fe7..95848bb127f5f 100644 --- a/recipes/bioconductor-pd.hg.u95av2/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95av2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95av2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3a4182b529bc07ec91277a95b1462468 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u95av2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u95b/meta.yaml b/recipes/bioconductor-pd.hg.u95b/meta.yaml index 5c34719af06f1..8d252d62d20d3 100644 --- a/recipes/bioconductor-pd.hg.u95b/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95b/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95b" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a7f10f91e920e191c5009fac8ca79c24 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u95b", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u95c/meta.yaml b/recipes/bioconductor-pd.hg.u95c/meta.yaml index e56011d16a928..b498166f902ea 100644 --- a/recipes/bioconductor-pd.hg.u95c/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95c/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95c" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 85655bf7a9ecd7aaa867e05899c5e3e4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u95c", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u95d/meta.yaml b/recipes/bioconductor-pd.hg.u95d/meta.yaml index 3dacf5a5cc3c1..ee978c70f173e 100644 --- a/recipes/bioconductor-pd.hg.u95d/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95d/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95d" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 946701ecfc9cccb46aaeb57a4d6fe1c5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u95d", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u95e/meta.yaml b/recipes/bioconductor-pd.hg.u95e/meta.yaml index cdac7d0b9bab1..51b85127f3579 100644 --- a/recipes/bioconductor-pd.hg.u95e/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95e/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95e" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9295e2fd1b4be6ff58477ea5a5de45ee build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u95e", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml b/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml index fcd4a33ca8f27..c94697cfd3954 100644 --- a/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml +++ b/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg18.60mer.expr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ee8d3813f74edce4e796933aa63999fb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg18.60mer.expr", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml b/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml index 209d6f26bb27b..f8c8caeeabca3 100644 --- a/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml +++ b/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ht.hg.u133.plus.pm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5b1c3dd0ab3f8b21154982c197512a7c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ht.hg.u133.plus.pm", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml b/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml index a599fd6dbd8db..10d4330dd368f 100644 --- a/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml +++ b/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ht.hg.u133a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 80a82f43083f95e1e9f5e2e2da2e288e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ht.hg.u133a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ht.mg.430a/meta.yaml b/recipes/bioconductor-pd.ht.mg.430a/meta.yaml index d40943fa17101..0ffa3f528e690 100644 --- a/recipes/bioconductor-pd.ht.mg.430a/meta.yaml +++ b/recipes/bioconductor-pd.ht.mg.430a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ht.mg.430a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 65ea4fae22d21ad70998ba3ea034dcc0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ht.mg.430a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hta.2.0/meta.yaml b/recipes/bioconductor-pd.hta.2.0/meta.yaml index 96fc7cc93730e..7e82318382efb 100644 --- a/recipes/bioconductor-pd.hta.2.0/meta.yaml +++ b/recipes/bioconductor-pd.hta.2.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.2" %} {% set name = "pd.hta.2.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8e13f85ece49c38da73eaf7b2247f5f0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hta.2.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hu6800/meta.yaml b/recipes/bioconductor-pd.hu6800/meta.yaml index 7dc594ce3fabe..9cb8265192e77 100644 --- a/recipes/bioconductor-pd.hu6800/meta.yaml +++ b/recipes/bioconductor-pd.hu6800/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hu6800" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9a3a3edde6d6f31b9e90dc32aa68875d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hu6800", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml b/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml index a741e0a6c9308..92f4d90dcf4f9 100644 --- a/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml +++ b/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.huex.1.0.st.v2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f4c4836c53447890b75b012efbdef3e9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.huex.1.0.st.v2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml index 64e47c869f52a..a6b0f80043946 100644 --- a/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.hugene.1.0.st.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8cb24c351aee5bf216180e4b19742506 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hugene.1.0.st.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml b/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml index ea64270d668c8..bc8bf2b9c2ee4 100644 --- a/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.hugene.1.1.st.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7a17ee4f7d258792be1d21be7d03deb0 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hugene.1.1.st.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml b/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml index 409673e5b749a..aded0828efe02 100644 --- a/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml +++ b/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.hugene.2.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e484209aa0c2a839c3445d91c1a799ce build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hugene.2.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml b/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml index b4e55987dadbe..4ba83c112fde7 100644 --- a/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml +++ b/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.hugene.2.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 164227f10b87f87059e4ae27b40f5238 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hugene.2.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.maize/meta.yaml b/recipes/bioconductor-pd.maize/meta.yaml index 08e4a585a46d8..6acdd12194b41 100644 --- a/recipes/bioconductor-pd.maize/meta.yaml +++ b/recipes/bioconductor-pd.maize/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.maize" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a1689518c8525d3dfa97e870f90b7a7b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.maize", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml b/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml index 6ad3366094538..d662313ff247e 100644 --- a/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml +++ b/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mapping250k.nsp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2786d00e1d621a9c415a599b4afe838b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mapping250k.nsp", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mapping250k.sty/meta.yaml b/recipes/bioconductor-pd.mapping250k.sty/meta.yaml index 04ae6d0f76244..431d2f563a670 100644 --- a/recipes/bioconductor-pd.mapping250k.sty/meta.yaml +++ b/recipes/bioconductor-pd.mapping250k.sty/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mapping250k.sty" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0db5992855eaf9b8f61f8bc2e57ef347 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mapping250k.sty", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml b/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml index 8453b2010cf8c..22b5b5394c56e 100644 --- a/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml +++ b/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mapping50k.hind240" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 83615dcb01eb381f0c69e07504809094 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mapping50k.hind240", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml b/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml index f0ac8da648f4f..351f1e536040b 100644 --- a/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml +++ b/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mapping50k.xba240" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: eb0f9250fe0d7b590ca9938fee88f2e7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mapping50k.xba240", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.margene.1.0.st/meta.yaml b/recipes/bioconductor-pd.margene.1.0.st/meta.yaml index 586b5883ac30e..6300298e4726a 100644 --- a/recipes/bioconductor-pd.margene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.margene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.margene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f670b192e4b453f13bb7cae154b5de42 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.margene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.margene.1.1.st/meta.yaml b/recipes/bioconductor-pd.margene.1.1.st/meta.yaml index 55ffdd6dfda0f..4a7d544a718bf 100644 --- a/recipes/bioconductor-pd.margene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.margene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.margene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: efd71aeb9c5ab36c2ddeccf9cb66ddec build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.margene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml index 8a0d04ac3eb19..408d867813d22 100644 --- a/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.medgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2a0048ccd5310ec5c45bb691f3c25885 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.medgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml index fe0bca8c284d1..f519411548246 100644 --- a/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.medgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d96894cfea509734af62110311100142 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.medgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.medicago/meta.yaml b/recipes/bioconductor-pd.medicago/meta.yaml index 26b8b1490b8c2..769fa2b2e172b 100644 --- a/recipes/bioconductor-pd.medicago/meta.yaml +++ b/recipes/bioconductor-pd.medicago/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.medicago" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0e3f00777919374619a9dc8244167068 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.medicago", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mg.u74a/meta.yaml b/recipes/bioconductor-pd.mg.u74a/meta.yaml index 60ac7a18bc7dc..e94ef1d820d7e 100644 --- a/recipes/bioconductor-pd.mg.u74a/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a855c7d2b80e9b8f9bbc1a3f83aca799 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mg.u74a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mg.u74av2/meta.yaml b/recipes/bioconductor-pd.mg.u74av2/meta.yaml index 82a3f943a5f07..12c4b3403f631 100644 --- a/recipes/bioconductor-pd.mg.u74av2/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74av2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74av2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 01c6e4da9c2ad0f1939482284dd5b421 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mg.u74av2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mg.u74b/meta.yaml b/recipes/bioconductor-pd.mg.u74b/meta.yaml index b8d715cc903d5..d3a265d3115ec 100644 --- a/recipes/bioconductor-pd.mg.u74b/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74b/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74b" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 47bb81abaceba6dfaab3e0987f28706c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mg.u74b", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mg.u74bv2/meta.yaml b/recipes/bioconductor-pd.mg.u74bv2/meta.yaml index d89e472d6734b..3cba6e2bcbf62 100644 --- a/recipes/bioconductor-pd.mg.u74bv2/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74bv2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74bv2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dbb6cd5b16bd5cafbf654744bc2d5c5c build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mg.u74bv2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mg.u74c/meta.yaml b/recipes/bioconductor-pd.mg.u74c/meta.yaml index b6d655fdb12b2..d34eec569ed78 100644 --- a/recipes/bioconductor-pd.mg.u74c/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74c/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74c" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 01f10eae99481f03d1d5a6a2c2f01733 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mg.u74c", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mg.u74cv2/meta.yaml b/recipes/bioconductor-pd.mg.u74cv2/meta.yaml index db3aa3aef3958..dded57370137e 100644 --- a/recipes/bioconductor-pd.mg.u74cv2/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74cv2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74cv2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b60943b90b95a24fcf93f8c245fd88be build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mg.u74cv2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mirna.1.0/meta.yaml b/recipes/bioconductor-pd.mirna.1.0/meta.yaml index 63eacb6291fbd..cc8a6f4292057 100644 --- a/recipes/bioconductor-pd.mirna.1.0/meta.yaml +++ b/recipes/bioconductor-pd.mirna.1.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mirna.1.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8dfeb82a9da6d6f73e5fb716a2867a34 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mirna.1.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mirna.2.0/meta.yaml b/recipes/bioconductor-pd.mirna.2.0/meta.yaml index 569cf51670331..39fb38a4ddbc3 100644 --- a/recipes/bioconductor-pd.mirna.2.0/meta.yaml +++ b/recipes/bioconductor-pd.mirna.2.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mirna.2.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: aab53cbc62fbd7727ca0303aeb1dca13 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mirna.2.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mirna.3.0/meta.yaml b/recipes/bioconductor-pd.mirna.3.0/meta.yaml index 6e83b6b7f4847..1fa7ec6d77b92 100644 --- a/recipes/bioconductor-pd.mirna.3.0/meta.yaml +++ b/recipes/bioconductor-pd.mirna.3.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mirna.3.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1265f1969c618b3b5121e6a77ba57009 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mirna.3.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mirna.3.1/meta.yaml b/recipes/bioconductor-pd.mirna.3.1/meta.yaml index e968576995635..5efcf883ca1ee 100644 --- a/recipes/bioconductor-pd.mirna.3.1/meta.yaml +++ b/recipes/bioconductor-pd.mirna.3.1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.8.1" %} {% set name = "pd.mirna.3.1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 296b3584ee5e9416c9018353d3e29c6c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mirna.3.1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.11.1' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.11.1' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mirna.4.0/meta.yaml b/recipes/bioconductor-pd.mirna.4.0/meta.yaml index 14517e4896b52..a3ad36ee6f9cf 100644 --- a/recipes/bioconductor-pd.mirna.4.0/meta.yaml +++ b/recipes/bioconductor-pd.mirna.4.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mirna.4.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: cae1a18c02aaa20a2f05172103e9d938 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mirna.4.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.moe430a/meta.yaml b/recipes/bioconductor-pd.moe430a/meta.yaml index 70887f8731119..e9ab0dd8f57dd 100644 --- a/recipes/bioconductor-pd.moe430a/meta.yaml +++ b/recipes/bioconductor-pd.moe430a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.moe430a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f9a7cb62140e42c2a82177548a1c73fb build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.moe430a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.moe430b/meta.yaml b/recipes/bioconductor-pd.moe430b/meta.yaml index 2cfad28753931..72a0e356ab58c 100644 --- a/recipes/bioconductor-pd.moe430b/meta.yaml +++ b/recipes/bioconductor-pd.moe430b/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.moe430b" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c19d2ee5e7e87703cf73afa33a5f3156 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.moe430b", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml index 14aee2e8a08a6..d83f930bddeed 100644 --- a/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.moex.1.0.st.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 57427e63b2d44258c12d796eada1897b build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.moex.1.0.st.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml index e452a31afec54..890fc6f4cb1c6 100644 --- a/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.mogene.1.0.st.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c3767385af3b9a120c777adb6d6e3364 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mogene.1.0.st.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml b/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml index c541512b2793c..09713fc997bd3 100644 --- a/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.mogene.1.1.st.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3d6c5d29e4d8a0b0152e109b68f82c37 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mogene.1.1.st.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml b/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml index 0cd167f8e7dea..9c9a7d684131a 100644 --- a/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml +++ b/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.mogene.2.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 71326d6bd85de02490171696f923d053 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mogene.2.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml b/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml index aef43e3a54ceb..499af455820e9 100644 --- a/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml +++ b/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.mogene.2.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2c7fc5644eae98359cb945ff16d072a2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mogene.2.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mouse430.2/meta.yaml b/recipes/bioconductor-pd.mouse430.2/meta.yaml index 6064430c2092b..205b87d6bbb36 100644 --- a/recipes/bioconductor-pd.mouse430.2/meta.yaml +++ b/recipes/bioconductor-pd.mouse430.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mouse430.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7f37397a57b06d15101ef86fa6242ca4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mouse430.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mouse430a.2/meta.yaml b/recipes/bioconductor-pd.mouse430a.2/meta.yaml index e3e97c992a487..328c8998bd334 100644 --- a/recipes/bioconductor-pd.mouse430a.2/meta.yaml +++ b/recipes/bioconductor-pd.mouse430a.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mouse430a.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0c28f564a1fa23f59c936d42c156796d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mouse430a.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mta.1.0/meta.yaml b/recipes/bioconductor-pd.mta.1.0/meta.yaml index e0a52461a85e0..7deeae0d5bdfb 100644 --- a/recipes/bioconductor-pd.mta.1.0/meta.yaml +++ b/recipes/bioconductor-pd.mta.1.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mta.1.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0f737b4f1f1353733e56e2df637f554b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mta.1.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mu11ksuba/meta.yaml b/recipes/bioconductor-pd.mu11ksuba/meta.yaml index 6d8393f88932e..94eb4e26e996d 100644 --- a/recipes/bioconductor-pd.mu11ksuba/meta.yaml +++ b/recipes/bioconductor-pd.mu11ksuba/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mu11ksuba" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 56be58b3f444ccb9572dc4c3882964b2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mu11ksuba", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mu11ksubb/meta.yaml b/recipes/bioconductor-pd.mu11ksubb/meta.yaml index 250416e090676..11001e1c78fc9 100644 --- a/recipes/bioconductor-pd.mu11ksubb/meta.yaml +++ b/recipes/bioconductor-pd.mu11ksubb/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mu11ksubb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c45b0ebe777b99cec38499826cc1b457 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mu11ksubb", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml b/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml index 0ceee2111c0df..104d2cb3a3b15 100644 --- a/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml +++ b/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "pd.nugo.hs1a520180" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 88a836472f0f9aab2e1d54e4bad7d6af build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.nugo.hs1a520180", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml b/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml index 4492a301ca5b0..3114b806849f1 100644 --- a/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml +++ b/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "pd.nugo.mm1a520177" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5cd64895eaddaf4cae1c48db9468c079 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.nugo.mm1a520177", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml b/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml index d4123ffc506a8..0127427f2b795 100644 --- a/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ovigene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 88cfedfe10dd357539305051a69d31a1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ovigene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml b/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml index 04d4af36fef2b..1c6bc4fd9fc71 100644 --- a/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ovigene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d6158cacd32a1892975fddd8dc8bb3f2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ovigene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.pae.g1a/meta.yaml b/recipes/bioconductor-pd.pae.g1a/meta.yaml index 4d4d8c40e7ec4..78b855cedb8e9 100644 --- a/recipes/bioconductor-pd.pae.g1a/meta.yaml +++ b/recipes/bioconductor-pd.pae.g1a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.pae.g1a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d96462eb35c63b30772bccae2a27a8cd build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.pae.g1a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml b/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml index 6f3fd0d8d595d..5db40654cc0d4 100644 --- a/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml +++ b/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.plasmodium.anopheles" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ae55b1451ceaed951f68213c0433f3d0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.plasmodium.anopheles", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.poplar/meta.yaml b/recipes/bioconductor-pd.poplar/meta.yaml index 725ba844d814a..56d765944b6ab 100644 --- a/recipes/bioconductor-pd.poplar/meta.yaml +++ b/recipes/bioconductor-pd.poplar/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.poplar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9c33b7528e5a47654aeacf61b71058a8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.poplar", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.porcine/meta.yaml b/recipes/bioconductor-pd.porcine/meta.yaml index 82c47a2bdff34..3c508d25653f1 100644 --- a/recipes/bioconductor-pd.porcine/meta.yaml +++ b/recipes/bioconductor-pd.porcine/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.porcine" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5df404babadb1d6faef73e249c819a72 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.porcine", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml index a9f0bf892744a..60c46a620aa02 100644 --- a/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.porgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 203fc56b0e2904fa7063c4a325e038f1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.porgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml index 430150b714537..d719ca62d0871 100644 --- a/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.porgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3a31d325861925a7428241207c461a1d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.porgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml index 2fc33f0100628..2d107b381b133 100644 --- a/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rabgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7f1e33f4767a4c4653bdaff2b79989a0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rabgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml index 364c9cedad143..4695d505632f7 100644 --- a/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rabgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2492695661309f5e6628612685460ee5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rabgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rae230a/meta.yaml b/recipes/bioconductor-pd.rae230a/meta.yaml index 9ed5fd10cc095..663454610c8b4 100644 --- a/recipes/bioconductor-pd.rae230a/meta.yaml +++ b/recipes/bioconductor-pd.rae230a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rae230a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fa4a1c29d3457b1db82b1010c5f72412 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rae230a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rae230b/meta.yaml b/recipes/bioconductor-pd.rae230b/meta.yaml index f83f7dcb76548..46e25943b634f 100644 --- a/recipes/bioconductor-pd.rae230b/meta.yaml +++ b/recipes/bioconductor-pd.rae230b/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rae230b" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 10e2e70bb7538119127cd65f636f93b6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rae230b", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml index b7e51f74b747a..519e76f5d2ad1 100644 --- a/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.raex.1.0.st.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e2160b549f63ffcc9222d88d82d4d393 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.raex.1.0.st.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml index fd93c7e228cab..83bbe9f667204 100644 --- a/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.ragene.1.0.st.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 122cb69603e705218d01d70f48e90cad build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ragene.1.0.st.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml b/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml index d5b1e4f5f14b0..7acf2c90841f4 100644 --- a/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.ragene.1.1.st.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7301ab6472849395ccb800c39807e969 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ragene.1.1.st.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml b/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml index fe928c01c0ba1..d353b093c0f97 100644 --- a/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml +++ b/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.ragene.2.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 37157b09f009fef368b54e47711c313b build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ragene.2.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml b/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml index e57d364d6bd4e..97f536d4fe7f2 100644 --- a/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml +++ b/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.ragene.2.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 53adfa5ff2c7e466da83b807dbc7b237 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ragene.2.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rat230.2/meta.yaml b/recipes/bioconductor-pd.rat230.2/meta.yaml index 2e706cdde08a6..b9a674841bfcf 100644 --- a/recipes/bioconductor-pd.rat230.2/meta.yaml +++ b/recipes/bioconductor-pd.rat230.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rat230.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 286b1a7868ef6c795ebeb6dd8a5d5920 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rat230.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml index 6ea3f356da10a..9200e31904ff5 100644 --- a/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rcngene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9c7c5ef4d4f5ed92d9130d77a99a0685 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rcngene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml index 7f3111b1fbbf6..d5109147ee4f8 100644 --- a/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rcngene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9781549447d90b5423e820fff5cc6273 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rcngene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rg.u34a/meta.yaml b/recipes/bioconductor-pd.rg.u34a/meta.yaml index 377e2433efbcc..814b06a1e7993 100644 --- a/recipes/bioconductor-pd.rg.u34a/meta.yaml +++ b/recipes/bioconductor-pd.rg.u34a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rg.u34a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ac3a6cc203dabb8faab85b97f1a7ae3c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rg.u34a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rg.u34b/meta.yaml b/recipes/bioconductor-pd.rg.u34b/meta.yaml index 3e06011a43a95..3bd194cf18f4d 100644 --- a/recipes/bioconductor-pd.rg.u34b/meta.yaml +++ b/recipes/bioconductor-pd.rg.u34b/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rg.u34b" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 757966b66795d388c7169816d31977ad build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rg.u34b", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rg.u34c/meta.yaml b/recipes/bioconductor-pd.rg.u34c/meta.yaml index 58acea111a8eb..0be8eaeea6991 100644 --- a/recipes/bioconductor-pd.rg.u34c/meta.yaml +++ b/recipes/bioconductor-pd.rg.u34c/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rg.u34c" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bc9cb7b208972ac2901235bdabdee5b2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rg.u34c", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml index 0a72cd95d1d5f..0b394c279d5fa 100644 --- a/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rhegene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6469add6928e663529df4df98fcdd7a8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rhegene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml index dc6fc4ec8900f..9f7b2da4be891 100644 --- a/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rhegene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4f63424ab52283a95731767dce6623cd build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rhegene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rhesus/meta.yaml b/recipes/bioconductor-pd.rhesus/meta.yaml index e760022f0a205..168eb0a7c0836 100644 --- a/recipes/bioconductor-pd.rhesus/meta.yaml +++ b/recipes/bioconductor-pd.rhesus/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rhesus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 51efcfe1384ac956ff93bf0530965054 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rhesus", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rice/meta.yaml b/recipes/bioconductor-pd.rice/meta.yaml index b9ce05cd1da4f..cc3172d469287 100644 --- a/recipes/bioconductor-pd.rice/meta.yaml +++ b/recipes/bioconductor-pd.rice/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rice" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9c456981b3d0b99a96ac6c71e3eb7c8a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rice", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml index 29985fdc1fa4f..6d55e5903b9cc 100644 --- a/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rjpgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 066f5dbacc1110e42ce4d457ad3b9306 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rjpgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml index d72c006ebbc88..f1cce02ab6f8c 100644 --- a/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rjpgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 265503774b15e0f4e71ac53a276a80f2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rjpgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rn.u34/meta.yaml b/recipes/bioconductor-pd.rn.u34/meta.yaml index fce938a21f5ae..7ba2751df2778 100644 --- a/recipes/bioconductor-pd.rn.u34/meta.yaml +++ b/recipes/bioconductor-pd.rn.u34/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rn.u34" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1728c547f1383bffab330796505119ec build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rn.u34", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rta.1.0/meta.yaml b/recipes/bioconductor-pd.rta.1.0/meta.yaml index 8fbd60597c1f6..96549451b50b6 100644 --- a/recipes/bioconductor-pd.rta.1.0/meta.yaml +++ b/recipes/bioconductor-pd.rta.1.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.2" %} {% set name = "pd.rta.1.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 90752a892a103c7fe4cd6c86e61a61db build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rta.1.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml index 14e2235bfc16b..1377c31afcc2c 100644 --- a/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rusgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0b9b00fee58ef211e041395052344483 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rusgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml index 3461cf3b2f6c9..ce4353bf56c14 100644 --- a/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rusgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 228837c2de4a4b106806cb7f384564fa build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rusgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.s.aureus/meta.yaml b/recipes/bioconductor-pd.s.aureus/meta.yaml index c900149e19766..7bb76e909c429 100644 --- a/recipes/bioconductor-pd.s.aureus/meta.yaml +++ b/recipes/bioconductor-pd.s.aureus/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.s.aureus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f173ae6e4316aaa2eafbde92d5868a5a build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.s.aureus", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.soybean/meta.yaml b/recipes/bioconductor-pd.soybean/meta.yaml index 010526d295f82..9a179dc85bbc3 100644 --- a/recipes/bioconductor-pd.soybean/meta.yaml +++ b/recipes/bioconductor-pd.soybean/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.soybean" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6dbe167be9d40c1d9096485afb4525f0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.soybean", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml b/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml index 072fa4b68f2a2..a347597e89b5a 100644 --- a/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.soygene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b264df0648ec35d04f91e0ef8e26ac95 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.soygene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml b/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml index e8615e564f1ec..a1729ed3dabec 100644 --- a/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.soygene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4a911a4a4b5de927fe6239e500a2993f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.soygene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.sugar.cane/meta.yaml b/recipes/bioconductor-pd.sugar.cane/meta.yaml index ea2c076dbe86a..1ac46bfb035b6 100644 --- a/recipes/bioconductor-pd.sugar.cane/meta.yaml +++ b/recipes/bioconductor-pd.sugar.cane/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.sugar.cane" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bd7eb8b1a1c9ac77359358a5347330fb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.sugar.cane", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.tomato/meta.yaml b/recipes/bioconductor-pd.tomato/meta.yaml index 499efa24cc9b0..f934a7a17e110 100644 --- a/recipes/bioconductor-pd.tomato/meta.yaml +++ b/recipes/bioconductor-pd.tomato/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.tomato" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ce78f6ee43d72e017608413dd4d50580 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.tomato", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.u133.x3p/meta.yaml b/recipes/bioconductor-pd.u133.x3p/meta.yaml index bd1109ab7bf75..8831a79d5d391 100644 --- a/recipes/bioconductor-pd.u133.x3p/meta.yaml +++ b/recipes/bioconductor-pd.u133.x3p/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.u133.x3p" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e3f343e32273667f851e26d7b8a7a5db build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.u133.x3p", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.vitis.vinifera/meta.yaml b/recipes/bioconductor-pd.vitis.vinifera/meta.yaml index e5fa0473c18b9..65c61d4bfd7fd 100644 --- a/recipes/bioconductor-pd.vitis.vinifera/meta.yaml +++ b/recipes/bioconductor-pd.vitis.vinifera/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.vitis.vinifera" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 104a8ac33a9baa25a61f953679795696 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.vitis.vinifera", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.wheat/meta.yaml b/recipes/bioconductor-pd.wheat/meta.yaml index 7528bceb33c0b..2880ec9932dab 100644 --- a/recipes/bioconductor-pd.wheat/meta.yaml +++ b/recipes/bioconductor-pd.wheat/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.wheat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 38a7183c8d3b874cf62391a9e9169bb9 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.wheat", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.x.laevis.2/meta.yaml b/recipes/bioconductor-pd.x.laevis.2/meta.yaml index 4d9af187348ba..85c3ad7eb268f 100644 --- a/recipes/bioconductor-pd.x.laevis.2/meta.yaml +++ b/recipes/bioconductor-pd.x.laevis.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.x.laevis.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 32416957e3cdc11ad4dbfcd9141ff113 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.x.laevis.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.x.tropicalis/meta.yaml b/recipes/bioconductor-pd.x.tropicalis/meta.yaml index 55d5ba4d4b85f..6670ccd4bafab 100644 --- a/recipes/bioconductor-pd.x.tropicalis/meta.yaml +++ b/recipes/bioconductor-pd.x.tropicalis/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.x.tropicalis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 79a4de91831e4b0153495e12b9c6e8d3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.x.tropicalis", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.xenopus.laevis/meta.yaml b/recipes/bioconductor-pd.xenopus.laevis/meta.yaml index 279aa750ba211..95dc899a279f5 100644 --- a/recipes/bioconductor-pd.xenopus.laevis/meta.yaml +++ b/recipes/bioconductor-pd.xenopus.laevis/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.xenopus.laevis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6d5c2c9e8e3891770b1c6e9dcd823c0d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.xenopus.laevis", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.yeast.2/meta.yaml b/recipes/bioconductor-pd.yeast.2/meta.yaml index aa48be6c21621..26d834b6f5f33 100644 --- a/recipes/bioconductor-pd.yeast.2/meta.yaml +++ b/recipes/bioconductor-pd.yeast.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.yeast.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 780f5139ee9cda46c9e38122538ce129 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.yeast.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.yg.s98/meta.yaml b/recipes/bioconductor-pd.yg.s98/meta.yaml index 31794da957b8a..9747d83c970c7 100644 --- a/recipes/bioconductor-pd.yg.s98/meta.yaml +++ b/recipes/bioconductor-pd.yg.s98/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.yg.s98" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: caec3e8f29918f078b2dc7c76f4a74e2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.yg.s98", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml index 49fea51353521..3bb4402a2e409 100644 --- a/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.zebgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 54fcf757b8069e95dd7e2f3ff74ae050 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.zebgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml index bfb5ed075f4bc..bb23b5798ea1e 100644 --- a/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.zebgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d87028cd9024bc33be518635cf2f48fc build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.zebgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.zebrafish/meta.yaml b/recipes/bioconductor-pd.zebrafish/meta.yaml index fe16ec6bb090a..c747bdcc950f4 100644 --- a/recipes/bioconductor-pd.zebrafish/meta.yaml +++ b/recipes/bioconductor-pd.zebrafish/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.zebrafish" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 101f09a9d9304d1d8fbcc7f4812897b1 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.zebrafish", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pdatk/build_failure.linux-64.yaml b/recipes/bioconductor-pdatk/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..8c604002d4745 --- /dev/null +++ b/recipes/bioconductor-pdatk/build_failure.linux-64.yaml @@ -0,0 +1,10 @@ +recipe_sha: 635aae6bed8d84cc4ff74353dbdc5a5f9128c7c2618b5cb2c1d55e0a4340da36 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + /opt/conda/conda-bld/bioconductor-pdatk_1702300846111/test_tmp/run_test.sh: line 7: -e: command not found +category: |- + test failure +log: |- + 13:26:37 BIOCONDA INFO (OUT) export SRC_DIR=/opt/conda/conda-bld/bioconductor-pdatk_1702300846111/test_tmp + 13:26:37 BIOCONDA INFO (OUT) + -e 'library('\''PDATK'\'')' + 13:26:37 BIOCONDA INFO (OUT) /opt/conda/conda-bld/bioconductor-pdatk_1702300846111/test_tmp/run_test.sh: line 7: -e: command not found diff --git a/recipes/bioconductor-pdatk/meta.yaml b/recipes/bioconductor-pdatk/meta.yaml index a10c49dde85f7..e154475d539d2 100644 --- a/recipes/bioconductor-pdatk/meta.yaml +++ b/recipes/bioconductor-pdatk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "PDATK" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ffb59256d71d12b3fea031e2936445a + md5: 7593f074493a9b3123e757f9f265d05c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pdatk", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), msigdbr, BiocStyle, rmarkdown, knitr, HDF5Array requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-coregx >=2.4.0,<2.5.0' - - 'bioconductor-genefu >=2.32.0,<2.33.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-piano >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-survcomp >=1.50.0,<1.51.0' - - 'bioconductor-switchbox >=1.36.0,<1.37.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-genefu >=2.34.0,<2.35.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-piano >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-survcomp >=1.52.0,<1.53.0' + - 'bioconductor-switchbox >=1.38.0,<1.39.0' - r-base - r-caret - r-clusterrepro @@ -52,18 +53,18 @@ requirements: - r-survminer - r-verification run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-coregx >=2.4.0,<2.5.0' - - 'bioconductor-genefu >=2.32.0,<2.33.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-piano >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-survcomp >=1.50.0,<1.51.0' - - 'bioconductor-switchbox >=1.36.0,<1.37.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-genefu >=2.34.0,<2.35.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-piano >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-survcomp >=1.52.0,<1.53.0' + - 'bioconductor-switchbox >=1.38.0,<1.39.0' - r-base - r-caret - r-clusterrepro @@ -84,11 +85,11 @@ requirements: - r-verification test: commands: - - 'R -e "library(''{{ name }}'')"' + - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Pancreatic Ductal Adenocarcinoma Tool-Kit' - description: 'Pancreatic ductal adenocarcinoma (PDA) has a relatively poor prognosis and is one of the most lethal cancers. Molecular classification of gene expression profiles holds the potential to identify meaningful subtypes which can inform therapeutic strategy in the clinical setting. The Pancreatic Cancer Adenocarcinoma Tool-Kit (PDATK) provides an S4 class-based interface for performing unsupervised subtype discovery, cross-cohort meta-clustering, gene-expression-based classification, and subsequent survival analysis to identify prognostically useful subtypes in pancreatic cancer and beyond. Two novel methods, Consensus Subtypes in Pancreatic Cancer (CSPC) and Pancreatic Cancer Overall Survival Predictor (PCOSP) are included for consensus-based meta-clustering and overall-survival prediction, respectively. Additionally, four published subtype classifiers and three published prognostic gene signatures are included to allow users to easily recreate published results, apply existing classifiers to new data, and benchmark the relative performance of new methods. The use of existing Bioconductor classes as input to all PDATK classes and methods enables integration with existing Bioconductor datasets, including the 21 pancreatic cancer patient cohorts available in the MetaGxPancreas data package. PDATK has been used to replicate results from Sandhu et al (2019) and an additional paper is in the works using CSPC to validate subtypes from the included published classifiers, both of which use the data available in MetaGxPancreas. The inclusion of subtype centroids and prognostic gene signatures from these and other publications will enable researchers and clinicians to classify novel patient gene expression data, allowing the direct clinical application of the classifiers included in PDATK. Overall, PDATK provides a rich set of tools to identify and validate useful prognostic and molecular subtypes based on gene-expression data, benchmark new classifiers against existing ones, and apply discovered classifiers on novel patient data to inform clinical decision making.' + description: 'Pancreatic ductal adenocarcinoma (PDA) has a relatively poor prognosis and is one of the most lethal cancers. Molecular classification of gene expression profiles holds the potential to identify meaningful subtypes which can inform therapeutic strategy in the clinical setting. The Pancreatic Cancer Adenocarcinoma Tool-Kit (PDATK) provides an S4 class-based interface for performing unsupervised subtype discovery, cross-cohort meta-clustering, gene-expression-based classification, and subsequent survival analysis to identify prognostically useful subtypes in pancreatic cancer and beyond. Two novel methods, Consensus Subtypes in Pancreatic Cancer (CSPC) and Pancreatic Cancer Overall Survival Predictor (PCOSP) are included for consensus-based meta-clustering and overall-survival prediction, respectively. Additionally, four published subtype classifiers and three published prognostic gene signatures are included to allow users to easily recreate published results, apply existing classifiers to new data, and benchmark the relative performance of new methods. The use of existing Bioconductor classes as input to all PDATK classes and methods enables integration with existing Bioconductor datasets, including the 21 pancreatic cancer patient cohorts available in the MetaGxPancreas data package. PDATK has been used to replicate results from Sandhu et al (2019) [https://doi.org/10.1200/cci.18.00102] and an additional paper is in the works using CSPC to validate subtypes from the included published classifiers, both of which use the data available in MetaGxPancreas. The inclusion of subtype centroids and prognostic gene signatures from these and other publications will enable researchers and clinicians to classify novel patient gene expression data, allowing the direct clinical application of the classifiers included in PDATK. Overall, PDATK provides a rich set of tools to identify and validate useful prognostic and molecular subtypes based on gene-expression data, benchmark new classifiers against existing ones, and apply discovered classifiers on novel patient data to inform clinical decision making.' license_file: LICENSE diff --git a/recipes/bioconductor-pdinfobuilder/meta.yaml b/recipes/bioconductor-pdinfobuilder/meta.yaml index eab66da1b8744..b94711d5f3961 100644 --- a/recipes/bioconductor-pdinfobuilder/meta.yaml +++ b/recipes/bioconductor-pdinfobuilder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "pdInfoBuilder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46f59ac69b5b94cc24cdb49cc12d28ac + md5: 67c0c8df22f95792e50c1e6c4b6eba2a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pdinfobuilder", max_pin="x.x") }}' requirements: host: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - libblas - liblapack run: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' diff --git a/recipes/bioconductor-peacoqc/meta.yaml b/recipes/bioconductor-peacoqc/meta.yaml index a6054ffe7608f..2a019595f29fb 100644 --- a/recipes/bioconductor-peacoqc/meta.yaml +++ b/recipes/bioconductor-peacoqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "PeacoQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 35cce4a53dfc774f2606eed22e09da17 + md5: fa296e0522b97273b692874b5ec23b97 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-peacoqc", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' - r-base - r-circlize - r-ggplot2 - r-gridextra - r-plyr run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' - r-base - r-circlize - r-ggplot2 diff --git a/recipes/bioconductor-peakpanther/meta.yaml b/recipes/bioconductor-peakpanther/meta.yaml index cc70a7e482192..d56a1978bcd39 100644 --- a/recipes/bioconductor-peakpanther/meta.yaml +++ b/recipes/bioconductor-peakpanther/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "peakPantheR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 654760a5537dfdc83125d3cd253f2124 + md5: 9753434861181af826b86fbc734b5850 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-peakpanther", max_pin="x.x") }}' noarch: generic # Suggests: testthat, devtools, faahKO, msdata, knitr, rmarkdown, pander, BiocStyle requirements: host: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-base - r-bslib - 'r-doparallel >=1.0.11' @@ -39,8 +40,8 @@ requirements: - 'r-stringr >=1.2.0' - 'r-xml >=3.98.1.10' run: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-base - r-bslib - 'r-doparallel >=1.0.11' diff --git a/recipes/bioconductor-peca/meta.yaml b/recipes/bioconductor-peca/meta.yaml index 1884e5ed624c3..5605c4a16cf73 100644 --- a/recipes/bioconductor-peca/meta.yaml +++ b/recipes/bioconductor-peca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "PECA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 658444c729d969dfd2f1a3edd43d3966 + md5: 43aed7fc555cb6ccbf70335add80f6dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-peca", max_pin="x.x") }}' noarch: generic # Suggests: SpikeIn requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rots >=1.28.0,<1.29.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rots >=1.30.0,<1.31.0' - r-aroma.affymetrix - r-aroma.core - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rots >=1.28.0,<1.29.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rots >=1.30.0,<1.31.0' - r-aroma.affymetrix - r-aroma.core - r-base diff --git a/recipes/bioconductor-peco/meta.yaml b/recipes/bioconductor-peco/meta.yaml index 4a1b3d0fa6fe4..42ee30969da6a 100644 --- a/recipes/bioconductor-peco/meta.yaml +++ b/recipes/bioconductor-peco/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "peco" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 47a4083ee1746cc79c437205b7eae854 + md5: 9a15c75c989ee10da1fb0ead1bbac99f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-peco", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-circular @@ -32,9 +33,9 @@ requirements: - r-foreach - 'r-genlasso >=1.4' run: - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-circular diff --git a/recipes/bioconductor-pedbarrayv10.db/meta.yaml b/recipes/bioconductor-pedbarrayv10.db/meta.yaml index d2a77ef59a613..1c9fa8f5fbffa 100644 --- a/recipes/bioconductor-pedbarrayv10.db/meta.yaml +++ b/recipes/bioconductor-pedbarrayv10.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "pedbarrayv10.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 25acc3bfee229015ecca1c7d688e5168 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pedbarrayv10.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pedbarrayv9.db/meta.yaml b/recipes/bioconductor-pedbarrayv9.db/meta.yaml index faf9c5826fd37..1d5180b7a344c 100644 --- a/recipes/bioconductor-pedbarrayv9.db/meta.yaml +++ b/recipes/bioconductor-pedbarrayv9.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "pedbarrayv9.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: da4b2f9c0a672e0c9ee53f017bacaff7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pedbarrayv9.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pengls/meta.yaml b/recipes/bioconductor-pengls/meta.yaml index c1a75c82cf20b..641c32b81fdc8 100644 --- a/recipes/bioconductor-pengls/meta.yaml +++ b/recipes/bioconductor-pengls/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "pengls" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bb111f7ec56fb1ce6cf319a56dbc3042 + md5: 7b4703b0839f4e46a97e208289a69345 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pengls", max_pin="x.x") }}' noarch: generic # Suggests: knitr,rmarkdown,testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-glmnet - r-nlme run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-glmnet - r-nlme diff --git a/recipes/bioconductor-pepdat/meta.yaml b/recipes/bioconductor-pepdat/meta.yaml index 89df237ee40a3..e632c11c7cf5c 100644 --- a/recipes/bioconductor-pepdat/meta.yaml +++ b/recipes/bioconductor-pepdat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "pepDat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c0f8c749db61b37d83728109a2e08df + md5: 4ce373369604b54b15e5992ebe9355b9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pepdat", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pepdat/post-link.sh b/recipes/bioconductor-pepdat/post-link.sh index f398190520806..18087b8b14b2d 100644 --- a/recipes/bioconductor-pepdat/post-link.sh +++ b/recipes/bioconductor-pepdat/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pepdat-1.20.0" +installBiocDataPackage.sh "pepdat-1.22.0" diff --git a/recipes/bioconductor-pepsnmr/meta.yaml b/recipes/bioconductor-pepsnmr/meta.yaml index 4720727dca64f..58ea6cbaff257 100644 --- a/recipes/bioconductor-pepsnmr/meta.yaml +++ b/recipes/bioconductor-pepsnmr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "PepsNMR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80a3c52dea0ca605a0988a664215b1a8 + md5: afd34a264a3af86ad7aec1d6163b0aab build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pepsnmr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown, rmarkdown, BiocStyle, PepsNMRData requirements: diff --git a/recipes/bioconductor-pepsnmrdata/meta.yaml b/recipes/bioconductor-pepsnmrdata/meta.yaml index ece4231e32bf7..bc0e5911ad73c 100644 --- a/recipes/bioconductor-pepsnmrdata/meta.yaml +++ b/recipes/bioconductor-pepsnmrdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "PepsNMRData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98f84b07316d8ec6aab7c64862c695d2 + md5: 96fc9090499b4460f72fb85a0428b357 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pepsnmrdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown, rmarkdown, BiocStyle requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pepsnmrdata/post-link.sh b/recipes/bioconductor-pepsnmrdata/post-link.sh index f40152b399244..31aa57da37b58 100644 --- a/recipes/bioconductor-pepsnmrdata/post-link.sh +++ b/recipes/bioconductor-pepsnmrdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pepsnmrdata-1.18.0" +installBiocDataPackage.sh "pepsnmrdata-1.20.0" diff --git a/recipes/bioconductor-pepstat/meta.yaml b/recipes/bioconductor-pepstat/meta.yaml index 553e2eb03cf16..63ce17507e1e1 100644 --- a/recipes/bioconductor-pepstat/meta.yaml +++ b/recipes/bioconductor-pepstat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "pepStat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: da35a44e27569b966515d3baa63da1c1 + md5: 031af81c6bcac97b7262d978bfda2392 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pepstat", max_pin="x.x") }}' noarch: generic # Suggests: pepDat, Pviz, knitr, shiny requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-data.table - r-fields - r-ggplot2 - r-plyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-data.table - r-fields diff --git a/recipes/bioconductor-pepxmltab/meta.yaml b/recipes/bioconductor-pepxmltab/meta.yaml index 967fd5813d88b..44ccd49357088 100644 --- a/recipes/bioconductor-pepxmltab/meta.yaml +++ b/recipes/bioconductor-pepxmltab/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "pepXMLTab" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eae67a9f54e44fbce148fb9e5077fdd0 + md5: 71d6bcb41c5a79bc2cfdd375c6468250 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pepxmltab", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: diff --git a/recipes/bioconductor-periodicdna/meta.yaml b/recipes/bioconductor-periodicdna/meta.yaml index 8ec4ccf2ef572..d85c082208a88 100644 --- a/recipes/bioconductor-periodicdna/meta.yaml +++ b/recipes/bioconductor-periodicdna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "periodicDNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb823cba035d96f14027fc949ba7df9b + md5: 60036578bc6ec2c45d1c4b57ae96ad03 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-periodicdna", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, reticulate, testthat, covr, knitr, rmarkdown, pkgdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-ggplot2 - r-magrittr - r-zoo run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-ggplot2 diff --git a/recipes/bioconductor-pfam.db/meta.yaml b/recipes/bioconductor-pfam.db/meta.yaml index 34aaa02a5dce7..d5113df6b0741 100644 --- a/recipes/bioconductor-pfam.db/meta.yaml +++ b/recipes/bioconductor-pfam.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "PFAM.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 729496d021868b74cbecfd156066d0e9 + md5: f98f5d1e5d335e6bbf1ea6426cde67bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pfam.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pfam.db/post-link.sh b/recipes/bioconductor-pfam.db/post-link.sh index 97165541e6661..c837f5c6d710e 100644 --- a/recipes/bioconductor-pfam.db/post-link.sh +++ b/recipes/bioconductor-pfam.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pfam.db-3.17.0" +installBiocDataPackage.sh "pfam.db-3.18.0" diff --git a/recipes/bioconductor-pfamanalyzer/meta.yaml b/recipes/bioconductor-pfamanalyzer/meta.yaml index 6f220cb9fcb37..d17c3a7853043 100644 --- a/recipes/bioconductor-pfamanalyzer/meta.yaml +++ b/recipes/bioconductor-pfamanalyzer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "pfamAnalyzeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d3921913adbae5d53442475b60ee78d + md5: 20159a7f365760efda4827ae6fff80d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pfamanalyzer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-pgca/meta.yaml b/recipes/bioconductor-pgca/meta.yaml index 408fa2cd1793b..bccdf859ffd7e 100644 --- a/recipes/bioconductor-pgca/meta.yaml +++ b/recipes/bioconductor-pgca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "pgca" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3285cff9d2bd68e50c1f8d51f61e22e0 + md5: 43c58c5b347ebf060a9e6afdc8aa8e93 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pgca", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown requirements: diff --git a/recipes/bioconductor-phantasus/meta.yaml b/recipes/bioconductor-phantasus/meta.yaml index f7b71859045be..12893d324c41d 100644 --- a/recipes/bioconductor-phantasus/meta.yaml +++ b/recipes/bioconductor-phantasus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.2" %} +{% set version = "1.22.2" %} {% set name = "phantasus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 010a7126b3a72bf9c3a89e45cd789d23 + md5: 84c6e2dce18e76a3268130cdd236ba59 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phantasus", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-assertthat - r-base - r-ccapp @@ -48,13 +50,14 @@ requirements: - r-stringr - r-svglite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-assertthat - r-base - r-ccapp diff --git a/recipes/bioconductor-phantasuslite/build.sh b/recipes/bioconductor-phantasuslite/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-phantasuslite/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-phantasuslite/meta.yaml b/recipes/bioconductor-phantasuslite/meta.yaml new file mode 100644 index 0000000000000..8f7dc38016eeb --- /dev/null +++ b/recipes/bioconductor-phantasuslite/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "phantasusLite" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5fe0e101ac53a89dd49e077d5fb4c07d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phantasuslite", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rhdf5, GEOquery +requirements: + host: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-rhdf5client >=1.24.0,<1.25.0' + - r-base + - r-data.table + - r-httr + - r-stringr + run: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-rhdf5client >=1.24.0,<1.25.0' + - r-base + - r-data.table + - r-httr + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Loading and annotation RNA-Seq counts matrices' + description: 'PhantasusLite – a lightweight package with helper functions of general interest extracted from phantasus package. In parituclar it simplifies working with public RNA-seq datasets from GEO by providing access to the remote HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects.' + license_file: LICENSE + diff --git a/recipes/bioconductor-pharmacogx/meta.yaml b/recipes/bioconductor-pharmacogx/meta.yaml index fe20c276b51b7..b3ec539112cf6 100644 --- a/recipes/bioconductor-pharmacogx/meta.yaml +++ b/recipes/bioconductor-pharmacogx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.0" %} +{% set version = "3.6.0" %} {% set name = "PharmacoGx" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a5db5607c2e34052f84c04aae7a19ca + md5: a786bf3c0ace641195cfb3b00823cda3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pharmacogx", max_pin="x.x") }}' # Suggests: pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown, BiocStyle, R.utils requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-coregx >=2.4.0,<2.5.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-catools @@ -43,13 +44,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-coregx >=2.4.0,<2.5.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-catools diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml b/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml index 1f87007d434f7..d94d17575001b 100644 --- a/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml +++ b/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.2" %} {% set name = "phastCons100way.UCSC.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 65aa706a567f7e328dbba0095f995cf1 build: - number: 13 + number: 14 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phastcons100way.ucsc.hg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml b/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml index 0f97e217028b1..bfb7828fb7da6 100644 --- a/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml +++ b/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.1" %} {% set name = "phastCons100way.UCSC.hg38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 878c757f9270b3410d11e4e4a4213c8e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phastcons100way.ucsc.hg38", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-phastcons30way.ucsc.hg38/meta.yaml b/recipes/bioconductor-phastcons30way.ucsc.hg38/meta.yaml index 26e57dffe6ed9..c1311660034c3 100644 --- a/recipes/bioconductor-phastcons30way.ucsc.hg38/meta.yaml +++ b/recipes/bioconductor-phastcons30way.ucsc.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "phastCons30way.UCSC.hg38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 754faee8463bc494c502540cb8f6ea8d build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phastcons30way.ucsc.hg38", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-phastcons35way.ucsc.mm39/meta.yaml b/recipes/bioconductor-phastcons35way.ucsc.mm39/meta.yaml index f874908947d57..1cd646da27c64 100644 --- a/recipes/bioconductor-phastcons35way.ucsc.mm39/meta.yaml +++ b/recipes/bioconductor-phastcons35way.ucsc.mm39/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.16.0" %} {% set name = "phastCons35way.UCSC.mm39" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 83fc2a2265bc341b6a00064a1286b5bc build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phastcons35way.ucsc.mm39", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml b/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml index 2fc48c1d9f445..8584071542d60 100644 --- a/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml +++ b/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.1" %} {% set name = "phastCons7way.UCSC.hg38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c2d87446b022c166c1c325ea2aef521d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phastcons7way.ucsc.hg38", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-phemd/meta.yaml b/recipes/bioconductor-phemd/meta.yaml index 323cf23e779a4..ea542cdc06cb2 100644 --- a/recipes/bioconductor-phemd/meta.yaml +++ b/recipes/bioconductor-phemd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "phemd" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f2f4325b02cd7c6b4c96b69de58ec50a + md5: 8cefd4ddfea1dd2deb007acb6cebfb7a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phemd", max_pin="x.x") }}' noarch: generic -# Suggests: knitr +# Suggests: knitr, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-destiny >=3.14.0,<3.15.0' - - 'bioconductor-monocle >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-destiny >=3.16.0,<3.17.0' + - 'bioconductor-monocle >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-cowplot @@ -46,13 +47,13 @@ requirements: - r-transport - r-vgam run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-destiny >=3.14.0,<3.15.0' - - 'bioconductor-monocle >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-destiny >=3.16.0,<3.17.0' + - 'bioconductor-monocle >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-cowplot diff --git a/recipes/bioconductor-phenogeneranker/meta.yaml b/recipes/bioconductor-phenogeneranker/meta.yaml index b423258bb8175..930e12d2e9963 100644 --- a/recipes/bioconductor-phenogeneranker/meta.yaml +++ b/recipes/bioconductor-phenogeneranker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "PhenoGeneRanker" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c54470bf5e606eb9b28ba81ac9250305 + md5: a6530ed180fae6b4250bc56d3de24e19 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phenogeneranker", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-phenomis/meta.yaml b/recipes/bioconductor-phenomis/meta.yaml index 02939aac0a470..7d1a1238da6ff 100644 --- a/recipes/bioconductor-phenomis/meta.yaml +++ b/recipes/bioconductor-phenomis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "phenomis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 68bcdad2f28989d9cf025744aa994e91 + md5: 6fc3be4aed9fead1f2038fb3d2837854 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phenomis", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, biosigner, CLL, knitr, omicade4, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biodb >=1.8.0,<1.9.0' - - 'bioconductor-biodbchebi >=1.6.0,<1.7.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' + - 'bioconductor-biodbchebi >=1.8.0,<1.9.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-futile.logger @@ -44,14 +45,14 @@ requirements: - r-tidyr - r-venndiagram run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biodb >=1.8.0,<1.9.0' - - 'bioconductor-biodbchebi >=1.6.0,<1.7.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' + - 'bioconductor-biodbchebi >=1.8.0,<1.9.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-futile.logger diff --git a/recipes/bioconductor-phenopath/meta.yaml b/recipes/bioconductor-phenopath/meta.yaml index 2079195f58ac1..bc3a0995ad613 100644 --- a/recipes/bioconductor-phenopath/meta.yaml +++ b/recipes/bioconductor-phenopath/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "phenopath" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d5602a76199cdbdc31210788b9569c72 + md5: 1bbbcb87efbf78aa39ee07851d27f498 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phenopath", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -30,7 +31,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-phenotest/meta.yaml b/recipes/bioconductor-phenotest/meta.yaml index ed39526f9108c..58b9a36220404 100644 --- a/recipes/bioconductor-phenotest/meta.yaml +++ b/recipes/bioconductor-phenotest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "phenoTest" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cedbc33a7165cbb547d8bf62db8de022 + md5: 20bd295654c25854160e8a1aad42d8e8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phenotest", max_pin="x.x") }}' noarch: generic # Suggests: GSEABase, GO.db requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-heatplus >=3.8.0,<3.9.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-heatplus >=3.10.0,<3.11.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - - 'bioconductor-hopach >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-hopach >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-bma - r-ellipse @@ -42,17 +43,17 @@ requirements: - r-survival - r-xtable run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-heatplus >=3.8.0,<3.9.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-heatplus >=3.10.0,<3.11.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - - 'bioconductor-hopach >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-hopach >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-bma - r-ellipse diff --git a/recipes/bioconductor-phenstat/meta.yaml b/recipes/bioconductor-phenstat/meta.yaml index 0da5e272bc69f..c766d7ff7dc15 100644 --- a/recipes/bioconductor-phenstat/meta.yaml +++ b/recipes/bioconductor-phenstat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.36.0" %} +{% set version = "2.38.0" %} {% set name = "PhenStat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73057858116719f9411fe66000677aa2 + md5: f28cba815b5f6e8b3350c926d1d05907 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phenstat", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-car - r-corrplot @@ -37,7 +38,7 @@ requirements: - r-reshape - r-smoothwin run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-car - r-corrplot diff --git a/recipes/bioconductor-philr/meta.yaml b/recipes/bioconductor-philr/meta.yaml index afea06135912c..225cd7a47bc4c 100644 --- a/recipes/bioconductor-philr/meta.yaml +++ b/recipes/bioconductor-philr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "philr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 16ca92ff095dc3125adfee5cc63a6177 + md5: d55e931af78335bd6378fba38c5f54a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-philr", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia requirements: host: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-ape - r-base - r-ggplot2 - r-phangorn - r-tidyr run: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-ape - r-base - r-ggplot2 diff --git a/recipes/bioconductor-phipdata/meta.yaml b/recipes/bioconductor-phipdata/meta.yaml index b34c62b91219d..2c96fe878d6dc 100644 --- a/recipes/bioconductor-phipdata/meta.yaml +++ b/recipes/bioconductor-phipdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "PhIPData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ac34fb97c8b145805e1e0d3b876c21e8 + md5: fdb81e6f685727bbbe4584f42ca33797 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phipdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr, withr requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli test: diff --git a/recipes/bioconductor-phosphonormalizer/meta.yaml b/recipes/bioconductor-phosphonormalizer/meta.yaml index 4a77350d28cf3..83fa2d9b82923 100644 --- a/recipes/bioconductor-phosphonormalizer/meta.yaml +++ b/recipes/bioconductor-phosphonormalizer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "phosphonormalizer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f61fb102338add2c5407d1cf9ea82feb + md5: b0146ac595b90e20d854404e6fa427bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phosphonormalizer", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-phosr/meta.yaml b/recipes/bioconductor-phosr/meta.yaml index f7e0eec29e307..c27015e7252dc 100644 --- a/recipes/bioconductor-phosr/meta.yaml +++ b/recipes/bioconductor-phosr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "PhosR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 378bad4ffeacf7daaac34ba1f3dfafb7 + md5: 49f34b9174257536ac2a912530d69d10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phosr", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown, org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle, stringr, calibrate requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-dendextend @@ -47,12 +48,12 @@ requirements: - r-stringi - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-dendextend diff --git a/recipes/bioconductor-phylop35way.ucsc.mm39/meta.yaml b/recipes/bioconductor-phylop35way.ucsc.mm39/meta.yaml index 8ff0e9d94e577..891cac36e766a 100644 --- a/recipes/bioconductor-phylop35way.ucsc.mm39/meta.yaml +++ b/recipes/bioconductor-phylop35way.ucsc.mm39/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.16.0" %} {% set name = "phyloP35way.UCSC.mm39" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2c34eef5f20eace04efd47673cdf1062 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phylop35way.ucsc.mm39", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-phyloprofile/meta.yaml b/recipes/bioconductor-phyloprofile/meta.yaml index 0cece8597d94a..c9851553e3706 100644 --- a/recipes/bioconductor-phyloprofile/meta.yaml +++ b/recipes/bioconductor-phyloprofile/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.5" %} +{% set version = "1.16.0" %} {% set name = "PhyloProfile" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd16fd6e4d6e6ed690b6780e2b381508 + md5: 96200a149b95297ba34dee53963493a1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phyloprofile", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biodist >=1.72.0,<1.73.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-omadb >=2.16.0,<2.17.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biodist >=1.74.0,<1.75.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-omadb >=2.18.0,<2.19.0' - r-ape - r-base - r-colourpicker @@ -40,17 +41,19 @@ requirements: - r-rcurl - r-shiny - r-shinybs + - r-shinycssloaders - r-shinyfiles - r-shinyjs + - r-stringr - r-xml2 - r-yaml - r-zoo run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biodist >=1.72.0,<1.73.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-omadb >=2.16.0,<2.17.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biodist >=1.74.0,<1.75.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-omadb >=2.18.0,<2.19.0' - r-ape - r-base - r-colourpicker @@ -65,8 +68,10 @@ requirements: - r-rcurl - r-shiny - r-shinybs + - r-shinycssloaders - r-shinyfiles - r-shinyjs + - r-stringr - r-xml2 - r-yaml - r-zoo diff --git a/recipes/bioconductor-phyloprofiledata/meta.yaml b/recipes/bioconductor-phyloprofiledata/meta.yaml index 4cf4ebb33acf0..f08883286f7df 100644 --- a/recipes/bioconductor-phyloprofiledata/meta.yaml +++ b/recipes/bioconductor-phyloprofiledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "PhyloProfileData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3be065a86910a062e9b63540157ff949 + md5: 68dda32e9151c0aba4eb5b29c0313f83 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phyloprofiledata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, markdown requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-phyloprofiledata/post-link.sh b/recipes/bioconductor-phyloprofiledata/post-link.sh index 967b824fdd6e4..7f47b649e3562 100644 --- a/recipes/bioconductor-phyloprofiledata/post-link.sh +++ b/recipes/bioconductor-phyloprofiledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "phyloprofiledata-1.14.0" +installBiocDataPackage.sh "phyloprofiledata-1.16.0" diff --git a/recipes/bioconductor-phyloseq/meta.yaml b/recipes/bioconductor-phyloseq/meta.yaml index 1da612a78b6e4..816a5356e24c3 100644 --- a/recipes/bioconductor-phyloseq/meta.yaml +++ b/recipes/bioconductor-phyloseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "phyloseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c159f15cbf12ce81298c1b4d1d1fe43b + md5: 335dc9dedba529ce34669dd881127e7c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phyloseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 2.4), DESeq2 (>= 1.16.1), genefilter (>= 1.58), knitr (>= 1.16), magrittr (>= 1.5), metagenomeSeq (>= 1.14), rmarkdown (>= 1.6), testthat (>= 1.0.2) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomformat >=1.28.0,<1.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomformat >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - 'r-ade4 >=1.7-4' - 'r-ape >=5.0' - r-base @@ -39,11 +40,11 @@ requirements: - 'r-scales >=0.4.0' - 'r-vegan >=2.5' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomformat >=1.28.0,<1.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomformat >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - 'r-ade4 >=1.7-4' - 'r-ape >=5.0' - r-base diff --git a/recipes/bioconductor-pi/meta.yaml b/recipes/bioconductor-pi/meta.yaml index 8a863f41dee2c..13cad610cab01 100644 --- a/recipes/bioconductor-pi/meta.yaml +++ b/recipes/bioconductor-pi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "Pi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b09c5d11dc5ba832eb809dc6d0009913 + md5: cb989f0e8a3a1ab90a4a319c860ef602 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pi", max_pin="x.x") }}' noarch: generic # Suggests: foreach, doParallel, BiocStyle, knitr, rmarkdown, png, GGally, gridExtra, ggforce, fgsea, RColorBrewer, ggpubr, rtracklayer, ggbio, Gviz, data.tree, jsonlite requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-suprahex >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-suprahex >=1.40.0,<1.41.0' - r-base - r-caret - r-dnet @@ -49,11 +50,11 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-suprahex >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-suprahex >=1.40.0,<1.41.0' - r-base - r-caret - r-dnet diff --git a/recipes/bioconductor-piano/meta.yaml b/recipes/bioconductor-piano/meta.yaml index 53acfc159e0f9..947eddd07883a 100644 --- a/recipes/bioconductor-piano/meta.yaml +++ b/recipes/bioconductor-piano/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "piano" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1dce4336105325c4f7200406542ba3fe + md5: 84b0ce2cca9fb11110bd82113e066e82 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-piano", max_pin="x.x") }}' noarch: generic # Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-dt - r-gplots @@ -37,10 +38,10 @@ requirements: - r-shinyjs - r-visnetwork run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-dt - r-gplots diff --git a/recipes/bioconductor-pickgene/meta.yaml b/recipes/bioconductor-pickgene/meta.yaml index e320a7ba7ddca..2ac35c4ab1be0 100644 --- a/recipes/bioconductor-pickgene/meta.yaml +++ b/recipes/bioconductor-pickgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "pickgene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 70c09c4cc929410aca20e9a4c1aae523 + md5: 250b3649eff783447f1d2c34f67bf3ca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pickgene", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-pics/meta.yaml b/recipes/bioconductor-pics/meta.yaml index 7ba57e9eb4425..29900a517454a 100644 --- a/recipes/bioconductor-pics/meta.yaml +++ b/recipes/bioconductor-pics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.44.0" %} +{% set version = "2.46.0" %} {% set name = "PICS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: efd0dc25199e80b8b905bc5cb4043400 + md5: 04ed3fdb7f1db15654e9974438495e43 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pics", max_pin="x.x") }}' # Suggests: rtracklayer, parallel, knitr +# SystemRequirements: gsl requirements: host: - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - libblas - liblapack + - gsl run: - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base + - gsl build: - {{ compiler('c') }} - automake diff --git a/recipes/bioconductor-pig.db0/meta.yaml b/recipes/bioconductor-pig.db0/meta.yaml index 04e11d645142e..15e8ede99ee85 100644 --- a/recipes/bioconductor-pig.db0/meta.yaml +++ b/recipes/bioconductor-pig.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "pig.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d4ea227fc9495dc815bb3ad2387a7e26 + md5: 85aaccdbdb969825957db45db3fb7801 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pig.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pig.db0/post-link.sh b/recipes/bioconductor-pig.db0/post-link.sh index 0b4239037a5b6..ccf6ee98e3660 100644 --- a/recipes/bioconductor-pig.db0/post-link.sh +++ b/recipes/bioconductor-pig.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pig.db0-3.17.0" +installBiocDataPackage.sh "pig.db0-3.18.0" diff --git a/recipes/bioconductor-pigengene/meta.yaml b/recipes/bioconductor-pigengene/meta.yaml index c0adf6351ca07..6200d1de33d16 100644 --- a/recipes/bioconductor-pigengene/meta.yaml +++ b/recipes/bioconductor-pigengene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "Pigengene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e8dfb7f626a2cf129ffce0986a6ee6c9 + md5: 2d7b090a6d6fad6cf62c987970663167 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pigengene", max_pin="x.x") }}' noarch: generic # Suggests: org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), biomaRt (>= 2.30.0), knitr, AnnotationDbi, energy requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-reactomepa >=1.44.0,<1.45.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-reactomepa >=1.46.0,<1.47.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - 'r-bnlearn >=4.7' - 'r-c50 >=0.1.2' @@ -44,15 +45,15 @@ requirements: - 'r-pheatmap >=1.0.8' - r-wgcna run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-reactomepa >=1.44.0,<1.45.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-reactomepa >=1.46.0,<1.47.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - 'r-bnlearn >=4.7' - 'r-c50 >=0.1.2' diff --git a/recipes/bioconductor-ping/meta.yaml b/recipes/bioconductor-ping/meta.yaml index 90020f35dd6a7..05e5b3f99f186 100644 --- a/recipes/bioconductor-ping/meta.yaml +++ b/recipes/bioconductor-ping/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.44.0" %} +{% set version = "2.46.0" %} {% set name = "PING" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c30c9725a93000736ebb0e890f6efc44 + md5: 703e11e3d890a3cf2b48c15d4c76ea87 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ping", max_pin="x.x") }}' # Suggests: parallel, ShortRead, rtracklayer requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-pics >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-pics >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fda - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-pics >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-pics >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fda build: diff --git a/recipes/bioconductor-pipecomp/meta.yaml b/recipes/bioconductor-pipecomp/meta.yaml index 2133ccf7b66c8..f2a38e18004db 100644 --- a/recipes/bioconductor-pipecomp/meta.yaml +++ b/recipes/bioconductor-pipecomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "pipeComp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a2b7cb51586dade4ebeaa1d1d85c06f + md5: ccc688331233bccee84104cbbb9b5d81 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pipecomp", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-aricode - r-base - r-circlize @@ -49,13 +50,13 @@ requirements: - r-uwot - r-viridislite run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-aricode - r-base - r-circlize diff --git a/recipes/bioconductor-pipeframe/meta.yaml b/recipes/bioconductor-pipeframe/meta.yaml index 33725a2823fd5..eab0329b0160a 100644 --- a/recipes/bioconductor-pipeframe/meta.yaml +++ b/recipes/bioconductor-pipeframe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "pipeFrame" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 75006944af02f9c62b4e851fca8e0e0e + md5: 142f8d049aa03cec36050c2b0ccc87d9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pipeframe", max_pin="x.x") }}' noarch: generic # Suggests: BiocManager, knitr, rtracklayer, testthat, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base - r-digest - r-magrittr - r-rmarkdown - r-visnetwork run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base - r-digest - r-magrittr diff --git a/recipes/bioconductor-planet/meta.yaml b/recipes/bioconductor-planet/meta.yaml index ff48e269b2eae..3b2c110ad4fd1 100644 --- a/recipes/bioconductor-planet/meta.yaml +++ b/recipes/bioconductor-planet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "planet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cee64675bce4d388dd7f348ff68900d1 + md5: dbd74bc4dd3583d6ebbd871b251ecd6d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-planet", max_pin="x.x") }}' noarch: generic # Suggests: ggplot2, testthat, tidyr, scales, minfi, EpiDISH, knitr, rmarkdown requirements: @@ -37,6 +38,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Placental DNA methylation analysis tools' - description: 'This package contains R functions to infer additional biological variables to supplemental DNA methylation analysis of placental data. This includes inferring ethnicity/ancestry, gestational age, and cell composition from placental DNA methylation array (450k/850k) data. The package comes with an example processed placental dataset.' + description: 'This package contains R functions to predict biological variables to from placnetal DNA methylation data generated from infinium arrays. This includes inferring ethnicity/ancestry, gestational age, and cell composition from placental DNA methylation array (450k/850k) data.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' diff --git a/recipes/bioconductor-planttfhunter/meta.yaml b/recipes/bioconductor-planttfhunter/meta.yaml index 2ab1ade95a55c..2d4836f3fc65b 100644 --- a/recipes/bioconductor-planttfhunter/meta.yaml +++ b/recipes/bioconductor-planttfhunter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "planttfhunter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 95ba952e191581983529908ece129c54 + md5: 94bf35ef27114ae40bdd4be243dfb8fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-planttfhunter", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>= 3.0.0) # SystemRequirements: HMMER requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml b/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml index 4d28ad9cf4a33..5ce91658cfd34 100644 --- a/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml +++ b/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "plasmodiumanophelescdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 54c5c326977d6358c40cacf34cb2aca2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plasmodiumanophelescdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml b/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml index a02c4b7775cd5..7a007c04ba9cd 100644 --- a/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml +++ b/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "plasmodiumanophelesprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 281683dab923168c2eedb7b08c528935 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plasmodiumanophelesprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-plasmut/build.sh b/recipes/bioconductor-plasmut/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-plasmut/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-plasmut/meta.yaml b/recipes/bioconductor-plasmut/meta.yaml new file mode 100644 index 0000000000000..7af4ecae4a8c9 --- /dev/null +++ b/recipes/bioconductor-plasmut/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.0.0" %} +{% set name = "plasmut" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8681d905157c0cbb8b46e48cbe4ecde9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plasmut", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf, BiocStyle, biocViews, testthat (>= 3.0.0) +requirements: + host: + - r-base + - r-dplyr + - r-tibble + run: + - r-base + - r-dplyr + - r-tibble +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Stratifying mutations observed in cell-free DNA and white blood cells as germline, hematopoietic, or somatic' + description: 'A Bayesian method for quantifying the liklihood that a given plasma mutation arises from clonal hematopoesis or the underlying tumor. It requires sequencing data of the mutation in plasma and white blood cells with the number of distinct and mutant reads in both tissues. We implement a Monte Carlo importance sampling method to assess the likelihood that a mutation arises from the tumor relative to non-tumor origin.' + diff --git a/recipes/bioconductor-plgem/meta.yaml b/recipes/bioconductor-plgem/meta.yaml index 4b7ee6e985e04..2bc338a763d0a 100644 --- a/recipes/bioconductor-plgem/meta.yaml +++ b/recipes/bioconductor-plgem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "plgem" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 384f0e272bf6bca492d6b6fa3b10bbc6 + md5: caa3e3fe048da49643b34bde9fcb834a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plgem", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-plier/meta.yaml b/recipes/bioconductor-plier/meta.yaml index 7efe1ff38926d..55b9c161f346c 100644 --- a/recipes/bioconductor-plier/meta.yaml +++ b/recipes/bioconductor-plier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "plier" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3ada0e5da50940e184dd56e4f15c2aac + md5: f16a09bf8bccc7f5596d55ed0577a593 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plier", max_pin="x.x") }}' requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-plogo2/meta.yaml b/recipes/bioconductor-plogo2/meta.yaml index 47f580c06cbc6..0b50bf78d9598 100644 --- a/recipes/bioconductor-plogo2/meta.yaml +++ b/recipes/bioconductor-plogo2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "PloGO2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c885f0334d65006c9d06c9670f337b8 + md5: a9d28e5ed4822c97721db2c841ce3eec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plogo2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' - r-base - r-httr - r-lattice - r-openxlsx - r-xtable run: - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' - r-base - r-httr - r-lattice diff --git a/recipes/bioconductor-plotgardener/meta.yaml b/recipes/bioconductor-plotgardener/meta.yaml index 2862ea7a65f6a..e7cb36e9c2ed0 100644 --- a/recipes/bioconductor-plotgardener/meta.yaml +++ b/recipes/bioconductor-plotgardener/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.2" %} +{% set version = "1.8.1" %} {% set name = "plotgardener" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 08318dcfcb24afd0efc11e1cd81dd7a6 + md5: 7459452ce71af8384d3df8340a7c3db0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plotgardener", max_pin="x.x") }}' # Suggests: AnnotationDbi, AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures, GenomeInfoDb, GenomicRanges, ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, pdftools, png, rmarkdown, scales, showtext, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' - r-base - r-curl - r-data.table @@ -36,8 +39,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' - r-base - r-curl - r-data.table diff --git a/recipes/bioconductor-plotgardenerdata/meta.yaml b/recipes/bioconductor-plotgardenerdata/meta.yaml index a575a778f4be1..9a02df7d187eb 100644 --- a/recipes/bioconductor-plotgardenerdata/meta.yaml +++ b/recipes/bioconductor-plotgardenerdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "plotgardenerData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 82519e095b0f464cd59388d4146d21db + md5: 96055b11818bd59c0c91977b34973608 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plotgardenerdata", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-plotgardenerdata/post-link.sh b/recipes/bioconductor-plotgardenerdata/post-link.sh index 40c8cd63e1efd..44e9cf40f78cf 100644 --- a/recipes/bioconductor-plotgardenerdata/post-link.sh +++ b/recipes/bioconductor-plotgardenerdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "plotgardenerdata-1.6.0" +installBiocDataPackage.sh "plotgardenerdata-1.8.0" diff --git a/recipes/bioconductor-plotgrouper/meta.yaml b/recipes/bioconductor-plotgrouper/meta.yaml index 1d887cfbba08c..c6e6e6c5bff30 100644 --- a/recipes/bioconductor-plotgrouper/meta.yaml +++ b/recipes/bioconductor-plotgrouper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "plotGrouper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5bfb2cb4a73da0fa5aaa637ca56e2f99 + md5: aca262974325a32b1d28d58d28e4e012 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plotgrouper", max_pin="x.x") }}' noarch: generic # Suggests: knitr, htmltools, BiocStyle, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-plpe/meta.yaml b/recipes/bioconductor-plpe/meta.yaml index 4da5eb67c552d..5818330d03f6a 100644 --- a/recipes/bioconductor-plpe/meta.yaml +++ b/recipes/bioconductor-plpe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "PLPE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a03620bea737c30691c47836a5a62e2f + md5: 1a4887a4c08676e0ce69331caacc297e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plpe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lpe >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lpe >=1.76.0,<1.77.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lpe >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lpe >=1.76.0,<1.77.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-plyinteractions/build.sh b/recipes/bioconductor-plyinteractions/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-plyinteractions/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-plyinteractions/meta.yaml b/recipes/bioconductor-plyinteractions/meta.yaml new file mode 100644 index 0000000000000..19e57bfea4e2f --- /dev/null +++ b/recipes/bioconductor-plyinteractions/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.0.0" %} +{% set name = "plyinteractions" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e072613b18768f43d832eaa32354bbc9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plyinteractions", max_pin="x.x") }}' + noarch: generic +# Suggests: tidyverse, BSgenome.Mmusculus.UCSC.mm10, Biostrings, BiocParallel, scales, HiContactsData, rtracklayer, BiocStyle, covr, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), RefManageR +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-dplyr + - r-rlang + - r-tibble + - r-tidyselect + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-dplyr + - r-rlang + - r-tibble + - r-tidyselect +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Extending tidy verbs to genomic interactions' + description: 'Operate on `GInteractions` objects as tabular data using `dplyr`-like verbs. The functions and methods in `plyinteractions` provide a grammatical approach to manipulate `GInteractions`, to facilitate their integration in genomic analysis workflows.' + diff --git a/recipes/bioconductor-plyranges/meta.yaml b/recipes/bioconductor-plyranges/meta.yaml index cee8917eb76bc..b8bbe45eb1171 100644 --- a/recipes/bioconductor-plyranges/meta.yaml +++ b/recipes/bioconductor-plyranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "plyranges" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1afddfe644bc0efd5e2af427d1d9e9e1 + md5: 23b74165be3c4a855e6a49d8c0f1bab1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plyranges", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 2.1.0), HelloRanges, HelloRangesData, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, covr, ggplot2 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-magrittr - 'r-rlang >=0.2.0' - 'r-tidyselect >=1.0.0' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-magrittr diff --git a/recipes/bioconductor-pmm/meta.yaml b/recipes/bioconductor-pmm/meta.yaml index 9c766f9eaa537..370e01487e660 100644 --- a/recipes/bioconductor-pmm/meta.yaml +++ b/recipes/bioconductor-pmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "pmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bb0cdf8f45d20c01984eb90fdf84c93a + md5: 43957004fa9664b15f4bca34f7ea975e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pmm", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-pmp/meta.yaml b/recipes/bioconductor-pmp/meta.yaml index 815b949774a12..ffe645d75fd11 100644 --- a/recipes/bioconductor-pmp/meta.yaml +++ b/recipes/bioconductor-pmp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "pmp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ae759e61d37da021af27182c987264a7 + md5: 07feec54f330f10904aae29238f79369 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pmp", max_pin="x.x") }}' noarch: generic # Suggests: testthat, covr, knitr, rmarkdown, BiocStyle, gridExtra, magick requirements: host: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-matrixstats - r-missforest - r-reshape2 run: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-matrixstats diff --git a/recipes/bioconductor-pocrcannotation.db/meta.yaml b/recipes/bioconductor-pocrcannotation.db/meta.yaml index 1da24ace53dd7..0918cbf3fda7b 100644 --- a/recipes/bioconductor-pocrcannotation.db/meta.yaml +++ b/recipes/bioconductor-pocrcannotation.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "POCRCannotation.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: da1d4dacc5fffb9c5dfea55649974aa5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pocrcannotation.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-podcall/meta.yaml b/recipes/bioconductor-podcall/meta.yaml index fd7ab13b42a15..9e63932878f83 100644 --- a/recipes/bioconductor-podcall/meta.yaml +++ b/recipes/bioconductor-podcall/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "PoDCall" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f8244df4ed33630558e25e740b18b3b + md5: e079c4df0c773e27d396662c928ac51b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-podcall", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: @@ -53,6 +54,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Positive Droplet Calling for DNA Methylation Droplet Digital PCR' - description: 'Reads files exported from ''QuantaSoft'' containing amplitude values from a run of ddPCR (96 well plate) and robustly sets thresholds to determine positive droplets for each channel of each individual well. Concentration and normalized concentration in addition to other metrics is then calculated for each well. Results are returned as a table, optionally written to file, as well as optional plots (scatterplot and histogram) for both channels per well written to file. The package includes a shiny application which provides an interactive and user-friendly interface to the full functionality of PoDCall.' + description: 'Reads files exported from ''QX Manager or QuantaSoft'' containing amplitude values from a run of ddPCR (96 well plate) and robustly sets thresholds to determine positive droplets for each channel of each individual well. Concentration and normalized concentration in addition to other metrics is then calculated for each well. Results are returned as a table, optionally written to file, as well as optional plots (scatterplot and histogram) for both channels per well written to file. The package includes a shiny application which provides an interactive and user-friendly interface to the full functionality of PoDCall.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-podkat/meta.yaml b/recipes/bioconductor-podkat/meta.yaml index 25dd36027bbcf..9678b6fcdff8a 100644 --- a/recipes/bioconductor-podkat/meta.yaml +++ b/recipes/bioconductor-podkat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "podkat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2d1ac828841d66fe3450803679df6c97 + md5: b06fbdc3f282bde5ec8df0d062d3ecb6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-podkat", max_pin="x.x") }}' # Suggests: BSgenome.Hsapiens.UCSC.hg38.masked, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24), VariantAnnotation, SummarizedExperiment, knitr # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-matrix - 'r-rcpp >=0.11.1' - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-matrix - 'r-rcpp >=0.11.1' diff --git a/recipes/bioconductor-pogos/meta.yaml b/recipes/bioconductor-pogos/meta.yaml index f09afba07cf48..426527de50e5d 100644 --- a/recipes/bioconductor-pogos/meta.yaml +++ b/recipes/bioconductor-pogos/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "pogos" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7a5e5764a5fdd26c7864e71e8dfab96d + md5: 14955bb127999aaa92633bc1ce3a1227 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pogos", max_pin="x.x") }}' noarch: generic # Suggests: knitr, DT, ontologyPlot, testthat, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-ontoproc >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-ontoproc >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - 'r-httr >=1.3.1' - 'r-rjson >=0.2.15' - r-shiny run: - - 'bioconductor-ontoproc >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-ontoproc >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - 'r-httr >=1.3.1' diff --git a/recipes/bioconductor-polyester/meta.yaml b/recipes/bioconductor-polyester/meta.yaml index daebb81f896f5..7fa24f5ce3bc9 100644 --- a/recipes/bioconductor-polyester/meta.yaml +++ b/recipes/bioconductor-polyester/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "polyester" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6737b2c8ec5c8b1415e784d632e0840c + md5: acc47ee29fb9c22fb1ad4bbfafe8fd4d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-polyester", max_pin="x.x") }}' noarch: generic # Suggests: knitr, ballgown, markdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-logspline run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-logspline test: diff --git a/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml b/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml index a963c8fbefadf..bd986aeb518f3 100644 --- a/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml +++ b/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.2" %} {% set name = "PolyPhen.Hsapiens.dbSNP131" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,24 +13,25 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 763e9cd4afd97b36f7e659f5454ef61f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-polyphen.hsapiens.dbsnp131", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-rsqlite >=0.11.0' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-rsqlite >=0.11.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-poma/meta.yaml b/recipes/bioconductor-poma/meta.yaml index df2809ab82fee..fffe40d372e0b 100644 --- a/recipes/bioconductor-poma/meta.yaml +++ b/recipes/bioconductor-poma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "POMA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: acdda87011b0add03854dc75df78fe2b + md5: 89690c830c8b6120d4d436f05e34f4eb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-poma", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, ggraph, knitr, patchwork, plotly, tidyverse, testthat (>= 2.3.2) requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mixomics >=6.24.0,<6.25.0' - - 'bioconductor-rankprod >=3.26.0,<3.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' + - 'bioconductor-rankprod >=3.28.0,<3.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom - r-caret @@ -45,13 +46,13 @@ requirements: - r-uwot - r-vegan run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mixomics >=6.24.0,<6.25.0' - - 'bioconductor-rankprod >=3.26.0,<3.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' + - 'bioconductor-rankprod >=3.28.0,<3.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom - r-caret diff --git a/recipes/bioconductor-poplarcdf/meta.yaml b/recipes/bioconductor-poplarcdf/meta.yaml index e498d9b89ead7..abe70a10b697e 100644 --- a/recipes/bioconductor-poplarcdf/meta.yaml +++ b/recipes/bioconductor-poplarcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "poplarcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 556e7f8f6f76436552d8044ef29279cb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-poplarcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-poplarprobe/meta.yaml b/recipes/bioconductor-poplarprobe/meta.yaml index fbe45b20cc09b..8844ecc8570be 100644 --- a/recipes/bioconductor-poplarprobe/meta.yaml +++ b/recipes/bioconductor-poplarprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "poplarprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 87a608cd86084a06973a88e9b51f799a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-poplarprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-porcine.db/meta.yaml b/recipes/bioconductor-porcine.db/meta.yaml index 3baabe5d742c9..345d8a9eba876 100644 --- a/recipes/bioconductor-porcine.db/meta.yaml +++ b/recipes/bioconductor-porcine.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "porcine.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4a86b3e696d267dca673b4e9276d6368 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-porcine.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.ss.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.ss.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.ss.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.ss.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-porcinecdf/meta.yaml b/recipes/bioconductor-porcinecdf/meta.yaml index d05d5a922f835..11979dc62adb7 100644 --- a/recipes/bioconductor-porcinecdf/meta.yaml +++ b/recipes/bioconductor-porcinecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "porcinecdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 32a60b93829c06a935895fab0a469228 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-porcinecdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-porcineprobe/meta.yaml b/recipes/bioconductor-porcineprobe/meta.yaml index 35c05fe4ea718..5d0f2c7ddf24a 100644 --- a/recipes/bioconductor-porcineprobe/meta.yaml +++ b/recipes/bioconductor-porcineprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "porcineprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5ac483b6329a012d4c9954e3dee8869e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-porcineprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-powertcr/meta.yaml b/recipes/bioconductor-powertcr/meta.yaml index 56035aad2d4fb..8df9efbe126d8 100644 --- a/recipes/bioconductor-powertcr/meta.yaml +++ b/recipes/bioconductor-powertcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "powerTCR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a1ea8721802f5c9366953c388f888d67 + md5: 6033da999bfcba4c2e80a45e358c3855 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-powertcr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics requirements: diff --git a/recipes/bioconductor-powsc/meta.yaml b/recipes/bioconductor-powsc/meta.yaml index 34d53c13d6475..9d658ab0472af 100644 --- a/recipes/bioconductor-powsc/meta.yaml +++ b/recipes/bioconductor-powsc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "POWSC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 68f052aeb186749e50a9f2bbb5cbe3f6 + md5: e2ed51f94e9a1b37aa91fe74a007f4d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-powsc", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mast >=1.26.0,<1.27.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mast >=1.28.0,<1.29.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-pheatmap - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mast >=1.26.0,<1.27.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mast >=1.28.0,<1.29.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-pheatmap diff --git a/recipes/bioconductor-ppcseq/meta.yaml b/recipes/bioconductor-ppcseq/meta.yaml index 0603999607703..bb0514df5b5e6 100644 --- a/recipes/bioconductor-ppcseq/meta.yaml +++ b/recipes/bioconductor-ppcseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ppcseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dc7a246fc82400b73aa46ba102e9e3ee + md5: 5a95706ac4269643dd1eb6efd4bccb67 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ppcseq", max_pin="x.x") }}' # Suggests: knitr, testthat, BiocStyle, rmarkdown # SystemRequirements: GNU make requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - r-benchmarkme - 'r-bh >=1.66.0' - r-dplyr - r-foreach - - r-furrr - - r-future <1.33 - r-ggplot2 - r-lifecycle - r-magrittr - r-purrr - 'r-rcpp >=0.12.0' - 'r-rcppeigen >=0.3.3.3.0' + - 'r-rcppparallel >=5.0.1' - r-rlang - 'r-rstan >=2.18.1' - - 'r-rstantools >=2.0.0' + - 'r-rstantools >=2.1.1' - 'r-stanheaders >=2.18.0' - r-tibble - r-tidybayes @@ -45,23 +45,22 @@ requirements: - libblas - liblapack run: - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - r-benchmarkme - 'r-bh >=1.66.0' - r-dplyr - r-foreach - - r-furrr - - r-future <1.33 - r-ggplot2 - r-lifecycle - r-magrittr - r-purrr - 'r-rcpp >=0.12.0' - 'r-rcppeigen >=0.3.3.3.0' + - 'r-rcppparallel >=5.0.1' - r-rlang - 'r-rstan >=2.18.1' - - 'r-rstantools >=2.0.0' + - 'r-rstantools >=2.1.1' - 'r-stanheaders >=2.18.0' - r-tibble - r-tidybayes diff --git a/recipes/bioconductor-ppinfer/meta.yaml b/recipes/bioconductor-ppinfer/meta.yaml index ad0b1aad6d7d1..a413c32921519 100644 --- a/recipes/bioconductor-ppinfer/meta.yaml +++ b/recipes/bioconductor-ppinfer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "PPInfer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5157ef584ef792c5ff0cb55de3da9eba + md5: f6b346ab6e0c90b546825aa50fb52b59 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ppinfer", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' - - 'bioconductor-yeastexpdata >=0.46.0,<0.47.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' + - 'bioconductor-yeastexpdata >=0.48.0,<0.49.0' - r-base - r-ggplot2 - r-httr - r-igraph - r-kernlab run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' - - 'bioconductor-yeastexpdata >=0.46.0,<0.47.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' + - 'bioconductor-yeastexpdata >=0.48.0,<0.49.0' - r-base - r-ggplot2 - r-httr diff --git a/recipes/bioconductor-pqsfinder/meta.yaml b/recipes/bioconductor-pqsfinder/meta.yaml index 112d56bf8879b..d89644da4851d 100644 --- a/recipes/bioconductor-pqsfinder/meta.yaml +++ b/recipes/bioconductor-pqsfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "pqsfinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 498ce0ee8270dbdff5c63f84e4c8717d + md5: c1201a86985850d5ace97c629e2d4864 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pqsfinder", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi # SystemRequirements: GNU make, C++11 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-bh >=1.78.0' - 'r-rcpp >=0.12.3' - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-bh >=1.78.0' - 'r-rcpp >=0.12.3' diff --git a/recipes/bioconductor-pram/meta.yaml b/recipes/bioconductor-pram/meta.yaml index b198a21d7c48a..6e6332cc06696 100644 --- a/recipes/bioconductor-pram/meta.yaml +++ b/recipes/bioconductor-pram/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "pram" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8737ac32a1a9f2e17fded29baf810970 + md5: 129a8e2cbbf4abab07038d3b7899c58e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pram", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-data.table >=1.11.8' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-data.table >=1.11.8' test: diff --git a/recipes/bioconductor-prebs/meta.yaml b/recipes/bioconductor-prebs/meta.yaml index e7ba1de006868..8be0337f23ffe 100644 --- a/recipes/bioconductor-prebs/meta.yaml +++ b/recipes/bioconductor-prebs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "prebs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c460d482da9e9b3357490dc60b494517 + md5: 847264218e6725926f1b56aacd09b541 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prebs", max_pin="x.x") }}' noarch: generic # Suggests: prebsdata, hgu133plus2cdf, hgu133plus2probe requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rpa >=1.56.0,<1.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rpa >=1.58.0,<1.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rpa >=1.56.0,<1.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rpa >=1.58.0,<1.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-prebsdata/meta.yaml b/recipes/bioconductor-prebsdata/meta.yaml index 2f4e2bf53fa33..1b3a2dde647b4 100644 --- a/recipes/bioconductor-prebsdata/meta.yaml +++ b/recipes/bioconductor-prebsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "prebsdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 96c0666ea91a4bd5b5c8dbc584f873b3 + md5: a1c6aee2732035357adc3e2cb99d6bcc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prebsdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prebsdata/post-link.sh b/recipes/bioconductor-prebsdata/post-link.sh index 34de2b2ebc061..816d1ef0dbdd3 100644 --- a/recipes/bioconductor-prebsdata/post-link.sh +++ b/recipes/bioconductor-prebsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prebsdata-1.36.0" +installBiocDataPackage.sh "prebsdata-1.38.0" diff --git a/recipes/bioconductor-precisetad/meta.yaml b/recipes/bioconductor-precisetad/meta.yaml index c11fc03892901..47324c027359e 100644 --- a/recipes/bioconductor-precisetad/meta.yaml +++ b/recipes/bioconductor-precisetad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "preciseTAD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d90370e884f035d71c774706abf96f2 + md5: 5e6495261bf370abf46d979aace7f363 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-precisetad", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocCheck, BiocManager, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rcgh >=1.30.0,<1.31.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rcgh >=1.32.0,<1.33.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - r-cluster @@ -39,10 +40,10 @@ requirements: - r-prroc - r-randomforest run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rcgh >=1.30.0,<1.31.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rcgh >=1.32.0,<1.33.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - r-cluster diff --git a/recipes/bioconductor-precisetadhub/meta.yaml b/recipes/bioconductor-precisetadhub/meta.yaml index b9aadfa5e8254..d4dc0c0f45d28 100644 --- a/recipes/bioconductor-precisetadhub/meta.yaml +++ b/recipes/bioconductor-precisetadhub/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "preciseTADhub" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e0da7747a2ae263545ef3e426701fd6 + md5: bff4bbf0a4ac1abf21ff72ad4346795c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-precisetadhub", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, markdown, BiocStyle, preciseTAD requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-precisetadhub/post-link.sh b/recipes/bioconductor-precisetadhub/post-link.sh index e29d34389daa1..ff7494e2c8d04 100644 --- a/recipes/bioconductor-precisetadhub/post-link.sh +++ b/recipes/bioconductor-precisetadhub/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "precisetadhub-1.8.0" +installBiocDataPackage.sh "precisetadhub-1.10.0" diff --git a/recipes/bioconductor-preda/meta.yaml b/recipes/bioconductor-preda/meta.yaml index f930ab14e4aaf..2c12240a90381 100644 --- a/recipes/bioconductor-preda/meta.yaml +++ b/recipes/bioconductor-preda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "PREDA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9660d5fd5b0221d82953b8bf43e631e7 + md5: 6f051dc3182b2d70715d84a12e39dd57 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-preda", max_pin="x.x") }}' noarch: generic # Suggests: quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - 'r-lokern >=1.0.9' run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - 'r-lokern >=1.0.9' test: diff --git a/recipes/bioconductor-predasampledata/meta.yaml b/recipes/bioconductor-predasampledata/meta.yaml index 58b45e3f02932..1d617501f624f 100644 --- a/recipes/bioconductor-predasampledata/meta.yaml +++ b/recipes/bioconductor-predasampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.40.0" %} +{% set version = "0.42.0" %} {% set name = "PREDAsampledata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 478b0cd1f601998cfefcca0fdf60eb3d + md5: 5acce57384c00a56d658281ba4fa57e5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-predasampledata", max_pin="x.x") }}' noarch: generic # Suggests: hgu133plus2.db, hgu133plus2cdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-preda >=1.46.0,<1.47.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-preda >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-preda >=1.46.0,<1.47.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-preda >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-predasampledata/post-link.sh b/recipes/bioconductor-predasampledata/post-link.sh index 52ddf15f66bff..abc7050325f76 100644 --- a/recipes/bioconductor-predasampledata/post-link.sh +++ b/recipes/bioconductor-predasampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "predasampledata-0.40.0" +installBiocDataPackage.sh "predasampledata-0.42.0" diff --git a/recipes/bioconductor-preprocesscore/build.sh b/recipes/bioconductor-preprocesscore/build.sh index 203597e1fddf9..c1d13421f5f1e 100644 --- a/recipes/bioconductor-preprocesscore/build.sh +++ b/recipes/bioconductor-preprocesscore/build.sh @@ -8,4 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --configure-args="--disable-threading" --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-preprocesscore/meta.yaml b/recipes/bioconductor-preprocesscore/meta.yaml index 9237faa672b3e..d43ce20f0865a 100644 --- a/recipes/bioconductor-preprocesscore/meta.yaml +++ b/recipes/bioconductor-preprocesscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.1" %} +{% set version = "1.64.0" %} {% set name = "preprocessCore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ef397708852e43e7b3fb42dfe9194d4 + md5: 2116c6363074b59becdaf7a1e88caf91 build: number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-preprocesscore", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-primeviewcdf/meta.yaml b/recipes/bioconductor-primeviewcdf/meta.yaml index ddd2fcbf84023..352d7095f852b 100644 --- a/recipes/bioconductor-primeviewcdf/meta.yaml +++ b/recipes/bioconductor-primeviewcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "primeviewcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 71e39a59a5907e9b8a8dba58d36eee50 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-primeviewcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-primeviewprobe/meta.yaml b/recipes/bioconductor-primeviewprobe/meta.yaml index 9f3a51a54987e..73bf4d160c889 100644 --- a/recipes/bioconductor-primeviewprobe/meta.yaml +++ b/recipes/bioconductor-primeviewprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "primeviewprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 87cc56a8da4fb742ab1558ce1d3d26cc build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-primeviewprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-primirtss/meta.yaml b/recipes/bioconductor-primirtss/meta.yaml index 8c7d1f158dfb0..7ba8ad1cb4071 100644 --- a/recipes/bioconductor-primirtss/meta.yaml +++ b/recipes/bioconductor-primirtss/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "primirTSS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3dfadad951f97d12b55332c5eff234d6 + md5: ead295f564f0e3c4c9d9c8bfa568e745 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-primirtss", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' - 'bioconductor-phastcons100way.ucsc.hg38 >=3.7.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - 'r-dplyr >=0.7.6' - 'r-purrr >=0.2.5' @@ -42,18 +43,18 @@ requirements: - 'r-tibble >=1.4.2' - 'r-tidyr >=0.8.1' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' - 'bioconductor-phastcons100way.ucsc.hg38 >=3.7.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - 'r-dplyr >=0.7.6' - 'r-purrr >=0.2.5' diff --git a/recipes/bioconductor-prince/meta.yaml b/recipes/bioconductor-prince/meta.yaml index a2cef262d826a..f898336ea68c0 100644 --- a/recipes/bioconductor-prince/meta.yaml +++ b/recipes/bioconductor-prince/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "PrInCE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4341628e51ae0ee0129c0d8036bab10d + md5: 98e7e0b9a7e620e0e4ab55436b5c289b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prince", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - 'r-dplyr >=0.7.4' - 'r-forecast >=8.2' @@ -39,8 +40,8 @@ requirements: - 'r-tester >=0.1.7' - 'r-tidyr >=0.8.99' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - 'r-dplyr >=0.7.4' - 'r-forecast >=8.2' diff --git a/recipes/bioconductor-proactiv/meta.yaml b/recipes/bioconductor-proactiv/meta.yaml index b3149a802a75b..475fc41ef36eb 100644 --- a/recipes/bioconductor-proactiv/meta.yaml +++ b/recipes/bioconductor-proactiv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "proActiv" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4681528e213cee2381e40f66ba06a214 + md5: 3aaa83b78fb2e017358c24ab185506ca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-proactiv", max_pin="x.x") }}' noarch: generic # Suggests: testthat, rmarkdown, knitr, Rtsne, gridExtra requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr @@ -40,16 +41,16 @@ requirements: - r-scales - r-tibble run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-probamr/meta.yaml b/recipes/bioconductor-probamr/meta.yaml index 52604dbff010f..2afdefe586872 100644 --- a/recipes/bioconductor-probamr/meta.yaml +++ b/recipes/bioconductor-probamr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "proBAMr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e55435900db79ff363dd274ae7abc343 + md5: 0b5a894a54fb0d56f940b75e025c0d47 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-probamr", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-process/meta.yaml b/recipes/bioconductor-process/meta.yaml index 6d3f897f897f6..3d680a0f15bea 100644 --- a/recipes/bioconductor-process/meta.yaml +++ b/recipes/bioconductor-process/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "PROcess" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 605613c9cdcffbaf4c7d332e93e66937 + md5: 9a9b6e6d31c1c45fb08e1f7cf00f0170 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-process", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-icens >=1.72.0,<1.73.0' + - 'bioconductor-icens >=1.74.0,<1.75.0' - r-base run: - - 'bioconductor-icens >=1.72.0,<1.73.0' + - 'bioconductor-icens >=1.74.0,<1.75.0' - r-base test: commands: diff --git a/recipes/bioconductor-procoil/meta.yaml b/recipes/bioconductor-procoil/meta.yaml index 679fe920302b5..c05235fe4603e 100644 --- a/recipes/bioconductor-procoil/meta.yaml +++ b/recipes/bioconductor-procoil/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "procoil" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d4ab86952e13fcb2719019f2f21c40d8 + md5: 5536c056587bff646a606dec3437fa5d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-procoil", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-kebabs >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-kebabs >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-kebabs >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-kebabs >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-proda/meta.yaml b/recipes/bioconductor-proda/meta.yaml index 95ef3bb8a2674..5a6afff59963e 100644 --- a/recipes/bioconductor-proda/meta.yaml +++ b/recipes/bioconductor-proda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "proDA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7900e3d2213cb542d3095140fe54bda3 + md5: 906f58f351f6a657aafcb3f6a670cc9f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-proda", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), MSnbase, dplyr, stringr, readr, tidyr, tibble, limma, DEP, numDeriv, pheatmap, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-extradistr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-extradistr test: diff --git a/recipes/bioconductor-prodata/meta.yaml b/recipes/bioconductor-prodata/meta.yaml index f64eac848efe7..8b8c68696cd5a 100644 --- a/recipes/bioconductor-prodata/meta.yaml +++ b/recipes/bioconductor-prodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "ProData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a4c17dd4a55240fdeab52f3301e19f6 + md5: 73f3449db86899c83d61173f6bd02a79 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prodata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prodata/post-link.sh b/recipes/bioconductor-prodata/post-link.sh index 966db4c8593cf..fd3bd80e9d246 100644 --- a/recipes/bioconductor-prodata/post-link.sh +++ b/recipes/bioconductor-prodata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prodata-1.38.0" +installBiocDataPackage.sh "prodata-1.40.0" diff --git a/recipes/bioconductor-profileplyr/meta.yaml b/recipes/bioconductor-profileplyr/meta.yaml index 080c30cc6af96..760ca42727502 100644 --- a/recipes/bioconductor-profileplyr/meta.yaml +++ b/recipes/bioconductor-profileplyr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "profileplyr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3975e32d9f4494ea85312b1a009ac8ce + md5: bc6ac2ac1050660a2cb45a11ebbd1a67 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-profileplyr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown, png, Cairo requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-chipseeker >=1.36.0,<1.37.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-enrichedheatmap >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgreat >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-soggi >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-chipseeker >=1.38.0,<1.39.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-enrichedheatmap >=1.32.0,<1.33.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgreat >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-soggi >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base @@ -54,25 +55,25 @@ requirements: - r-tidyr - r-tiff run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-chipseeker >=1.36.0,<1.37.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-enrichedheatmap >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgreat >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-soggi >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-chipseeker >=1.38.0,<1.39.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-enrichedheatmap >=1.32.0,<1.33.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgreat >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-soggi >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base diff --git a/recipes/bioconductor-profilescoredist/meta.yaml b/recipes/bioconductor-profilescoredist/meta.yaml index bedbfef8f41f1..7be23f4741047 100644 --- a/recipes/bioconductor-profilescoredist/meta.yaml +++ b/recipes/bioconductor-profilescoredist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "profileScoreDist" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61e62770ee189714e138987ad490fb96 + md5: 59d0f0bd369e20aa7be8352e5cf46830 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-profilescoredist", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, MotifDb requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-progeny/meta.yaml b/recipes/bioconductor-progeny/meta.yaml index cbb4a9c2e9064..b6dfccddd3534 100644 --- a/recipes/bioconductor-progeny/meta.yaml +++ b/recipes/bioconductor-progeny/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "progeny" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bdb55828f59d804d05e3bddb43c20367 + md5: 9798ea9424f4115b980496038619f009 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-progeny", max_pin="x.x") }}' noarch: generic # Suggests: airway, biomaRt, BiocFileCache, broom, Seurat, SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl, pheatmap, tibble, rmarkdown, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-decoupler >=2.6.0,<2.7.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-decoupler >=2.8.0,<2.9.0' - r-base - r-dplyr - r-ggplot2 @@ -31,8 +32,8 @@ requirements: - r-reshape2 - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-decoupler >=2.6.0,<2.7.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-decoupler >=2.8.0,<2.9.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-projectr/meta.yaml b/recipes/bioconductor-projectr/meta.yaml index a6ff976b635cf..b84111fbdebb1 100644 --- a/recipes/bioconductor-projectr/meta.yaml +++ b/recipes/bioconductor-projectr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "projectR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,42 +11,53 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef6439c75fc8aa471312a4a03dde8dfb + md5: 7351d9a1c593186a6adb189ebd3ff9d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-projectr", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, gridExtra, grid, testthat, devtools, knitr, rmarkdown, ComplexHeatmap +# Suggests: BiocStyle, CoGAPS, gridExtra, grid, testthat, devtools, rmarkdown, knitr, rmarkdown, ComplexHeatmap, gplots requirements: host: - - 'bioconductor-cogaps >=3.19.0,<3.20.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-cluster + - r-cowplot - r-dplyr - r-ggalluvial - r-ggplot2 + - r-ggrepel + - r-matrix + - r-matrixmodels - r-nmf - r-rcolorbrewer - r-reshape2 - r-rocr - r-scales + - r-tsne + - r-umap - r-viridis run: - - 'bioconductor-cogaps >=3.19.0,<3.20.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-cluster + - r-cowplot - r-dplyr - r-ggalluvial - r-ggplot2 + - r-ggrepel + - r-matrix + - r-matrixmodels - r-nmf - r-rcolorbrewer - r-reshape2 - r-rocr - r-scales + - r-tsne + - r-umap - r-viridis test: commands: diff --git a/recipes/bioconductor-proloc/meta.yaml b/recipes/bioconductor-proloc/meta.yaml index 9a4fbacdab1db..230e1d8a522c7 100644 --- a/recipes/bioconductor-proloc/meta.yaml +++ b/recipes/bioconductor-proloc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.1" %} +{% set version = "1.42.0" %} {% set name = "pRoloc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4300b0c722aeef0f0fd76d37bcb56149 + md5: 309ce5a09f91050bdf916ab18389d7a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-proloc", max_pin="x.x") }}' # Suggests: testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.41.0), dplyr, akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape, magick requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-mlinterfaces >=1.80.0,<1.81.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-mlinterfaces >=1.82.0,<1.83.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - r-caret - r-class @@ -56,12 +57,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-mlinterfaces >=1.80.0,<1.81.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-mlinterfaces >=1.82.0,<1.83.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - r-caret - r-class diff --git a/recipes/bioconductor-prolocdata/meta.yaml b/recipes/bioconductor-prolocdata/meta.yaml index caef916fdfc2a..fb5d1764fc6b7 100644 --- a/recipes/bioconductor-prolocdata/meta.yaml +++ b/recipes/bioconductor-prolocdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "pRolocdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3cf7b5644c6af5a158d0291d9b597cd2 + md5: 8aafd04221b21588077788ec79272e1a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prolocdata", max_pin="x.x") }}' noarch: generic # Suggests: pRoloc (>= 1.13.8), testthat, SummarizedExperiment requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prolocdata/post-link.sh b/recipes/bioconductor-prolocdata/post-link.sh index bc590e3d40f51..58c959a4f2622 100644 --- a/recipes/bioconductor-prolocdata/post-link.sh +++ b/recipes/bioconductor-prolocdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prolocdata-1.38.0" +installBiocDataPackage.sh "prolocdata-1.40.0" diff --git a/recipes/bioconductor-prolocgui/meta.yaml b/recipes/bioconductor-prolocgui/meta.yaml index 654796709e1ee..92ba43b5a6797 100644 --- a/recipes/bioconductor-prolocgui/meta.yaml +++ b/recipes/bioconductor-prolocgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "pRolocGUI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9696984952c5868c1550fbb89db5eb6d + md5: a9947bbed5501a1c2c68f7c35364c1da build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prolocgui", max_pin="x.x") }}' noarch: generic # Suggests: pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-proloc >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-proloc >=1.42.0,<1.43.0' - r-base - r-colorspace - r-colourpicker @@ -39,10 +40,10 @@ requirements: - r-shinyjs - r-shinywidgets run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-proloc >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-proloc >=1.42.0,<1.43.0' - r-base - r-colorspace - r-colourpicker diff --git a/recipes/bioconductor-promise/build_failure.linux-64.yaml b/recipes/bioconductor-promise/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..cf404d42c073a --- /dev/null +++ b/recipes/bioconductor-promise/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5b781e0fa5e8b6eb7b4e980f15193540530dbd5b63b9a1fb5db07f32907673c6 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.2s + conda-forge/linux-64 + conda-forge/noarch + bioconda/linux-64 + pkgs/main/linux-64 + pkgs/main/noarch + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gbioconda/linux-64 + [] 1.3s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/linux-64 + pkgs/main/noarch + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.4s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/linux-64 100% + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/linux-64 + [] 1.5s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.6s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.7s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch 100%[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/r/noarch + pkgs/main/noarch + [] 1.8s + conda-forge/linux-64 + conda-forge/noarch 100% + pkgs/r/linux-64 [2K[1A[2K[1A[2K[1A[2K[0G[] 1.9s + conda-forge/linux-64 + conda-forge/noarch 100% + pkgs/r/linux-64 [2K[1A[2K[1A[2K[1A[2K[0Gconda-forge/noarch + pkgs/r/linux-64 + [] 2.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.9s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.9s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.6s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.7s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.8s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.9s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.0s + conda-forge/linux-64 100%[2K[1A[2K[0Gconda-forge/linux-64 + [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.2MB/s 0.0s + opt/conda/conda-bld/noarch 748.0 B @ 15.0MB/s 0.0s + [?25hTraceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3089, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2879, in test + environ.create_env(metadata.config.test_prefix, actions, config=metadata.config, + File "/opt/conda/lib/python3.8/site-packages/conda_build/environ.py", line 1052, in create_env + display_actions(actions, index) + File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in display_actions + actions['LINK'] = [index[d] for d in actions['LINK']] + File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in + actions['LINK'] = [index[d] for d in actions['LINK']] + KeyError: Dist(channel='conda-forge', dist_name='python-3.12.1-hab00c5b_0_cpython', name='python', fmt='.conda', version='3.12.1', build_string='hab00c5b_0_cpython', build_number=0, base_url=None, platform=None) +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-promise/meta.yaml b/recipes/bioconductor-promise/meta.yaml index aeac8a19e26de..17795839b7288 100644 --- a/recipes/bioconductor-promise/meta.yaml +++ b/recipes/bioconductor-promise/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "PROMISE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 89f8708d951f68b7e63c5cb57cc4b182 + md5: ad7b8b2fcd0ba52ad47eb9ff23097a4e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-promise", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base test: commands: diff --git a/recipes/bioconductor-proper/meta.yaml b/recipes/bioconductor-proper/meta.yaml index 0aa0c569bc782..4bb762b00bf39 100644 --- a/recipes/bioconductor-proper/meta.yaml +++ b/recipes/bioconductor-proper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "PROPER" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95670318c035e13983013b9802b91a8e + md5: 6f91ce4b3f5feee476a991fc1072c521 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-proper", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle,DESeq2,DSS,knitr requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base run: - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base test: commands: diff --git a/recipes/bioconductor-props/meta.yaml b/recipes/bioconductor-props/meta.yaml index e22e75404825b..31a4de48bbbe6 100644 --- a/recipes/bioconductor-props/meta.yaml +++ b/recipes/bioconductor-props/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "PROPS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 00746ca2b4edfa8b4d462491b777039f + md5: 20b285908014c5e85775518ea72349c0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-props", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-bnlearn - r-reshape2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-bnlearn - r-reshape2 diff --git a/recipes/bioconductor-prostar/meta.yaml b/recipes/bioconductor-prostar/meta.yaml index 1946540dc3a1b..7833b98683be8 100644 --- a/recipes/bioconductor-prostar/meta.yaml +++ b/recipes/bioconductor-prostar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.1" %} +{% set version = "1.34.3" %} {% set name = "Prostar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 24a2213ce5e4ff844a53fdc1453d5abe + md5: ab3095af56a61bfe4fe81279dffcae21 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prostar", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, BiocManager, testthat, shinyTree, knitr, colourpicker, gtools, XML, R.utils, RColorBrewer, DT, shinyWidgets, sass, rclipboard +# Suggests: BiocStyle, BiocManager, testthat requirements: host: - - 'bioconductor-dapar >=1.32.0,<1.33.0' - - 'bioconductor-dapardata >=1.30.0,<1.31.0' + - 'bioconductor-dapar >=1.34.0,<1.35.0' + - 'bioconductor-dapardata >=1.32.0,<1.33.0' - r-base + - r-colourpicker - r-data.table + - r-dt - r-future - r-ggplot2 - r-gplots + - r-gtools - r-highcharter - r-htmlwidgets + - r-knitr - r-later - r-promises + - r-r.utils + - r-rclipboard + - r-rcolorbrewer - r-rhandsontable + - r-sass - r-shiny - r-shinyace - r-shinybs @@ -40,22 +49,33 @@ requirements: - r-shinyjqui - r-shinyjs - r-shinythemes + - r-shinytree + - r-shinywidgets - r-tibble - r-vioplot - r-webshot + - r-xml run: - - 'bioconductor-dapar >=1.32.0,<1.33.0' - - 'bioconductor-dapardata >=1.30.0,<1.31.0' + - 'bioconductor-dapar >=1.34.0,<1.35.0' + - 'bioconductor-dapardata >=1.32.0,<1.33.0' - r-base + - r-colourpicker - r-data.table + - r-dt - r-future - r-ggplot2 - r-gplots + - r-gtools - r-highcharter - r-htmlwidgets + - r-knitr - r-later - r-promises + - r-r.utils + - r-rclipboard + - r-rcolorbrewer - r-rhandsontable + - r-sass - r-shiny - r-shinyace - r-shinybs @@ -63,9 +83,12 @@ requirements: - r-shinyjqui - r-shinyjs - r-shinythemes + - r-shinytree + - r-shinywidgets - r-tibble - r-vioplot - r-webshot + - r-xml test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prostatecancercamcap/meta.yaml b/recipes/bioconductor-prostatecancercamcap/meta.yaml index 4d29f05598ac7..b01bd5c2727ae 100644 --- a/recipes/bioconductor-prostatecancercamcap/meta.yaml +++ b/recipes/bioconductor-prostatecancercamcap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "prostateCancerCamcap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ff2a0d04db22bce6d2d1722e718edeb5 + md5: 5a27ee47f07162569e5e1e06ffd69886 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prostatecancercamcap", max_pin="x.x") }}' noarch: generic # Suggests: GEOquery requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prostatecancercamcap/post-link.sh b/recipes/bioconductor-prostatecancercamcap/post-link.sh index f05e7e90c4971..884e3a7cda119 100644 --- a/recipes/bioconductor-prostatecancercamcap/post-link.sh +++ b/recipes/bioconductor-prostatecancercamcap/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prostatecancercamcap-1.28.0" +installBiocDataPackage.sh "prostatecancercamcap-1.30.0" diff --git a/recipes/bioconductor-prostatecancergrasso/meta.yaml b/recipes/bioconductor-prostatecancergrasso/meta.yaml index a12622be233ab..642718a61eedf 100644 --- a/recipes/bioconductor-prostatecancergrasso/meta.yaml +++ b/recipes/bioconductor-prostatecancergrasso/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "prostateCancerGrasso" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cc2f4713d5950c0fcd99dd320adbdb2d + md5: c331c996d943a14687439dfdf37b8029 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prostatecancergrasso", max_pin="x.x") }}' noarch: generic # Suggests: GEOquery requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prostatecancergrasso/post-link.sh b/recipes/bioconductor-prostatecancergrasso/post-link.sh index b7bec21917d26..544c52ea34897 100644 --- a/recipes/bioconductor-prostatecancergrasso/post-link.sh +++ b/recipes/bioconductor-prostatecancergrasso/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prostatecancergrasso-1.28.0" +installBiocDataPackage.sh "prostatecancergrasso-1.30.0" diff --git a/recipes/bioconductor-prostatecancerstockholm/meta.yaml b/recipes/bioconductor-prostatecancerstockholm/meta.yaml index 09bd6e6c8db4f..483e6a2239ac4 100644 --- a/recipes/bioconductor-prostatecancerstockholm/meta.yaml +++ b/recipes/bioconductor-prostatecancerstockholm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "prostateCancerStockholm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f2ec2d712681d173c561a57451acae94 + md5: 49326bf3b6f66be78fa1e6d6768b5538 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prostatecancerstockholm", max_pin="x.x") }}' noarch: generic # Suggests: GEOquery requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prostatecancerstockholm/post-link.sh b/recipes/bioconductor-prostatecancerstockholm/post-link.sh index 09ddf03cf328d..b347e68cf857d 100644 --- a/recipes/bioconductor-prostatecancerstockholm/post-link.sh +++ b/recipes/bioconductor-prostatecancerstockholm/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prostatecancerstockholm-1.28.0" +installBiocDataPackage.sh "prostatecancerstockholm-1.30.0" diff --git a/recipes/bioconductor-prostatecancertaylor/meta.yaml b/recipes/bioconductor-prostatecancertaylor/meta.yaml index 5babe7d413b01..00ac0962d4074 100644 --- a/recipes/bioconductor-prostatecancertaylor/meta.yaml +++ b/recipes/bioconductor-prostatecancertaylor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "prostateCancerTaylor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d41f91c630547581ccabf8159a79d889 + md5: c90ff79776e9a658d4cf05e9a29706a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prostatecancertaylor", max_pin="x.x") }}' noarch: generic # Suggests: GEOquery, org.Hs.eg.db requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prostatecancertaylor/post-link.sh b/recipes/bioconductor-prostatecancertaylor/post-link.sh index f127abf7081f2..814031af6bc79 100644 --- a/recipes/bioconductor-prostatecancertaylor/post-link.sh +++ b/recipes/bioconductor-prostatecancertaylor/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prostatecancertaylor-1.28.0" +installBiocDataPackage.sh "prostatecancertaylor-1.30.0" diff --git a/recipes/bioconductor-prostatecancervarambally/meta.yaml b/recipes/bioconductor-prostatecancervarambally/meta.yaml index b88d542ce7ef5..65f3a1df66b5c 100644 --- a/recipes/bioconductor-prostatecancervarambally/meta.yaml +++ b/recipes/bioconductor-prostatecancervarambally/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "prostateCancerVarambally" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8008e839c2e72aee55433f2361efb0cb + md5: cf8fc1872af8c5c2b47372ce94ed4c5c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prostatecancervarambally", max_pin="x.x") }}' noarch: generic # Suggests: GEOquery requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prostatecancervarambally/post-link.sh b/recipes/bioconductor-prostatecancervarambally/post-link.sh index f89b0acc823e7..6a6d1ca836881 100644 --- a/recipes/bioconductor-prostatecancervarambally/post-link.sh +++ b/recipes/bioconductor-prostatecancervarambally/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prostatecancervarambally-1.28.0" +installBiocDataPackage.sh "prostatecancervarambally-1.30.0" diff --git a/recipes/bioconductor-proteinprofiles/meta.yaml b/recipes/bioconductor-proteinprofiles/meta.yaml index 45df829cdd2d0..ac403d2f66889 100644 --- a/recipes/bioconductor-proteinprofiles/meta.yaml +++ b/recipes/bioconductor-proteinprofiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "proteinProfiles" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ffcc07e3926008e6f478089073aa6443 + md5: 491483ff7b360413ae0eafa5ac07de14 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-proteinprofiles", max_pin="x.x") }}' noarch: generic # Suggests: testthat requirements: diff --git a/recipes/bioconductor-proteodisco/meta.yaml b/recipes/bioconductor-proteodisco/meta.yaml index 0a74dbf806d1b..6e6ba09dfda9e 100644 --- a/recipes/bioconductor-proteodisco/meta.yaml +++ b/recipes/bioconductor-proteodisco/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "ProteoDisco" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3f18bfe0ae324151bd6a6ff32f1ea99 + md5: f69597248b6cbbdb2c1029a1dd3b39cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-proteodisco", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi (>= 1.54.1), BSgenome (>= 1.60.0), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.3), BiocStyle (>= 2.20.1), DelayedArray (>= 0.18.0), devtools (>= 2.4.2), knitr (>= 1.33), matrixStats (>= 0.59.0), markdown (>= 1.1), org.Hs.eg.db (>= 3.13.0), purrr (>= 0.3.4), RCurl (>= 1.98.1.3), readr (>= 1.4.0), ggplot2 (>= 3.3.5), rmarkdown (>= 2.9), rtracklayer (>= 1.52.0), seqinr (>= 4.2.8), stringr (>= 1.4.0), reshape2 (>= 1.4.4), scales (>= 1.1.1), testthat (>= 3.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-cleaver >=1.38.0,<1.39.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-cleaver >=1.40.0,<1.41.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-checkmate >=2.0.0' - 'r-dplyr >=1.0.6' @@ -41,17 +42,17 @@ requirements: - 'r-tibble >=3.1.2' - 'r-tidyr >=1.1.3' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-cleaver >=1.38.0,<1.39.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-cleaver >=1.40.0,<1.41.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-checkmate >=2.0.0' - 'r-dplyr >=1.0.6' diff --git a/recipes/bioconductor-proteomm/meta.yaml b/recipes/bioconductor-proteomm/meta.yaml index 5207b937a4d19..18d262626a71c 100644 --- a/recipes/bioconductor-proteomm/meta.yaml +++ b/recipes/bioconductor-proteomm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "ProteoMM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c9f13f6998275db7f5a4374f3ae69883 + md5: 6497729c8cc0221c898927dcddeb00e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-proteomm", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base - r-gdata - r-ggplot2 @@ -29,7 +30,7 @@ requirements: - r-gtools - r-matrixstats run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base - r-gdata - r-ggplot2 diff --git a/recipes/bioconductor-protgear/meta.yaml b/recipes/bioconductor-protgear/meta.yaml index 97862f28cf361..6d3a0b7331dc4 100644 --- a/recipes/bioconductor-protgear/meta.yaml +++ b/recipes/bioconductor-protgear/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "protGear" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d7b1ec8bb2be4491137f53da1b9f5f7 + md5: db63dca71894a3ebbf3b8b78512bccb4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-protgear", max_pin="x.x") }}' noarch: generic # Suggests: gridExtra (>= 2.3), png (>= 0.1-7) , magick (>= 2.7.3) , ggplotify (>= 0.1.0) , scales (>= 1.1.1) , shinythemes (>= 1.2.0) , shinyjs (>= 2.0.0) , shinyWidgets (>= 0.6.2) , shinycssloaders (>= 1.0.0) , shinyalert (>= 3.0.0) , shinyFiles (>= 0.9.1) , shinyFeedback (>= 0.3.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - 'r-data.table >=1.14.0' - 'r-dplyr >=0.8.0' @@ -54,10 +55,10 @@ requirements: - 'r-tibble >=3.1.0' - 'r-tidyr >=1.1.3' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - 'r-data.table >=1.14.0' - 'r-dplyr >=0.8.0' diff --git a/recipes/bioconductor-protgenerics/meta.yaml b/recipes/bioconductor-protgenerics/meta.yaml index 15ba078511ed3..99dbefecd9faf 100644 --- a/recipes/bioconductor-protgenerics/meta.yaml +++ b/recipes/bioconductor-protgenerics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "ProtGenerics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7848b0ce11174fd3e995eb39dc57766a + md5: 5d55c00588169aa089bb457e2d94669a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-protgenerics", max_pin="x.x") }}' noarch: generic # Suggests: testthat requirements: diff --git a/recipes/bioconductor-psea/meta.yaml b/recipes/bioconductor-psea/meta.yaml index d3bcfe4d2b3da..2460bda29bef8 100644 --- a/recipes/bioconductor-psea/meta.yaml +++ b/recipes/bioconductor-psea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "PSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dfe8429c4952bb970f612fb15cfe8545 + md5: c8f9f8210c265d722d76668e19a6fd7c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-psea", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-psichomics/meta.yaml b/recipes/bioconductor-psichomics/meta.yaml index cf57efd937530..34f50e50ef81c 100644 --- a/recipes/bioconductor-psichomics/meta.yaml +++ b/recipes/bioconductor-psichomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "psichomics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5a9ad76e280bfbe775fda70657d72adc + md5: 8d6d1c34972e5d4b389d9263ab2077db build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-psichomics", max_pin="x.x") }}' # Suggests: testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi, spelling requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-recount >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-recount >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-colourpicker @@ -59,13 +60,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-recount >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-recount >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-colourpicker diff --git a/recipes/bioconductor-psmatch/meta.yaml b/recipes/bioconductor-psmatch/meta.yaml index 2946b78c9dfa2..86c4f75515374 100644 --- a/recipes/bioconductor-psmatch/meta.yaml +++ b/recipes/bioconductor-psmatch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "PSMatch" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 17a718dd3fa26d78a2584f90bc5b0631 + md5: 4c63ca3d541af4e5925bcc2bde7d67ea build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-psmatch", max_pin="x.x") }}' noarch: generic # Suggests: msdata, rpx, mzID, mzR, Spectra, SummarizedExperiment, BiocStyle, rmarkdown, knitr, factoextra, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-igraph - r-matrix run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-igraph - r-matrix diff --git a/recipes/bioconductor-psygenet2r/meta.yaml b/recipes/bioconductor-psygenet2r/meta.yaml index d8785e016a310..4550ccfe6407e 100644 --- a/recipes/bioconductor-psygenet2r/meta.yaml +++ b/recipes/bioconductor-psygenet2r/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.2" %} +{% set version = "1.34.0" %} {% set name = "psygenet2r" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ce5ce92ebd24818a539a905621b0f4e2 + md5: 69234da568b765050beb79aa46205114 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-psygenet2r", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-bgeedb >=2.26.0,<2.27.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-bgeedb >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-ggplot2 - r-igraph @@ -34,11 +35,11 @@ requirements: - r-reshape2 - r-stringr run: - - 'bioconductor-bgeedb >=2.26.0,<2.27.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-bgeedb >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-ggplot2 - r-igraph diff --git a/recipes/bioconductor-ptairdata/meta.yaml b/recipes/bioconductor-ptairdata/meta.yaml index 65052ec0ce765..47412396819e7 100644 --- a/recipes/bioconductor-ptairdata/meta.yaml +++ b/recipes/bioconductor-ptairdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ptairData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ede739875473864ed372a4fb877b1852 + md5: eea0fcfdd0047d72092a3b6beb326129 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ptairdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-signal run: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-signal - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ptairdata/post-link.sh b/recipes/bioconductor-ptairdata/post-link.sh index 1f8d934053b1f..8d2982bffafe3 100644 --- a/recipes/bioconductor-ptairdata/post-link.sh +++ b/recipes/bioconductor-ptairdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ptairdata-1.8.0" +installBiocDataPackage.sh "ptairdata-1.10.0" diff --git a/recipes/bioconductor-ptairms/meta.yaml b/recipes/bioconductor-ptairms/meta.yaml index f69b15f2e94b9..dbf733b5430bc 100644 --- a/recipes/bioconductor-ptairms/meta.yaml +++ b/recipes/bioconductor-ptairms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ptairMS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d7e194913f9006f5782be7aa4944714 + md5: 771ce745db55fad5684a47026df33abe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ptairms", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), ptairData, ropls requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-bit64 - r-chron @@ -46,9 +47,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-bit64 - r-chron @@ -80,6 +81,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Pre-processing PTR-TOF-MS Data' - description: 'This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the ''sample by features'' table of peak intensities in addition to the sample and feature metadata (as a single ExpressionSet object for subsequent statistical analysis). This package also permit usefull tools for cohorts management as analyzing data progressively, visualization tools and quality control. The steps include calibration, expiration detection, peak detection and quantification, feature alignment, missing value imputation and feature annotation. Applications to exhaled air and cell culture in headspace are described in the vignettes and examples. This package was used for data analysis of Gassin Delyle study on adults undergoing invasive mechanical ventilation in the intensive care unit due to severe COVID-19 or non-COVID-19 acute respiratory distress syndrome (ARDS), and permit to identfy four potentiel biomarquers of the infection.' + description: 'This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the ''sample by features'' table of peak intensities in addition to the sample and feature metadata (as a singl=1.56.0,<1.57.0' - - 'bioconductor-lobstahs >=1.26.0,<1.27.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-lobstahs >=1.28.0,<1.29.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base run: - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-lobstahs >=1.26.0,<1.27.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-lobstahs >=1.28.0,<1.29.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pth2o2lipids/post-link.sh b/recipes/bioconductor-pth2o2lipids/post-link.sh index 1a5c3167d93b6..db6d6c3fc4d12 100644 --- a/recipes/bioconductor-pth2o2lipids/post-link.sh +++ b/recipes/bioconductor-pth2o2lipids/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pth2o2lipids-1.26.0" +installBiocDataPackage.sh "pth2o2lipids-1.28.0" diff --git a/recipes/bioconductor-puma/meta.yaml b/recipes/bioconductor-puma/meta.yaml index c7823e3ecf680..991e8eb47bf36 100644 --- a/recipes/bioconductor-puma/meta.yaml +++ b/recipes/bioconductor-puma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.42.0" %} +{% set version = "3.44.0" %} {% set name = "puma" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ec485bb2cd3bc9d97a2badb8b1c0be2d + md5: ed1d90c9c9b7751611b0f32edf0a1ffb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-puma", max_pin="x.x") }}' # Suggests: pumadata, affydata, snow, limma, ROCR,annotate requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-mclust - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-mclust build: diff --git a/recipes/bioconductor-pumadata/meta.yaml b/recipes/bioconductor-pumadata/meta.yaml index b67c027c521de..a621ddfcce813 100644 --- a/recipes/bioconductor-pumadata/meta.yaml +++ b/recipes/bioconductor-pumadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.36.0" %} +{% set version = "2.38.0" %} {% set name = "pumadata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8201e94e0c66444c72b8f45bd3ca7020 + md5: 811d6234d1d4e310beb7111601b157b7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pumadata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-puma >=3.42.0,<3.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-puma >=3.44.0,<3.45.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-puma >=3.42.0,<3.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-puma >=3.44.0,<3.45.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pumadata/post-link.sh b/recipes/bioconductor-pumadata/post-link.sh index a66648cc03439..1b94fc5e7a3cf 100644 --- a/recipes/bioconductor-pumadata/post-link.sh +++ b/recipes/bioconductor-pumadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pumadata-2.36.0" +installBiocDataPackage.sh "pumadata-2.38.0" diff --git a/recipes/bioconductor-purecn/meta.yaml b/recipes/bioconductor-purecn/meta.yaml index 2c5bcc9a97740..a34ed6b085135 100644 --- a/recipes/bioconductor-purecn/meta.yaml +++ b/recipes/bioconductor-purecn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.4" %} +{% set version = "2.8.1" %} {% set name = "PureCN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ec5551dfa20ade4fa9d0bbb6767709c + md5: d668ed7c332244073d26762dd291004f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-purecn", max_pin="x.x") }}' noarch: generic # Suggests: BiocParallel, BiocStyle, PSCBS, R.utils, TxDb.Hsapiens.UCSC.hg19.knownGene, covr, knitr, optparse, org.Hs.eg.db, jsonlite, markdown, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-futile.logger @@ -45,20 +46,20 @@ requirements: - r-rcolorbrewer - r-vgam run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-futile.logger diff --git a/recipes/bioconductor-pvac/meta.yaml b/recipes/bioconductor-pvac/meta.yaml index 66f2c8112a2a8..904378bd67a73 100644 --- a/recipes/bioconductor-pvac/meta.yaml +++ b/recipes/bioconductor-pvac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "pvac" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: abfcf7faff5f1bc03741c07c72eb6c29 + md5: ae148a3c65e5b6efc44cfea7d208d918 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pvac", max_pin="x.x") }}' noarch: generic # Suggests: pbapply, affydata, ALLMLL, genefilter requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-pvca/meta.yaml b/recipes/bioconductor-pvca/meta.yaml index d0aad607a7176..c02a34e9d4f84 100644 --- a/recipes/bioconductor-pvca/meta.yaml +++ b/recipes/bioconductor-pvca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "pvca" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e0f8e4f5b7de7c8a1eac5199675c140c + md5: dcc72a578e6ec7d738fab213c4d27e20 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pvca", max_pin="x.x") }}' noarch: generic # Suggests: golubEsets requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-lme4 - r-matrix run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-lme4 - r-matrix diff --git a/recipes/bioconductor-pviz/meta.yaml b/recipes/bioconductor-pviz/meta.yaml index 9e8a823fee0fd..83a82e5290e48 100644 --- a/recipes/bioconductor-pviz/meta.yaml +++ b/recipes/bioconductor-pviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "Pviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a6f2ef898de7e8a4fb115b42f651872 + md5: 1a1513067c6a873f9523f20eb85f2878 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pviz", max_pin="x.x") }}' noarch: generic # Suggests: knitr, pepDat requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-data.table run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-data.table test: diff --git a/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml b/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml index 6fb8ca4fd431f..0fc2d9e14d907 100644 --- a/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml +++ b/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.34.0" %} +{% set version = "4.36.0" %} {% set name = "PWMEnrich.Dmelanogaster.background" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 907d3ff8c0fb527c01dbf099a075f732 + md5: b671ba0cff5c0c6017fd3f72d0afc547 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pwmenrich.dmelanogaster.background", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-pwmenrich >=4.36.0,<4.37.0' + - 'bioconductor-pwmenrich >=4.38.0,<4.39.0' - r-base run: - - 'bioconductor-pwmenrich >=4.36.0,<4.37.0' + - 'bioconductor-pwmenrich >=4.38.0,<4.39.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh b/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh index 46d30a6d9777d..f9aedbea31b16 100644 --- a/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh +++ b/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pwmenrich.dmelanogaster.background-4.34.0" +installBiocDataPackage.sh "pwmenrich.dmelanogaster.background-4.36.0" diff --git a/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml b/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml index f89270babbb6d..2cc73594c1eb4 100644 --- a/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml +++ b/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.34.0" %} +{% set version = "4.36.0" %} {% set name = "PWMEnrich.Hsapiens.background" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02021cd798df13ad0f124fdc481ebe33 + md5: 7c7b177c29fc31c7546d4e7160a9b977 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pwmenrich.hsapiens.background", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-pwmenrich >=4.36.0,<4.37.0' + - 'bioconductor-pwmenrich >=4.38.0,<4.39.0' - r-base run: - - 'bioconductor-pwmenrich >=4.36.0,<4.37.0' + - 'bioconductor-pwmenrich >=4.38.0,<4.39.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh b/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh index 00e6fb83781aa..5fd33b45910e0 100644 --- a/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh +++ b/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pwmenrich.hsapiens.background-4.34.0" +installBiocDataPackage.sh "pwmenrich.hsapiens.background-4.36.0" diff --git a/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml b/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml index 9a674ea664f6b..14f7a80059072 100644 --- a/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml +++ b/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.34.0" %} +{% set version = "4.36.0" %} {% set name = "PWMEnrich.Mmusculus.background" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e81cb70d4a4850829fa5a83003c75404 + md5: 5d54401a941d1efe7148da2ddc714d65 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pwmenrich.mmusculus.background", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-pwmenrich >=4.36.0,<4.37.0' + - 'bioconductor-pwmenrich >=4.38.0,<4.39.0' - r-base run: - - 'bioconductor-pwmenrich >=4.36.0,<4.37.0' + - 'bioconductor-pwmenrich >=4.38.0,<4.39.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh b/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh index cf21e15375be7..b583b5d163e55 100644 --- a/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh +++ b/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pwmenrich.mmusculus.background-4.34.0" +installBiocDataPackage.sh "pwmenrich.mmusculus.background-4.36.0" diff --git a/recipes/bioconductor-pwmenrich/meta.yaml b/recipes/bioconductor-pwmenrich/meta.yaml index 4b8dbaf802a26..e3e4139a4902f 100644 --- a/recipes/bioconductor-pwmenrich/meta.yaml +++ b/recipes/bioconductor-pwmenrich/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.36.0" %} +{% set version = "4.38.0" %} {% set name = "PWMEnrich" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d26185e888435e846dec08f4f6b566d + md5: ced56cbfbab381f5736f4f58fe26b9f8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pwmenrich", max_pin="x.x") }}' noarch: generic # Suggests: MotifDb, BSgenome, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' - r-base - r-evd - r-gdata run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' - r-base - r-evd - r-gdata diff --git a/recipes/bioconductor-pwomics/meta.yaml b/recipes/bioconductor-pwomics/meta.yaml index dfd46023a8190..9ad50be8600cb 100644 --- a/recipes/bioconductor-pwomics/meta.yaml +++ b/recipes/bioconductor-pwomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "pwOmics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9f2c44535d54b08ef853fd4d7fea7092 + md5: fcb2cc2e104a970552cc4f45ce4a1197 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pwomics", max_pin="x.x") }}' noarch: generic -# Suggests: ebdbNet, longitudinal, Mfuzz +# Suggests: ebdbNet, longitudinal, Mfuzz, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbiopaxparser >=2.40.0,<2.41.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbiopaxparser >=2.42.0,<2.43.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' - r-base - r-data.table - r-gplots - r-igraph run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbiopaxparser >=2.40.0,<2.41.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbiopaxparser >=2.42.0,<2.43.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' - r-base - r-data.table - r-gplots diff --git a/recipes/bioconductor-pwrewas.data/meta.yaml b/recipes/bioconductor-pwrewas.data/meta.yaml index c7be770b6480c..3c654ffcdf181 100644 --- a/recipes/bioconductor-pwrewas.data/meta.yaml +++ b/recipes/bioconductor-pwrewas.data/meta.yaml @@ -27,7 +27,7 @@ requirements: - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20230706 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-qckitfastq/meta.yaml b/recipes/bioconductor-qckitfastq/meta.yaml index 459c1c90d6de9..ecb59cbec82ca 100644 --- a/recipes/bioconductor-qckitfastq/meta.yaml +++ b/recipes/bioconductor-qckitfastq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "qckitfastq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,7 +11,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3c41af38fcd03a1f5e2bf17aa58969c0 + md5: 60955b37d9eb0868da1c5ecd262334e8 patches: - shared_timed_mutex.patch build: @@ -19,13 +19,14 @@ build: rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qckitfastq", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, kableExtra, testthat # SystemRequirements: GNU make requirements: host: - - 'bioconductor-rseqan >=1.20.0,<1.21.0' - - 'bioconductor-seqtools >=1.34.0,<1.35.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-rseqan >=1.22.0,<1.23.0' + - 'bioconductor-seqtools >=1.36.0,<1.37.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-data.table - r-dplyr @@ -37,9 +38,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-rseqan >=1.20.0,<1.21.0' - - 'bioconductor-seqtools >=1.34.0,<1.35.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-rseqan >=1.22.0,<1.23.0' + - 'bioconductor-seqtools >=1.36.0,<1.37.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-qcmetrics/meta.yaml b/recipes/bioconductor-qcmetrics/meta.yaml index 9a0b45ade18c7..2cdd85a42a547 100644 --- a/recipes/bioconductor-qcmetrics/meta.yaml +++ b/recipes/bioconductor-qcmetrics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "qcmetrics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6285c583fa47f8be686d506160602efc + md5: 68f2a395be6986c02f8473dbe25ed621 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qcmetrics", max_pin="x.x") }}' noarch: generic # Suggests: affy, MSnbase, ggplot2, lattice, mzR, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-knitr - r-pander - r-xtable run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-knitr - r-pander diff --git a/recipes/bioconductor-qdnaseq.hg19/meta.yaml b/recipes/bioconductor-qdnaseq.hg19/meta.yaml index c3c0694654834..bd3148547dbbb 100644 --- a/recipes/bioconductor-qdnaseq.hg19/meta.yaml +++ b/recipes/bioconductor-qdnaseq.hg19/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "QDNAseq.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b81f056006151fd4a2f55935ee57f67 + md5: 2b663d8771f16d55db88ec3321942ead build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qdnaseq.hg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-qdnaseq.hg19/post-link.sh b/recipes/bioconductor-qdnaseq.hg19/post-link.sh index 900524cd9f150..f95428a20b4fd 100644 --- a/recipes/bioconductor-qdnaseq.hg19/post-link.sh +++ b/recipes/bioconductor-qdnaseq.hg19/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "qdnaseq.hg19-1.30.0" +installBiocDataPackage.sh "qdnaseq.hg19-1.32.0" diff --git a/recipes/bioconductor-qdnaseq.mm10/meta.yaml b/recipes/bioconductor-qdnaseq.mm10/meta.yaml index a39e1bbf1d1de..a14c48bb16146 100644 --- a/recipes/bioconductor-qdnaseq.mm10/meta.yaml +++ b/recipes/bioconductor-qdnaseq.mm10/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "QDNAseq.mm10" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d7c1a5cec6ee30213a4389b40979b9ef + md5: 2d7b80c2bec7146aec28384b7875acca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qdnaseq.mm10", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-qdnaseq.mm10/post-link.sh b/recipes/bioconductor-qdnaseq.mm10/post-link.sh index 6f9e4ae2877cd..05c6fcc404271 100644 --- a/recipes/bioconductor-qdnaseq.mm10/post-link.sh +++ b/recipes/bioconductor-qdnaseq.mm10/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "qdnaseq.mm10-1.30.0" +installBiocDataPackage.sh "qdnaseq.mm10-1.32.0" diff --git a/recipes/bioconductor-qdnaseq/meta.yaml b/recipes/bioconductor-qdnaseq/meta.yaml index adfb87e341164..aae4b1e35a592 100644 --- a/recipes/bioconductor-qdnaseq/meta.yaml +++ b/recipes/bioconductor-qdnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "QDNAseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9d44cd046b4d2157547009cb1fdfa442 + md5: 589b066b44091955991b4f66ac86b9ee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qdnaseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 1.8.0), BSgenome (>= 1.38.0), digest (>= 0.6.20), GenomeInfoDb (>= 1.6.0), future (>= 1.22.1), parallelly (>= 1.28.1), R.cache (>= 0.13.0), QDNAseq.hg19, QDNAseq.mm10 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cghbase >=1.60.0,<1.61.0' - - 'bioconductor-cghcall >=2.62.0,<2.63.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' + - 'bioconductor-cghcall >=2.64.0,<2.65.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - 'r-future.apply >=1.8.1' - 'r-matrixstats >=0.60.0' - 'r-r.utils >=2.9.0' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cghbase >=1.60.0,<1.61.0' - - 'bioconductor-cghcall >=2.62.0,<2.63.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' + - 'bioconductor-cghcall >=2.64.0,<2.65.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - 'r-future.apply >=1.8.1' - 'r-matrixstats >=0.60.0' diff --git a/recipes/bioconductor-qfeatures/meta.yaml b/recipes/bioconductor-qfeatures/meta.yaml index 720858efa736e..f071f392d180f 100644 --- a/recipes/bioconductor-qfeatures/meta.yaml +++ b/recipes/bioconductor-qfeatures/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "QFeatures" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7b1b85fe9194b0d05f0049c1a43ebb8 + md5: 6833061a024bb9783b7d9a85bc282a88 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qfeatures", max_pin="x.x") }}' noarch: generic # Suggests: SingleCellExperiment, Matrix, HDF5Array, msdata, ggplot2, gplots, dplyr, limma, DT, shiny, shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute, norm, ComplexHeatmap requirements: host: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-lazyeval - r-plotly run: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-lazyeval diff --git a/recipes/bioconductor-qmtools/meta.yaml b/recipes/bioconductor-qmtools/meta.yaml index 2e6747f0bf6f8..8ec0b0553e167 100644 --- a/recipes/bioconductor-qmtools/meta.yaml +++ b/recipes/bioconductor-qmtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "qmtools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3dd6957b8b5e757e4acaa92338fc289e + md5: 941d7cbf1dc8c2622fe97bda18a2bf49 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qmtools", max_pin="x.x") }}' noarch: generic # Suggests: Rtsne, missForest, vsn, pcaMethods, pls, MsFeatures, impute, imputeLCMD, nlme, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-heatmaply @@ -33,9 +34,9 @@ requirements: - r-scales - r-vim run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-heatmaply diff --git a/recipes/bioconductor-qpcrnorm/meta.yaml b/recipes/bioconductor-qpcrnorm/meta.yaml index 11bb25b31ea50..72c295aba9034 100644 --- a/recipes/bioconductor-qpcrnorm/meta.yaml +++ b/recipes/bioconductor-qpcrnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "qpcrNorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 27b2a54f8a20b56b34273c690e85ca16 + md5: 43fa513309301e6d8e89fcef668c7b28 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qpcrnorm", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-qpgraph/meta.yaml b/recipes/bioconductor-qpgraph/meta.yaml index ea0a0c777fd9d..4287b9ed5aeb4 100644 --- a/recipes/bioconductor-qpgraph/meta.yaml +++ b/recipes/bioconductor-qpgraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.2" %} +{% set version = "2.36.0" %} {% set name = "qpgraph" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c8599307a26a9048d0094ea30862da09 + md5: 10be7ba90f9349fb4de4aa84e6fecaa4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qpgraph", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db, rlecuyer, snow, Category, GOstats requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-matrix >=1.5-0' - r-mvtnorm @@ -38,17 +39,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-matrix >=1.5-0' - r-mvtnorm diff --git a/recipes/bioconductor-qplexanalyzer/meta.yaml b/recipes/bioconductor-qplexanalyzer/meta.yaml index 10626e9250bcc..6b01c08b890cd 100644 --- a/recipes/bioconductor-qplexanalyzer/meta.yaml +++ b/recipes/bioconductor-qplexanalyzer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "qPLEXanalyzer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a45ddc801efbbb143d4bceb0edb67a7 + md5: d30edcfbf4e355e0c40bd7cf16d396fb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qplexanalyzer", max_pin="x.x") }}' noarch: generic # Suggests: gridExtra, knitr, qPLEXdata, rmarkdown, statmod, testthat, UniProt.ws, vdiffr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-assertthat - r-base - 'r-dplyr >=1.0.0' @@ -44,13 +45,13 @@ requirements: - r-tidyr - r-tidyselect run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-assertthat - r-base - 'r-dplyr >=1.0.0' diff --git a/recipes/bioconductor-qplexdata/meta.yaml b/recipes/bioconductor-qplexdata/meta.yaml index 02aab7e2337f6..d72d4ac30f891 100644 --- a/recipes/bioconductor-qplexdata/meta.yaml +++ b/recipes/bioconductor-qplexdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "qPLEXdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2ea69c2e1a071fd94fcb169af5c61422 + md5: af947f54391fc79c81308890b1e95d96 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qplexdata", max_pin="x.x") }}' noarch: generic +# Suggests: statmod requirements: host: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-qplexanalyzer >=1.18.0,<1.19.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-qplexanalyzer >=1.20.0,<1.21.0' - r-base - r-dplyr - r-knitr run: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-qplexanalyzer >=1.18.0,<1.19.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-qplexanalyzer >=1.20.0,<1.21.0' - r-base - r-dplyr - r-knitr - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-qplexdata/post-link.sh b/recipes/bioconductor-qplexdata/post-link.sh index b3776da8b113c..5bfe1edb7e282 100644 --- a/recipes/bioconductor-qplexdata/post-link.sh +++ b/recipes/bioconductor-qplexdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "qplexdata-1.18.0" +installBiocDataPackage.sh "qplexdata-1.20.0" diff --git a/recipes/bioconductor-qsea/meta.yaml b/recipes/bioconductor-qsea/meta.yaml index 25e311d360427..9bafebacc6db4 100644 --- a/recipes/bioconductor-qsea/meta.yaml +++ b/recipes/bioconductor-qsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "qsea" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8717b734a71f34dbf8b231134752afde + md5: 2891ba342f17500cee6391d1f388c3c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qsea", max_pin="x.x") }}' # Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown, BiocManager, MASS requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hmmcopy >=1.42.0,<1.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hmmcopy >=1.44.0,<1.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-gtools - r-zoo - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hmmcopy >=1.42.0,<1.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hmmcopy >=1.44.0,<1.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-gtools - r-zoo diff --git a/recipes/bioconductor-qsmooth/meta.yaml b/recipes/bioconductor-qsmooth/meta.yaml index 6ed95bf40b208..659687e2f8c11 100644 --- a/recipes/bioconductor-qsmooth/meta.yaml +++ b/recipes/bioconductor-qsmooth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "qsmooth" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 24fdc20a48b8eb73da6122e29420738e + md5: 471983d71a4b056b71b10fe15c3f7b1c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qsmooth", max_pin="x.x") }}' noarch: generic # Suggests: bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-hmisc run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-hmisc test: diff --git a/recipes/bioconductor-qsutils/meta.yaml b/recipes/bioconductor-qsutils/meta.yaml index 9524de10c95a7..67ebd30438806 100644 --- a/recipes/bioconductor-qsutils/meta.yaml +++ b/recipes/bioconductor-qsutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "QSutils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a9ad7bfbc8487c40238707a43d8607d3 + md5: 3a1816762d5d0d26145c352281211f80 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qsutils", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, ggplot2 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-ape - r-base - r-psych run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-ape - r-base - r-psych diff --git a/recipes/bioconductor-qsvar/meta.yaml b/recipes/bioconductor-qsvar/meta.yaml index 95ef83f52c2b6..1da9a23ce0762 100644 --- a/recipes/bioconductor-qsvar/meta.yaml +++ b/recipes/bioconductor-qsvar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "qsvaR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fda6f9c474c90089486be809da7b2955 + md5: e9531cc164f93967a5d5d0469d47f7c7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qsvar", max_pin="x.x") }}' noarch: generic # Suggests: BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-ggplot2 run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-qtlexperiment/build.sh b/recipes/bioconductor-qtlexperiment/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-qtlexperiment/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-qtlexperiment/meta.yaml b/recipes/bioconductor-qtlexperiment/meta.yaml new file mode 100644 index 0000000000000..d7d4285a69261 --- /dev/null +++ b/recipes/bioconductor-qtlexperiment/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.0.0" %} +{% set name = "QTLExperiment" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fe7642e0952c4c68e5417906dfb66fb3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qtlexperiment", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat, BiocStyle, knitr, rmarkdown, covr +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-ashr + - r-base + - r-checkmate + - r-collapse + - r-dplyr + - r-rlang + - r-tibble + - r-tidyr + - r-vroom + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-ashr + - r-base + - r-checkmate + - r-collapse + - r-dplyr + - r-rlang + - r-tibble + - r-tidyr + - r-vroom +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'S4 classes for QTL summary statistics and metadata' + description: 'QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states. It is based on the ''SummarizedExperiment'' class and contains functions for creating, merging, and subsetting objects. ''QTLExperiment'' also stores experiment metadata and has checks in place to ensure that transformations apply correctly.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-qtlizer/meta.yaml b/recipes/bioconductor-qtlizer/meta.yaml index eabb7717c1a6e..e151c4ba3c0fc 100644 --- a/recipes/bioconductor-qtlizer/meta.yaml +++ b/recipes/bioconductor-qtlizer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "Qtlizer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f1b7e4abafbf2a5ad5516d174fe1605 + md5: ea7e6227ebf6708e465681021fb77b19 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qtlizer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-curl - r-httr - r-stringi run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-curl - r-httr diff --git a/recipes/bioconductor-quantiseqr/meta.yaml b/recipes/bioconductor-quantiseqr/meta.yaml index ecf946508bbe4..92068f91ebef4 100644 --- a/recipes/bioconductor-quantiseqr/meta.yaml +++ b/recipes/bioconductor-quantiseqr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "quantiseqr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5917b18de8ecdfc1d3ad9683c14b0d4c + md5: 34cd21d2e59e1f8f58001fdcc49eaf44 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-quantiseqr", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery, knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat, tibble requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-limsolve @@ -31,9 +32,9 @@ requirements: - r-rlang - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-limsolve diff --git a/recipes/bioconductor-quantro/meta.yaml b/recipes/bioconductor-quantro/meta.yaml index 40605f161c433..78285b4ad918e 100644 --- a/recipes/bioconductor-quantro/meta.yaml +++ b/recipes/bioconductor-quantro/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "quantro" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 24fc384ea9ede169587bac30b26ba294 + md5: 3e7912df8d9bc50c461074539540f289 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-quantro", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - r-doparallel - r-foreach @@ -30,8 +31,8 @@ requirements: - r-iterators - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-quantsmooth/meta.yaml b/recipes/bioconductor-quantsmooth/meta.yaml index 601aeceed6b4a..3145b221ce689 100644 --- a/recipes/bioconductor-quantsmooth/meta.yaml +++ b/recipes/bioconductor-quantsmooth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "quantsmooth" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 02f6e69a0d90b985b5ea59123514d22f + md5: cb47e0040fd219ad15aebf094dd379cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-quantsmooth", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-quartpac/meta.yaml b/recipes/bioconductor-quartpac/meta.yaml index 41719f9389dda..ccaac8ad09882 100644 --- a/recipes/bioconductor-quartpac/meta.yaml +++ b/recipes/bioconductor-quartpac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "QuartPAC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dcfa63b6c83c62a6a6ceabd014aae563 + md5: 91af5166d133016b9beaa8539f0fcef7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-quartpac", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, rgl requirements: host: - - 'bioconductor-graphpac >=1.42.0,<1.43.0' - - 'bioconductor-ipac >=1.44.0,<1.45.0' - - 'bioconductor-spacepac >=1.38.0,<1.39.0' + - 'bioconductor-graphpac >=1.44.0,<1.45.0' + - 'bioconductor-ipac >=1.46.0,<1.47.0' + - 'bioconductor-spacepac >=1.40.0,<1.41.0' - r-base - r-data.table run: - - 'bioconductor-graphpac >=1.42.0,<1.43.0' - - 'bioconductor-ipac >=1.44.0,<1.45.0' - - 'bioconductor-spacepac >=1.38.0,<1.39.0' + - 'bioconductor-graphpac >=1.44.0,<1.45.0' + - 'bioconductor-ipac >=1.46.0,<1.47.0' + - 'bioconductor-spacepac >=1.40.0,<1.41.0' - r-base - r-data.table test: diff --git a/recipes/bioconductor-quasr/meta.yaml b/recipes/bioconductor-quasr/meta.yaml index ef705eccba5a3..c95104f9a8972 100644 --- a/recipes/bioconductor-quasr/meta.yaml +++ b/recipes/bioconductor-quasr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.1" %} +{% set version = "1.42.1" %} {% set name = "QuasR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,54 +11,55 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 08e936fb92d8ccfc031fb6ffeea50747 + md5: ace4fd8823c92add78b78c8e05b366aa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-quasr", max_pin="x.x") }}' # Suggests: Gviz, BiocStyle, GenomicAlignments, Rhisat2, knitr, rmarkdown, covr, testthat # SystemRequirements: GNU make requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbowtie >=1.40.0,<1.41.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbowtie >=1.42.0,<1.43.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbowtie >=1.40.0,<1.41.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbowtie >=1.42.0,<1.43.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-quaternaryprod/meta.yaml b/recipes/bioconductor-quaternaryprod/meta.yaml index c9c986003df15..335557456ba9f 100644 --- a/recipes/bioconductor-quaternaryprod/meta.yaml +++ b/recipes/bioconductor-quaternaryprod/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "QuaternaryProd" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad10afde46e2b65c39b96ba7333cf930 + md5: 73dfc14934979c18429472a3d6870ece build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-quaternaryprod", max_pin="x.x") }}' # Suggests: knitr requirements: host: diff --git a/recipes/bioconductor-qubic/meta.yaml b/recipes/bioconductor-qubic/meta.yaml index 10045a4ed6915..dfff731e76d06 100644 --- a/recipes/bioconductor-qubic/meta.yaml +++ b/recipes/bioconductor-qubic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "QUBIC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef7e2f43d1b1bf14a659a8643a0f5379 + md5: 728f7aca6c2d2913d424694e9b31c41c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qubic", max_pin="x.x") }}' # Suggests: QUBICdata, qgraph, fields, knitr, rmarkdown # SystemRequirements: C++11, Rtools (>= 3.1) requirements: diff --git a/recipes/bioconductor-qubicdata/meta.yaml b/recipes/bioconductor-qubicdata/meta.yaml index 9e299269570fc..349cf66d0a19b 100644 --- a/recipes/bioconductor-qubicdata/meta.yaml +++ b/recipes/bioconductor-qubicdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "QUBICdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 47be84c681eabf3ba1851a935762e23a + md5: 0670dfaee6f8d532cf3506428a5932c1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qubicdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-qubicdata/post-link.sh b/recipes/bioconductor-qubicdata/post-link.sh index 3d91df27a6fab..e44c7a49f8d46 100644 --- a/recipes/bioconductor-qubicdata/post-link.sh +++ b/recipes/bioconductor-qubicdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "qubicdata-1.28.0" +installBiocDataPackage.sh "qubicdata-1.30.0" diff --git a/recipes/bioconductor-qusage/meta.yaml b/recipes/bioconductor-qusage/meta.yaml index 5d2be31ad1f00..b458324664fca 100644 --- a/recipes/bioconductor-qusage/meta.yaml +++ b/recipes/bioconductor-qusage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "qusage" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d98b2598bdae73d4c17fe40586dd3afb + md5: f4675daa1494bbf070a084d05a2e672b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qusage", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-emmeans - r-fftw - r-nlme run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-emmeans - r-fftw diff --git a/recipes/bioconductor-qvalue/meta.yaml b/recipes/bioconductor-qvalue/meta.yaml index 2425f0321e6ae..255657b20155b 100644 --- a/recipes/bioconductor-qvalue/meta.yaml +++ b/recipes/bioconductor-qvalue/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "qvalue" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 380fe077649cd719ccc6abdf683f2be7 + md5: d6d57a60a814587681cf438b4e6ee9bc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qvalue", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: diff --git a/recipes/bioconductor-r10kcod.db/meta.yaml b/recipes/bioconductor-r10kcod.db/meta.yaml index 4a52c7c605332..fe56f9587a20a 100644 --- a/recipes/bioconductor-r10kcod.db/meta.yaml +++ b/recipes/bioconductor-r10kcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "r10kcod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4a7a25fee64294cfb5adccaa6cf28772 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-r10kcod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-r3cpet/meta.yaml b/recipes/bioconductor-r3cpet/meta.yaml index 4dbb3f662a152..8e04b83625ff9 100644 --- a/recipes/bioconductor-r3cpet/meta.yaml +++ b/recipes/bioconductor-r3cpet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "R3CPET" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7010509ac5d68785413f584462b19cd5 + md5: 4eaced963afa114068f2c36982e1add3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-r3cpet", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, TxDb.Hsapiens.UCSC.hg19.knownGene, biovizBase, biomaRt, AnnotationDbi, org.Hs.eg.db, shiny, ChIPpeakAnno requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-clvalid - r-data.table @@ -39,12 +40,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-clvalid - r-data.table diff --git a/recipes/bioconductor-r3cseq/meta.yaml b/recipes/bioconductor-r3cseq/meta.yaml index b84ee7f76b7b4..cf83b123ff451 100644 --- a/recipes/bioconductor-r3cseq/meta.yaml +++ b/recipes/bioconductor-r3cseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "r3Cseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7106a2893f7db6ba10481edcfc36186d + md5: 548b2dc3319fc848c932bcb142edbd61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-r3cseq", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Rnorvegicus.UCSC.rn5.masked requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-rcolorbrewer - r-sqldf - r-vgam run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-rcolorbrewer diff --git a/recipes/bioconductor-r453plus1toolbox/meta.yaml b/recipes/bioconductor-r453plus1toolbox/meta.yaml index 8df159384666f..8870d430d6725 100644 --- a/recipes/bioconductor-r453plus1toolbox/meta.yaml +++ b/recipes/bioconductor-r453plus1toolbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "R453Plus1Toolbox" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2e33a0e2ede03b423ce99fda54bcc54b + md5: 2d7ad69c3b68b4a635129d296599c210 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-r453plus1toolbox", max_pin="x.x") }}' # Suggests: rtracklayer, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-r2html - r-teachingdemos @@ -40,19 +41,19 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-r2html - r-teachingdemos diff --git a/recipes/bioconductor-r4rna/meta.yaml b/recipes/bioconductor-r4rna/meta.yaml index 4b298c5b3f270..5cb61ea244f9a 100644 --- a/recipes/bioconductor-r4rna/meta.yaml +++ b/recipes/bioconductor-r4rna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "R4RNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 29316712c46983e36ff86e8bd0ebd2a4 + md5: a77903559307ab481671650646dd85e5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-r4rna", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base test: commands: diff --git a/recipes/bioconductor-radiogx/meta.yaml b/recipes/bioconductor-radiogx/meta.yaml index 0547a675591b5..6aa2d3edaaaa0 100644 --- a/recipes/bioconductor-radiogx/meta.yaml +++ b/recipes/bioconductor-radiogx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "RadioGx" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 07e2cfb998c9754ffec01a7ca0dae866 + md5: a7e06ef2f71341c5252a5e2b874fdf17 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-radiogx", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, BiocStyle, knitr, pander, markdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-coregx >=2.4.0,<2.5.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-catools @@ -38,12 +39,12 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-coregx >=2.4.0,<2.5.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-catools diff --git a/recipes/bioconductor-rae230a.db/meta.yaml b/recipes/bioconductor-rae230a.db/meta.yaml index 1c69dfc10cf40..afeee8e0950b8 100644 --- a/recipes/bioconductor-rae230a.db/meta.yaml +++ b/recipes/bioconductor-rae230a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "rae230a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a2a80af1669fc038a64effbf5a4b246d build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rae230a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rae230acdf/meta.yaml b/recipes/bioconductor-rae230acdf/meta.yaml index 912b6a851adcc..650f0d564ab13 100644 --- a/recipes/bioconductor-rae230acdf/meta.yaml +++ b/recipes/bioconductor-rae230acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rae230acdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6f2281124e1be164d5fd599e84f6adbc build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rae230acdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rae230aprobe/meta.yaml b/recipes/bioconductor-rae230aprobe/meta.yaml index 63b5b3e81ddd0..b7441cbf4679b 100644 --- a/recipes/bioconductor-rae230aprobe/meta.yaml +++ b/recipes/bioconductor-rae230aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rae230aprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6f2d77e1d9c1e3afb96ef78b3202bb0b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rae230aprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rae230b.db/meta.yaml b/recipes/bioconductor-rae230b.db/meta.yaml index 82efc0b4d7aea..0273888d9117e 100644 --- a/recipes/bioconductor-rae230b.db/meta.yaml +++ b/recipes/bioconductor-rae230b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "rae230b.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4f0474ed22bf5ebd932dd6a4d9573551 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rae230b.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rae230bcdf/meta.yaml b/recipes/bioconductor-rae230bcdf/meta.yaml index 6f52923f1d90e..38c382de21f3c 100644 --- a/recipes/bioconductor-rae230bcdf/meta.yaml +++ b/recipes/bioconductor-rae230bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rae230bcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bd61c17402e9c04be1000c16e0356618 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rae230bcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rae230bprobe/meta.yaml b/recipes/bioconductor-rae230bprobe/meta.yaml index acd25efbdb3a0..242c7cdb4229c 100644 --- a/recipes/bioconductor-rae230bprobe/meta.yaml +++ b/recipes/bioconductor-rae230bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rae230bprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7bdb3a07e1f00de8ff510a69bdac4c53 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rae230bprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-raer/build.sh b/recipes/bioconductor-raer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-raer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-raer/meta.yaml b/recipes/bioconductor-raer/meta.yaml new file mode 100644 index 0000000000000..61beb51eb00aa --- /dev/null +++ b/recipes/bioconductor-raer/meta.yaml @@ -0,0 +1,80 @@ +{% set version = "1.0.0" %} +{% set name = "raer" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0b5c050626ce21756f90b4f9c967465b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-raer", max_pin="x.x") }}' +# Suggests: testthat (>= 3.0.0), knitr, DESeq2, edgeR, limma, rmarkdown, BiocStyle, ComplexHeatmap, TxDb.Hsapiens.UCSC.hg38.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, BSgenome.Hsapiens.NCBI.GRCh38, scater, scran, scuttle, AnnotationHub, covr, raerdata +# SystemRequirements: GNU make +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-cli + - r-data.table + - r-matrix + - r-r.utils + - libblas + - liblapack + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-cli + - r-data.table + - r-matrix + - r-r.utils + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'RNA editing tools in R' + description: 'Toolkit for identification and statistical testing of RNA editing signals from within R. Provides support for identifying sites from bulk-RNA and single cell RNA-seq datasets, and general methods for extraction of allelic read counts from alignment files. Facilitates annotation and exploratory analysis of editing signals using Bioconductor packages and resources.' + license_file: LICENSE + diff --git a/recipes/bioconductor-raerdata/meta.yaml b/recipes/bioconductor-raerdata/meta.yaml new file mode 100644 index 0000000000000..a93eb084ad4ba --- /dev/null +++ b/recipes/bioconductor-raerdata/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.0.0" %} +{% set name = "raerdata" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8f250d12f89396f8d4351da5045cf22c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-raerdata", max_pin="x.x") }}' + noarch: generic +# Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - r-base + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'A collection of datasets for use with raer package' + description: 'raerdata is an ExperimentHub package that provides a collection of files useful for demostrating functionality in the raer package. Datasets include 10x genomics scRNA-seq, bulk RNA-seq, and paired whole-genome and RNA-seq data. Additionally databases of human and mouse RNA editing sites are provided.' + license_file: LICENSE + diff --git a/recipes/bioconductor-raerdata/post-link.sh b/recipes/bioconductor-raerdata/post-link.sh new file mode 100644 index 0000000000000..f8c5dd141a4fe --- /dev/null +++ b/recipes/bioconductor-raerdata/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "raerdata-1.0.0" diff --git a/recipes/bioconductor-raerdata/pre-unlink.sh b/recipes/bioconductor-raerdata/pre-unlink.sh new file mode 100644 index 0000000000000..fe52b6b760486 --- /dev/null +++ b/recipes/bioconductor-raerdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ raerdata diff --git a/recipes/bioconductor-raex10stprobeset.db/meta.yaml b/recipes/bioconductor-raex10stprobeset.db/meta.yaml index 5a0fae703d91b..27cc03aa38783 100644 --- a/recipes/bioconductor-raex10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-raex10stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "raex10stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a386809ea8da340f315e378fa329b3ac build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-raex10stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml index e131376b0b124..98b38f78e2267 100644 --- a/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "raex10sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3a0c511a1073c67172770bc3e4b842b5 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-raex10sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-raexexonprobesetlocation/meta.yaml b/recipes/bioconductor-raexexonprobesetlocation/meta.yaml index e536a6c1c1889..370160c4212b6 100644 --- a/recipes/bioconductor-raexexonprobesetlocation/meta.yaml +++ b/recipes/bioconductor-raexexonprobesetlocation/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.15.0" %} {% set name = "RaExExonProbesetLocation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: d547bcd30685495283b32f0f86ecc79b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-raexexonprobesetlocation", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene10stprobeset.db/meta.yaml b/recipes/bioconductor-ragene10stprobeset.db/meta.yaml index a84b92471aa9b..d5ca4b4037b08 100644 --- a/recipes/bioconductor-ragene10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-ragene10stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "ragene10stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 358685c380b37027a064924069b9ee40 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene10stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml index b491aacb14471..4169739b0d7d0 100644 --- a/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "ragene10sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5ff95454493a72bfa2546d82d32fbec1 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene10sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene10stv1cdf/meta.yaml b/recipes/bioconductor-ragene10stv1cdf/meta.yaml index 1797ced105faf..f9095368dcbb5 100644 --- a/recipes/bioconductor-ragene10stv1cdf/meta.yaml +++ b/recipes/bioconductor-ragene10stv1cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ragene10stv1cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: df696e9dbf5b3f2761b6a0a5914be058 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene10stv1cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene10stv1probe/meta.yaml b/recipes/bioconductor-ragene10stv1probe/meta.yaml index 163ed6d32bf18..36db272a8a25c 100644 --- a/recipes/bioconductor-ragene10stv1probe/meta.yaml +++ b/recipes/bioconductor-ragene10stv1probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ragene10stv1probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 94978b6efb075aacf31ccdc8000e40fa build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene10stv1probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene11stprobeset.db/meta.yaml b/recipes/bioconductor-ragene11stprobeset.db/meta.yaml index 945be5c32fcb5..9605b8d84ad9a 100644 --- a/recipes/bioconductor-ragene11stprobeset.db/meta.yaml +++ b/recipes/bioconductor-ragene11stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "ragene11stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 86f7704c4852c514b3bc3221f7692ba3 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene11stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml index e90c54b294548..a4a85cda35e82 100644 --- a/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "ragene11sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f7fbe318547f911b520415a90b3440e9 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene11sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene20stprobeset.db/meta.yaml b/recipes/bioconductor-ragene20stprobeset.db/meta.yaml index 1fbbb3c6d6e9e..67108c15a1dd4 100644 --- a/recipes/bioconductor-ragene20stprobeset.db/meta.yaml +++ b/recipes/bioconductor-ragene20stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "ragene20stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 23a43899a22078f4c13b7b1d45176319 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene20stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml index 6a38b64f3ce7c..28fc801a28399 100644 --- a/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "ragene20sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b44c5f6ac2b2e3eb4d820d08f7a38644 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene20sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene21stprobeset.db/meta.yaml b/recipes/bioconductor-ragene21stprobeset.db/meta.yaml index 8739c96546c4c..0b4be17e863db 100644 --- a/recipes/bioconductor-ragene21stprobeset.db/meta.yaml +++ b/recipes/bioconductor-ragene21stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "ragene21stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6451885f99ce3873d5d4dbacdf968181 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene21stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml index 0aae6a57270bb..06c45bcb7dee6 100644 --- a/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "ragene21sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6ffe13e1594add0a5169b2083b608336 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene21sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-raggedexperiment/meta.yaml b/recipes/bioconductor-raggedexperiment/meta.yaml index b27b8f891f221..5caad78ba3f76 100644 --- a/recipes/bioconductor-raggedexperiment/meta.yaml +++ b/recipes/bioconductor-raggedexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "RaggedExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 05b6897d69250f287a753601e550080f + md5: 5704ce0834ff2770c489c3882ef4acec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-raggedexperiment", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, MultiAssayExperiment requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-raids/build.sh b/recipes/bioconductor-raids/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-raids/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-raids/meta.yaml b/recipes/bioconductor-raids/meta.yaml new file mode 100644 index 0000000000000..507252a73a248 --- /dev/null +++ b/recipes/bioconductor-raids/meta.yaml @@ -0,0 +1,66 @@ +{% set version = "1.0.0" %} +{% set name = "RAIDS" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 768d047b002bb44e1178d69233878818 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-raids", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat, knitr, rmarkdown, BiocStyle, withr, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 +requirements: + host: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genesis >=2.32.0,<2.33.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - r-base + - r-class + - r-proc + - r-rlang + run: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genesis >=2.32.0,<2.33.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - r-base + - r-class + - r-proc + - r-rlang +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'Apache License (>= 2)' + summary: 'Accurate Inference of Genetic Ancestry from Cancer Sequences' + description: 'This package implements specialized algorithms that enable genetic ancestry inference from various cancer sequences sources (RNA, Exome and Whole-Genome sequences). This package also implements a simulation algorithm that generates synthetic cancer-derived data. This code and analysis pipeline was designed and developed for the following publication: Belleau, P et al. Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.' + diff --git a/recipes/bioconductor-rain/meta.yaml b/recipes/bioconductor-rain/meta.yaml index 7d79f13920b07..f06f49eb3f548 100644 --- a/recipes/bioconductor-rain/meta.yaml +++ b/recipes/bioconductor-rain/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "rain" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9749ba6b883017a62470ef1ba33a5148 + md5: e523c08337422230710fd1f2a5a392cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rain", max_pin="x.x") }}' noarch: generic # Suggests: lattice, BiocStyle requirements: host: - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-gmp run: - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-gmp test: diff --git a/recipes/bioconductor-ramr/meta.yaml b/recipes/bioconductor-ramr/meta.yaml index 12bb7b578b6a0..196dcea668264 100644 --- a/recipes/bioconductor-ramr/meta.yaml +++ b/recipes/bioconductor-ramr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ramr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d61b7ccd6f2bf988a00a4e95d9307653 + md5: 6a6278f2ad74018661b9985eb978e90c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ramr", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, knitr, rmarkdown, gridExtra, annotatr, LOLA, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-dorng @@ -35,10 +36,10 @@ requirements: - r-matrixstats - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-dorng diff --git a/recipes/bioconductor-ramwas/meta.yaml b/recipes/bioconductor-ramwas/meta.yaml index 045ea8fdde6ff..233f285fb2a8e 100644 --- a/recipes/bioconductor-ramwas/meta.yaml +++ b/recipes/bioconductor-ramwas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "ramwas" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: be4fe215633bd48a9802b7ad6a22a39f + md5: ccbff0a1c4bd31c8ceb9d2641d6608d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ramwas", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, pander, BiocStyle, BSgenome.Ecoli.NCBI.20080805 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-digest - r-filematrix @@ -33,11 +34,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-digest - r-filematrix diff --git a/recipes/bioconductor-randomwalkrestartmh/meta.yaml b/recipes/bioconductor-randomwalkrestartmh/meta.yaml index c96acc8e7ac67..aad822b818c73 100644 --- a/recipes/bioconductor-randomwalkrestartmh/meta.yaml +++ b/recipes/bioconductor-randomwalkrestartmh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RandomWalkRestartMH" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 334449d593d86853a0203fcb7ccb4d6d + md5: ace5e6d73a365094a41a864a47deb893 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-randomwalkrestartmh", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-randpack/meta.yaml b/recipes/bioconductor-randpack/meta.yaml index a62a77797a627..626ee120a1935 100644 --- a/recipes/bioconductor-randpack/meta.yaml +++ b/recipes/bioconductor-randpack/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "randPack" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 074bd51f6b64411a009463888a08ffe4 + md5: 71791ade28f58d981a510c8b660ae1e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-randpack", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-randrotation/meta.yaml b/recipes/bioconductor-randrotation/meta.yaml index d05d67a6aa7d8..5d4447925d490 100644 --- a/recipes/bioconductor-randrotation/meta.yaml +++ b/recipes/bioconductor-randrotation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "randRotation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af48011b48390b6567ccda6141ee4f12 + md5: a05faf1fe582450a789fc2d58960fa97 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-randrotation", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocParallel, lme4, nlme, rmarkdown, BiocStyle, testthat (>= 2.1.0), limma, sva requirements: diff --git a/recipes/bioconductor-rankprod/meta.yaml b/recipes/bioconductor-rankprod/meta.yaml index 159db0a61e95b..2ebbe68585c00 100644 --- a/recipes/bioconductor-rankprod/meta.yaml +++ b/recipes/bioconductor-rankprod/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.26.0" %} +{% set version = "3.28.0" %} {% set name = "RankProd" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6fa483ed8d64249e1280088bc1fd78a4 + md5: 39f3eba64601984ad265d91f3a150180 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rankprod", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-raresim/meta.yaml b/recipes/bioconductor-raresim/meta.yaml index edae4c455e23d..fdd6a7e5a167e 100644 --- a/recipes/bioconductor-raresim/meta.yaml +++ b/recipes/bioconductor-raresim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "RAREsim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a227aacb1583b3ea793e127a30e6796f + md5: 6ec5b86f348e2d4ffb365da80651041e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-raresim", max_pin="x.x") }}' noarch: generic # Suggests: markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) requirements: diff --git a/recipes/bioconductor-rarevariantvis/meta.yaml b/recipes/bioconductor-rarevariantvis/meta.yaml index e41ef7739083e..a55ff5d23bcd9 100644 --- a/recipes/bioconductor-rarevariantvis/meta.yaml +++ b/recipes/bioconductor-rarevariantvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "RareVariantVis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,46 +11,47 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 679826e7c9df1bbb563a740f197fa2c2 + md5: 2157172a825bbc826d5c2f3d17a41987 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rarevariantvis", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-phastcons100way.ucsc.hg19 >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-googlevis - r-gtools run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-phastcons100way.ucsc.hg19 >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-googlevis - r-gtools diff --git a/recipes/bioconductor-rarr/meta.yaml b/recipes/bioconductor-rarr/meta.yaml index 46ecddaef2c4d..5f28e2f9eb0be 100644 --- a/recipes/bioconductor-rarr/meta.yaml +++ b/recipes/bioconductor-rarr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "Rarr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,13 +11,14 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d1368ed8413be31e3d59401f1642991 + md5: 94af864ae3de3557840993a429944ea2 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, covr, knitr, tinytest + run_exports: '{{ pin_subpackage("bioconductor-rarr", max_pin="x.x") }}' +# Suggests: BiocStyle, covr, knitr, tinytest, mockery # SystemRequirements: GNU make requirements: host: diff --git a/recipes/bioconductor-rat.db0/meta.yaml b/recipes/bioconductor-rat.db0/meta.yaml index 9664ceae6fa59..97008b6343456 100644 --- a/recipes/bioconductor-rat.db0/meta.yaml +++ b/recipes/bioconductor-rat.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "rat.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 86993da680822a050e85f1208713f3c8 + md5: cde666f86ec7b61beb8cf1037511f977 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rat.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rat.db0/post-link.sh b/recipes/bioconductor-rat.db0/post-link.sh index c3e3d4f5e5bbb..b40a101d33dc3 100644 --- a/recipes/bioconductor-rat.db0/post-link.sh +++ b/recipes/bioconductor-rat.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rat.db0-3.17.0" +installBiocDataPackage.sh "rat.db0-3.18.0" diff --git a/recipes/bioconductor-rat2302.db/meta.yaml b/recipes/bioconductor-rat2302.db/meta.yaml index 3837f56dc958d..2a342615aa394 100644 --- a/recipes/bioconductor-rat2302.db/meta.yaml +++ b/recipes/bioconductor-rat2302.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "rat2302.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b1404d8a16fec681f0fd682589a685ea build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rat2302.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rat2302cdf/meta.yaml b/recipes/bioconductor-rat2302cdf/meta.yaml index 4aaf5fcb18bd5..043a6a2d81dd8 100644 --- a/recipes/bioconductor-rat2302cdf/meta.yaml +++ b/recipes/bioconductor-rat2302cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rat2302cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a033730f79a11d45b4cd7e7c520f8052 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rat2302cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rat2302frmavecs/meta.yaml b/recipes/bioconductor-rat2302frmavecs/meta.yaml index 24f0971b2d763..5eb5dfee57f4f 100644 --- a/recipes/bioconductor-rat2302frmavecs/meta.yaml +++ b/recipes/bioconductor-rat2302frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.11" %} {% set name = "rat2302frmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 44d9f00c2f3806899c6605d1ba274066 build: - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rat2302frmavecs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-frma >=1.52.0,<1.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-frma >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-frma >=1.52.0,<1.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-frma >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rat2302probe/meta.yaml b/recipes/bioconductor-rat2302probe/meta.yaml index 531f316a7171b..e2c76e6e9f797 100644 --- a/recipes/bioconductor-rat2302probe/meta.yaml +++ b/recipes/bioconductor-rat2302probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rat2302probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d1d9215e52b9e845cc4d7c902536e0d6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rat2302probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ratchrloc/meta.yaml b/recipes/bioconductor-ratchrloc/meta.yaml index c07eec45d96dc..d3fe6a6509e9a 100644 --- a/recipes/bioconductor-ratchrloc/meta.yaml +++ b/recipes/bioconductor-ratchrloc/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.1.6" %} {% set name = "ratCHRLOC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6fecff4821a5a47e3bd38a2ff78173d5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ratchrloc", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rattoxfxcdf/meta.yaml b/recipes/bioconductor-rattoxfxcdf/meta.yaml index d529581444b92..73dd35e04127f 100644 --- a/recipes/bioconductor-rattoxfxcdf/meta.yaml +++ b/recipes/bioconductor-rattoxfxcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rattoxfxcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 912d0fa424615fcd92773ed174d5efdd build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rattoxfxcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rattoxfxprobe/meta.yaml b/recipes/bioconductor-rattoxfxprobe/meta.yaml index 525a470b0ffa1..f32aeb6966e55 100644 --- a/recipes/bioconductor-rattoxfxprobe/meta.yaml +++ b/recipes/bioconductor-rattoxfxprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rattoxfxprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 202791c72e8c956b9854fa4d9ba67a24 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rattoxfxprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rattus.norvegicus/meta.yaml b/recipes/bioconductor-rattus.norvegicus/meta.yaml index 5902d0a0bb074..3d57f0f02545d 100644 --- a/recipes/bioconductor-rattus.norvegicus/meta.yaml +++ b/recipes/bioconductor-rattus.norvegicus/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1" %} {% set name = "Rattus.norvegicus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5692fdeb0bc7f94e1db35f097cad99a9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rattus.norvegicus", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - 'bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene >=3.12.0,<3.13.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - 'bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene >=3.12.0,<3.13.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rawrr/meta.yaml b/recipes/bioconductor-rawrr/meta.yaml index 1bfc3b3af36a5..08f497e744570 100644 --- a/recipes/bioconductor-rawrr/meta.yaml +++ b/recipes/bioconductor-rawrr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.2" %} {% set name = "rawrr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: def45f50cec22561ffbc1022eed93032 + md5: 42213a8a733115af719162fc1a72d6a1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rawrr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 2.5), ExperimentHub, knitr, protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat # SystemRequirements: mono-runtime 4.x or higher (including System.Data library) on Linux/macOS, .Net Framework (>= 4.5.1) on Microsoft Windows. diff --git a/recipes/bioconductor-rbcbook1/meta.yaml b/recipes/bioconductor-rbcbook1/meta.yaml index cfead0d6598f5..59907071a6fca 100644 --- a/recipes/bioconductor-rbcbook1/meta.yaml +++ b/recipes/bioconductor-rbcbook1/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.0" %} {% set name = "RbcBook1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 849ecc7e9f264ce9bacce3f8a6d64c3f + md5: 16f681613c1c4d309b032c64cfe18c4a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbcbook1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-rpart run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-rpart test: diff --git a/recipes/bioconductor-rbec/meta.yaml b/recipes/bioconductor-rbec/meta.yaml index f657f26389496..92930222940ff 100644 --- a/recipes/bioconductor-rbec/meta.yaml +++ b/recipes/bioconductor-rbec/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "Rbec" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a954c964eccec52381d10c1344b4796c + md5: f295d8ade5faf2c0b770f2b075262116 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbec", max_pin="x.x") }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-dada2 >=1.28.0,<1.29.0' + - 'bioconductor-dada2 >=1.30.0,<1.31.0' - r-base - r-doparallel - r-foreach @@ -30,7 +31,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-dada2 >=1.28.0,<1.29.0' + - 'bioconductor-dada2 >=1.30.0,<1.31.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-rbgl/meta.yaml b/recipes/bioconductor-rbgl/meta.yaml index 02005957b371d..f201a7627ea36 100644 --- a/recipes/bioconductor-rbgl/meta.yaml +++ b/recipes/bioconductor-rbgl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "RBGL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f8bf9943c7d1fbf6ce2e027109a8b4f + md5: a18b5ad5c49f058b6f65a2bd0a4274d1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbgl", max_pin="x.x") }}' # Suggests: Rgraphviz, XML, RUnit, BiocGenerics, BiocStyle, knitr requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-bh - libblas - liblapack run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-bh build: diff --git a/recipes/bioconductor-rbioformats/meta.yaml b/recipes/bioconductor-rbioformats/meta.yaml index c75d3f2a6b06c..0b180c33b55f5 100644 --- a/recipes/bioconductor-rbioformats/meta.yaml +++ b/recipes/bioconductor-rbioformats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "RBioFormats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c2078329911e3b0b5979225dd524f28f + md5: cd83827dd164a9b44ba3d0d08fd77b38 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbioformats", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat, xml2 # SystemRequirements: Java (>= 1.7) requirements: host: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-rjava >=0.9-6' - openjdk run: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-rjava >=0.9-6' - openjdk diff --git a/recipes/bioconductor-rbioinf/meta.yaml b/recipes/bioconductor-rbioinf/meta.yaml index 0e6032254ba56..9cf94f1be6a6b 100644 --- a/recipes/bioconductor-rbioinf/meta.yaml +++ b/recipes/bioconductor-rbioinf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "RBioinf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a706a1b48cbed097dcb5ab1266fe0e90 + md5: ec036823fe8f50106f37436eec716add build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbioinf", max_pin="x.x") }}' # Suggests: Rgraphviz requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - libblas - liblapack run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-rbiopaxparser/meta.yaml b/recipes/bioconductor-rbiopaxparser/meta.yaml index 104a20d71ef31..b48a0a08c3e8a 100644 --- a/recipes/bioconductor-rbiopaxparser/meta.yaml +++ b/recipes/bioconductor-rbiopaxparser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.40.0" %} +{% set version = "2.42.0" %} {% set name = "rBiopaxParser" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee84f721ce8bafac32c3c847500b9481 + md5: 53e24a8896bf17bd56fe48d62427eb33 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbiopaxparser", max_pin="x.x") }}' noarch: generic # Suggests: Rgraphviz, RCurl, graph, RUnit, BiocGenerics, RBGL, igraph requirements: diff --git a/recipes/bioconductor-rbm/meta.yaml b/recipes/bioconductor-rbm/meta.yaml index 6d455e14c5162..216f62b73d664 100644 --- a/recipes/bioconductor-rbm/meta.yaml +++ b/recipes/bioconductor-rbm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "RBM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 836597b482a58256a1e2021fd9b411ff + md5: 4ae63966d6e9cfd1d3ce001f65a02abe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbm", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base test: commands: diff --git a/recipes/bioconductor-rbowtie/meta.yaml b/recipes/bioconductor-rbowtie/meta.yaml index 207599443dbf9..9263ed9e3b853 100644 --- a/recipes/bioconductor-rbowtie/meta.yaml +++ b/recipes/bioconductor-rbowtie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "Rbowtie" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5421ecbf4cfa6eb177dc24e71ab9360c + md5: 409fc50371b1eaf9be2af500aff05249 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbowtie", max_pin="x.x") }}' # Suggests: testthat, parallel, BiocStyle, knitr, rmarkdown # SystemRequirements: GNU make requirements: diff --git a/recipes/bioconductor-rbowtie2/meta.yaml b/recipes/bioconductor-rbowtie2/meta.yaml index 70f57c0c2e4ab..cf394a23f4368 100644 --- a/recipes/bioconductor-rbowtie2/meta.yaml +++ b/recipes/bioconductor-rbowtie2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "Rbowtie2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4410870693059284f2d83f0e66f0c343 + md5: dbba503f3134fdb9c6521c060ec2d5fc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbowtie2", max_pin="x.x") }}' # Suggests: knitr, testthat (>= 3.0.0), rmarkdown # SystemRequirements: C++11, GNU make, samtools requirements: host: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-magrittr - libblas - liblapack - - zlib run: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-magrittr - - zlib build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-rbsurv/meta.yaml b/recipes/bioconductor-rbsurv/meta.yaml index c4316931efc32..399aaa8374e09 100644 --- a/recipes/bioconductor-rbsurv/meta.yaml +++ b/recipes/bioconductor-rbsurv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.58.0" %} +{% set version = "2.60.0" %} {% set name = "rbsurv" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 77140e1902a32fa5df323496a5cbc7fb + md5: e2791c7a40004e031fd88e0995f4dc13 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbsurv", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-survival run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-survival test: diff --git a/recipes/bioconductor-rbwa/build.sh b/recipes/bioconductor-rbwa/build.sh index 9a888f987910c..578c85ee502d7 100644 --- a/recipes/bioconductor-rbwa/build.sh +++ b/recipes/bioconductor-rbwa/build.sh @@ -8,4 +8,4 @@ CXX=$CXX -I${PREFIX}/include -L${PREFIX}/lib CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rbwa/meta.yaml b/recipes/bioconductor-rbwa/meta.yaml index 374d5fce73c70..b777c8844fbd4 100644 --- a/recipes/bioconductor-rbwa/meta.yaml +++ b/recipes/bioconductor-rbwa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "Rbwa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fae3f23359b0d79625367cfb21ae2757 + md5: 036e0acc237e1249e5509df62d6c9968 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbwa", max_pin="x.x") }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown # SystemRequirements: GNU make requirements: @@ -40,4 +41,3 @@ about: summary: 'R wrapper for BWA-backtrack and BWA-MEM aligners' description: 'Provides an R wrapper for BWA alignment algorithms. Both BWA-backtrack and BWA-MEM are available. Convenience function to build a BWA index from a reference genome is also provided. Currently not supported for Windows machines.' license_file: LICENSE - diff --git a/recipes/bioconductor-rcas/meta.yaml b/recipes/bioconductor-rcas/meta.yaml index 007c19da31eb7..bfcfb29ffe1ef 100644 --- a/recipes/bioconductor-rcas/meta.yaml +++ b/recipes/bioconductor-rcas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.2" %} {% set name = "RCAS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af0a35923e6cd6eb176f8498cdf75951 + md5: 379c5b756cc12ca37913f7b51d8d29eb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcas", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, covr +# Suggests: testthat, covr, BiocManager # SystemRequirements: pandoc (>= 1.12.3) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomation >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomation >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-data.table @@ -51,17 +52,17 @@ requirements: - r-rsqlite - 'pandoc >=1.12.3' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomation >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomation >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-data.table diff --git a/recipes/bioconductor-rcaspar/meta.yaml b/recipes/bioconductor-rcaspar/meta.yaml index d6b239689a705..8d9c57743bd22 100644 --- a/recipes/bioconductor-rcaspar/meta.yaml +++ b/recipes/bioconductor-rcaspar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "RCASPAR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b3df5d1c22c9b55868fd054e5e07e516 + md5: 54a7734c80b26a4b0080fbdeb583af02 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcaspar", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-rcellminer/meta.yaml b/recipes/bioconductor-rcellminer/meta.yaml index ee2ba8cad5219..9ae4c09d89d57 100644 --- a/recipes/bioconductor-rcellminer/meta.yaml +++ b/recipes/bioconductor-rcellminer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "rcellminer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0c97d997df69e2442dfddc352db63d6e + md5: e74fd74daff68802d805b6bc0336499d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcellminer", max_pin="x.x") }}' noarch: generic # Suggests: knitr, RColorBrewer, sqldf, BiocGenerics, testthat, BiocStyle, jsonlite, heatmaply, glmnet, foreach, doSNOW, parallel, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-rcellminerdata >=2.22.0,<2.23.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-rcellminerdata >=2.24.0,<2.25.0' - r-base - r-ggplot2 - r-gplots - r-shiny - r-stringr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-rcellminerdata >=2.22.0,<2.23.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-rcellminerdata >=2.24.0,<2.25.0' - r-base - r-ggplot2 - r-gplots diff --git a/recipes/bioconductor-rcellminerdata/meta.yaml b/recipes/bioconductor-rcellminerdata/meta.yaml index 45c41b13a4544..6d0d65c26be67 100644 --- a/recipes/bioconductor-rcellminerdata/meta.yaml +++ b/recipes/bioconductor-rcellminerdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "rcellminerData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45f581dfcac9cd66a5cb2ca6f0706d7a + md5: 2f45852d4eeb438b6a1feb156200b2bc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcellminerdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, BiocStyle, rcellminer, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rcellminerdata/post-link.sh b/recipes/bioconductor-rcellminerdata/post-link.sh index db2270d4a5fbd..c6a6cbff8fe34 100644 --- a/recipes/bioconductor-rcellminerdata/post-link.sh +++ b/recipes/bioconductor-rcellminerdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rcellminerdata-2.22.0" +installBiocDataPackage.sh "rcellminerdata-2.24.0" diff --git a/recipes/bioconductor-rcgh/meta.yaml b/recipes/bioconductor-rcgh/meta.yaml index c94462cecac67..add2e2dfda8d6 100644 --- a/recipes/bioconductor-rcgh/meta.yaml +++ b/recipes/bioconductor-rcgh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "rCGH" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 517f6a662b4aa90862de3f26c5b48e10 + md5: 80510d5207fb0ad5d517a99b35734621 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcgh", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, BiocGenerics, RUnit requirements: host: - - 'bioconductor-acgh >=1.78.0,<1.79.0' - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-acgh >=1.80.0,<1.81.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-ggplot2 - r-lattice @@ -41,19 +42,19 @@ requirements: - r-plyr - 'r-shiny >=0.11.1' run: - - 'bioconductor-acgh >=1.78.0,<1.79.0' - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-acgh >=1.80.0,<1.81.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-ggplot2 - r-lattice diff --git a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml index b4de3e01687bd..b884d5531ab95 100644 --- a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml +++ b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RcisTarget.hg19.motifDBs.cisbpOnly.500bp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 74b4a09e41b8af5f638848ca86f3ec53 + md5: b8cdbfafeb9966332876fdf9be8dbb5a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp", max_pin="x.x") }}' noarch: generic requirements: host: @@ -26,7 +27,7 @@ requirements: - r-base - r-data.table - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh index 07379bec0ec86..6674b4221ffd9 100644 --- a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh +++ b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rcistarget.hg19.motifdbs.cisbponly.500bp-1.20.0" +installBiocDataPackage.sh "rcistarget.hg19.motifdbs.cisbponly.500bp-1.22.0" diff --git a/recipes/bioconductor-rcm/meta.yaml b/recipes/bioconductor-rcm/meta.yaml index 0bcfbcce34ece..78a7ec4e17ce7 100644 --- a/recipes/bioconductor-rcm/meta.yaml +++ b/recipes/bioconductor-rcm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "RCM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9be63e477e29d2fd363285ec9e89ea0b + md5: 2512426fe72a0dfede77816e98935ca1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcm", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-alabama - r-base - r-dbi @@ -35,8 +36,8 @@ requirements: - r-tseries - r-vgam run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-alabama - r-base - r-dbi diff --git a/recipes/bioconductor-rcollectl/meta.yaml b/recipes/bioconductor-rcollectl/meta.yaml index 3d0b3933b0e20..da65e37613492 100644 --- a/recipes/bioconductor-rcollectl/meta.yaml +++ b/recipes/bioconductor-rcollectl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "Rcollectl" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4eb21452f5d214449462f4a7d81b0b6 + md5: 855c39cf9aece9c63b3febc0c0d5654b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcollectl", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, knitcitations, sessioninfo, rmarkdown, testthat, covr # SystemRequirements: collectl diff --git a/recipes/bioconductor-rcpi/meta.yaml b/recipes/bioconductor-rcpi/meta.yaml index 2452d1d26bab5..5da588cf6c1df 100644 --- a/recipes/bioconductor-rcpi/meta.yaml +++ b/recipes/bioconductor-rcpi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.1" %} +{% set version = "1.38.0" %} {% set name = "Rcpi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1837722429b7d18ab4594197a3aeb350 + md5: 2f3697ca19200881f65d7d37f3d34e33 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcpi", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - r-base - r-doparallel - r-foreach @@ -30,8 +31,8 @@ requirements: - r-rjson - r-rlang run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-rcwl/meta.yaml b/recipes/bioconductor-rcwl/meta.yaml index 5d55d43dac0a0..fbd644f83afd4 100644 --- a/recipes/bioconductor-rcwl/meta.yaml +++ b/recipes/bioconductor-rcwl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Rcwl" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09262e7d3dc5c04ce919d8cebe9418a8 + md5: f427ee3f7f5ba2458f8f97b694b48a85 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcwl", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-batchtools - r-codetools @@ -32,9 +33,9 @@ requirements: - r-shiny - r-yaml run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-batchtools - r-codetools diff --git a/recipes/bioconductor-rcwlpipelines/build_failure.linux-64.yaml b/recipes/bioconductor-rcwlpipelines/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..6ae0fde6d9352 --- /dev/null +++ b/recipes/bioconductor-rcwlpipelines/build_failure.linux-64.yaml @@ -0,0 +1,61 @@ +recipe_sha: af004261d70c636e2d08ed30d7cbe6563df507346a88a94d377d6a64ee5d934a # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + package r-base-4.3.0-h0fc540b_0 requires icu >=72.1,<73.0a0, but none of the providers can be installed +category: |- + dependency issue +log: |- + 02:31:45 BIOCONDA INFO (OUT) RuntimeError: Solver could not find solution.Mamba failed to solve: + 02:31:45 BIOCONDA INFO (OUT) - r-base 4.3.* + 02:31:45 BIOCONDA INFO (OUT) - r-httr + 02:31:45 BIOCONDA INFO (OUT) - nodejs 14.* + 02:31:45 BIOCONDA INFO (OUT) - r-git2r + 02:31:45 BIOCONDA INFO (OUT) - bioconductor-s4vectors >=0.40.0,<0.41.0 + 02:31:45 BIOCONDA INFO (OUT) - r-rappdirs + 02:31:45 BIOCONDA INFO (OUT) - bioconductor-rcwl >=1.18.0,<1.19.0 + 02:31:45 BIOCONDA INFO (OUT) - bioconductor-biocfilecache >=2.10.0,<2.11.0 + 02:31:45 BIOCONDA INFO (OUT) + 02:31:45 BIOCONDA INFO (OUT) with channels: + 02:31:45 BIOCONDA INFO (OUT) - file:///opt/host-conda-bld + 02:31:45 BIOCONDA INFO (OUT) - conda-forge + 02:31:45 BIOCONDA INFO (OUT) - bioconda + 02:31:45 BIOCONDA INFO (OUT) - defaults + 02:31:45 BIOCONDA INFO (OUT) + 02:31:45 BIOCONDA INFO (OUT) The reported errors are: + 02:31:45 BIOCONDA INFO (OUT) - Encountered problems while solving: + 02:31:45 BIOCONDA INFO (OUT) - - package r-base-4.3.0-h0fc540b_0 requires icu >=72.1,<73.0a0, but none of the providers can be installed + 02:31:45 BIOCONDA INFO (OUT) - + 02:31:45 BIOCONDA INFO (OUT) + 02:31:45 BIOCONDA INFO (OUT) During handling of the above exception, another exception occurred: + 02:31:45 BIOCONDA INFO (OUT) + 02:31:45 BIOCONDA INFO (OUT) Traceback (most recent call last): + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/bin/conda-mambabuild", line 10, in + 02:31:45 BIOCONDA INFO (OUT) sys.exit(main()) + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + 02:31:45 BIOCONDA INFO (OUT) call_conda_build(action, config) + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + 02:31:45 BIOCONDA INFO (OUT) result = api.build( + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + 02:31:45 BIOCONDA INFO (OUT) return build_tree( + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + 02:31:45 BIOCONDA INFO (OUT) packages_from_this = build(metadata, stats, + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + 02:31:45 BIOCONDA INFO (OUT) output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + 02:31:45 BIOCONDA INFO (OUT) for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + 02:31:45 BIOCONDA INFO (OUT) conda_packages = finalize_outputs_pass( + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + 02:31:45 BIOCONDA INFO (OUT) fm = finalize_metadata( + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + 02:31:45 BIOCONDA INFO (OUT) build_unsat, host_unsat = add_upstream_pins(m, + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + 02:31:45 BIOCONDA INFO (OUT) host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + 02:31:45 BIOCONDA INFO (OUT) deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + 02:31:45 BIOCONDA INFO (OUT) actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + 02:31:45 BIOCONDA INFO (OUT) raise err + 02:31:45 BIOCONDA INFO (OUT) conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-base==4.3.0=h0fc540b_0"), MatchSpec("icu[version='>=72.1,<73.0a0']")} + diff --git a/recipes/bioconductor-rcwlpipelines/meta.yaml b/recipes/bioconductor-rcwlpipelines/meta.yaml index daa823b3014ed..f933217359628 100644 --- a/recipes/bioconductor-rcwlpipelines/meta.yaml +++ b/recipes/bioconductor-rcwlpipelines/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "RcwlPipelines" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c4531dad2b967b01fc7520ec5ad5e5d + md5: 5ff1c2848694b09cc639a56009392cf3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcwlpipelines", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle # SystemRequirements: nodejs requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-rcwl >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-rcwl >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-git2r - r-httr - r-rappdirs - - nodejs >=18 + - nodejs run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-rcwl >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-rcwl >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-git2r - r-httr - r-rappdirs - - nodejs >=18 + - nodejs test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rcx/meta.yaml b/recipes/bioconductor-rcx/meta.yaml index 50e3dbc1a19f1..63f9f80394e5d 100644 --- a/recipes/bioconductor-rcx/meta.yaml +++ b/recipes/bioconductor-rcx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "RCX" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04d1a91c0621fd0704b6653244ebc5e9 + md5: 4fdd9c350200e6854c3ed1db44572826 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcx", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown, base64enc, graph requirements: diff --git a/recipes/bioconductor-rcy3/meta.yaml b/recipes/bioconductor-rcy3/meta.yaml index ba7877a398d7a..e0c575aaae226 100644 --- a/recipes/bioconductor-rcy3/meta.yaml +++ b/recipes/bioconductor-rcy3/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.1" %} {% set name = "RCy3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a92632aee8b33ce6fb02007d5185e9d + md5: d4f51eaf382ede111f69aefd2660e383 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcy3", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, igraph, grDevices # SystemRequirements: Cytoscape (>= 3.7.1), CyREST (>= 3.8.0) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-base64enc - r-base64url @@ -36,13 +37,13 @@ requirements: - r-rcolorbrewer - r-rcurl - r-rjsonio - - r-uchardet + - r-stringi - r-uuid - r-xml - 'cytoscape >=3.7.1' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-base64enc - r-base64url @@ -55,7 +56,7 @@ requirements: - r-rcolorbrewer - r-rcurl - r-rjsonio - - r-uchardet + - r-stringi - r-uuid - r-xml - 'cytoscape >=3.7.1' diff --git a/recipes/bioconductor-rcyjs/meta.yaml b/recipes/bioconductor-rcyjs/meta.yaml index f6398c9c572c1..d1b93b6a7c224 100644 --- a/recipes/bioconductor-rcyjs/meta.yaml +++ b/recipes/bioconductor-rcyjs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "RCyjs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 17cff1b9dd82ea88c53dab0026483a8b + md5: b02526ea0ff36d61fdac395633bc4a4d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcyjs", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-browserviz >=2.22.0,<2.23.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-browserviz >=2.24.0,<2.25.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-base64enc - 'r-httpuv >=1.5.0' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-browserviz >=2.22.0,<2.23.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-browserviz >=2.24.0,<2.25.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-base64enc - 'r-httpuv >=1.5.0' diff --git a/recipes/bioconductor-rdgidb/meta.yaml b/recipes/bioconductor-rdgidb/meta.yaml index 8a80f191c2fba..60e0aeffac71e 100644 --- a/recipes/bioconductor-rdgidb/meta.yaml +++ b/recipes/bioconductor-rdgidb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "rDGIdb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2c908760f3b9a2722fc61aa3e3f02085 + md5: 5f3f78a4035bbb5597811f38c68b8e4f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rdgidb", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle,knitr,testthat requirements: diff --git a/recipes/bioconductor-rdisop/meta.yaml b/recipes/bioconductor-rdisop/meta.yaml index b513069f63ddb..a2c7a9d73dcd3 100644 --- a/recipes/bioconductor-rdisop/meta.yaml +++ b/recipes/bioconductor-rdisop/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "Rdisop" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 601cefd4030ddf03d7160eafbd882d58 + md5: 508c96aaea70daa872ec75712570f6da build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rdisop", max_pin="x.x") }}' # Suggests: RUnit # SystemRequirements: None requirements: diff --git a/recipes/bioconductor-rdrtoolbox/meta.yaml b/recipes/bioconductor-rdrtoolbox/meta.yaml index 985fed010963b..8cf36b1c8d51c 100644 --- a/recipes/bioconductor-rdrtoolbox/meta.yaml +++ b/recipes/bioconductor-rdrtoolbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "RDRToolbox" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fa5250922a670612beb7076f719c5eec + md5: 4b0e59a1ea48dd51e11d8d18666cf2d4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rdrtoolbox", max_pin="x.x") }}' noarch: generic # Suggests: golubEsets requirements: diff --git a/recipes/bioconductor-reactome.db/meta.yaml b/recipes/bioconductor-reactome.db/meta.yaml index 298a51b995f7e..242822e8bae25 100644 --- a/recipes/bioconductor-reactome.db/meta.yaml +++ b/recipes/bioconductor-reactome.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.84.0" %} +{% set version = "1.86.2" %} {% set name = "reactome.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ce62dbac370a30e260d8e45891939693 + md5: ff56f3908b347cb18e3e4ccedf7f584e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reactome.db", max_pin="x.x") }}' noarch: generic # Suggests: RSQLite requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +36,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: 'CC BY 4.0' summary: 'A set of annotation maps for reactome' - description: 'A set of annotation maps for reactome assembled using data from reactome' + description: 'A set of annotation maps for reactome assembled using data from reactome. This package has been created by a third-party developer, and is not affiliated with the Reactome team.' extra: parent_recipe: name: bioconductor-reactome.db diff --git a/recipes/bioconductor-reactome.db/post-link.sh b/recipes/bioconductor-reactome.db/post-link.sh index 876c20ee8f1c5..505cfbf3b984f 100644 --- a/recipes/bioconductor-reactome.db/post-link.sh +++ b/recipes/bioconductor-reactome.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "reactome.db-1.84.0" +installBiocDataPackage.sh "reactome.db-1.86.2" diff --git a/recipes/bioconductor-reactomecontentservice4r/meta.yaml b/recipes/bioconductor-reactomecontentservice4r/meta.yaml index 79c1cafcbf884..6e385b59f6091 100644 --- a/recipes/bioconductor-reactomecontentservice4r/meta.yaml +++ b/recipes/bioconductor-reactomecontentservice4r/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ReactomeContentService4R" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 50dd55d0d0765fb797dac403502775cf + md5: 3ec9de10a86259a6aae5308f6dfc0fa4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reactomecontentservice4r", max_pin="x.x") }}' noarch: generic # Suggests: pdftools, testthat, knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-reactomegraph4r/meta.yaml b/recipes/bioconductor-reactomegraph4r/meta.yaml index 082f8e215f520..3ae2c6b087f58 100644 --- a/recipes/bioconductor-reactomegraph4r/meta.yaml +++ b/recipes/bioconductor-reactomegraph4r/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ReactomeGraph4R" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4501886646fb5b54869a77a3456db1a5 + md5: 47a818d1c6d25db90a547d315d1189e8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reactomegraph4r", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, stringr, networkD3, visNetwork, wesanderson requirements: host: - - 'bioconductor-reactomecontentservice4r >=1.8.0,<1.9.0' + - 'bioconductor-reactomecontentservice4r >=1.10.0,<1.11.0' - r-base - r-data.table - r-doparallel @@ -33,7 +34,7 @@ requirements: - r-purrr - r-rlang run: - - 'bioconductor-reactomecontentservice4r >=1.8.0,<1.9.0' + - 'bioconductor-reactomecontentservice4r >=1.10.0,<1.11.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-reactomegsa.data/meta.yaml b/recipes/bioconductor-reactomegsa.data/meta.yaml index 33d4444292b5a..bec7f216b21da 100644 --- a/recipes/bioconductor-reactomegsa.data/meta.yaml +++ b/recipes/bioconductor-reactomegsa.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.1" %} {% set name = "ReactomeGSA.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c6b8b4eeacfc2f316c8c0aa021938f1 + md5: bd236d4d4078f99ea5d473fde1ff065f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reactomegsa.data", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-reactomegsa >=1.14.0,<1.15.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-reactomegsa >=1.16.0,<1.17.0' - r-base - r-seurat run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-reactomegsa >=1.14.0,<1.15.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-reactomegsa >=1.16.0,<1.17.0' - r-base - r-seurat - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-reactomegsa.data/post-link.sh b/recipes/bioconductor-reactomegsa.data/post-link.sh index 8712bc92d4982..7105dd31e819c 100644 --- a/recipes/bioconductor-reactomegsa.data/post-link.sh +++ b/recipes/bioconductor-reactomegsa.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "reactomegsa.data-1.14.0" +installBiocDataPackage.sh "reactomegsa.data-1.16.1" diff --git a/recipes/bioconductor-reactomegsa/meta.yaml b/recipes/bioconductor-reactomegsa/meta.yaml index 3e7ec0c8fb08d..eca696e84304c 100644 --- a/recipes/bioconductor-reactomegsa/meta.yaml +++ b/recipes/bioconductor-reactomegsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.1" %} {% set name = "ReactomeGSA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ceb80478cd55d9675e6d0a6093023cab + md5: c4ef9b68baf6957b7a3abf38bd4ffb39 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reactomegsa", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, ReactomeGSA.data, Biobase, devtools requirements: diff --git a/recipes/bioconductor-reactomepa/meta.yaml b/recipes/bioconductor-reactomepa/meta.yaml index 22181302d424b..7157cb19579aa 100644 --- a/recipes/bioconductor-reactomepa/meta.yaml +++ b/recipes/bioconductor-reactomepa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "ReactomePA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4f827baf24cebacfc6d5960d8639ada5 + md5: c31f563d1848fd0bafdbedb6b7f9bb66 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reactomepa", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, clusterProfiler, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - r-base - 'r-ggplot2 >=3.3.5' - r-ggraph - r-gson - r-igraph run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - r-base - 'r-ggplot2 >=3.3.5' - r-ggraph diff --git a/recipes/bioconductor-readqpcr/meta.yaml b/recipes/bioconductor-readqpcr/meta.yaml index 90b685245eff9..999355ab15670 100644 --- a/recipes/bioconductor-readqpcr/meta.yaml +++ b/recipes/bioconductor-readqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "ReadqPCR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8b34a2498b00f76095ad92c8ccc11eb + md5: b92a0fe88b39abffbc0c46c36a76a8de build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-readqpcr", max_pin="x.x") }}' noarch: generic # Suggests: qpcR requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-rebet/meta.yaml b/recipes/bioconductor-rebet/meta.yaml index ab5de905c1863..8771d5bd544a0 100644 --- a/recipes/bioconductor-rebet/meta.yaml +++ b/recipes/bioconductor-rebet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "REBET" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d7dc401e0d069b5ab67336904d617402 + md5: fc1e4bc02e112473630da74fce831189 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rebet", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-asset >=2.18.0,<2.19.0' + - 'bioconductor-asset >=2.20.0,<2.21.0' - r-base - libblas - liblapack run: - - 'bioconductor-asset >=2.18.0,<2.19.0' + - 'bioconductor-asset >=2.20.0,<2.21.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-rebook/meta.yaml b/recipes/bioconductor-rebook/meta.yaml index 189c783a94af4..8ea103b7b63c5 100644 --- a/recipes/bioconductor-rebook/meta.yaml +++ b/recipes/bioconductor-rebook/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "rebook" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b71e3b95cce07920b7ce27a330f581ff + md5: 05a8502e7f25563382e9e277b3199339 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rebook", max_pin="x.x") }}' noarch: generic # Suggests: testthat, igraph, XML, BiocManager, RCurl, bookdown, rappdirs, yaml, BiocParallel, OSCA.intro, OSCA.workflows requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-dir.expiry >=1.8.0,<1.9.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-dir.expiry >=1.10.0,<1.11.0' - r-base - r-codedepends - r-filelock - 'r-knitr >=1.32' - r-rmarkdown run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-dir.expiry >=1.8.0,<1.9.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-dir.expiry >=1.10.0,<1.11.0' - r-base - r-codedepends - r-filelock diff --git a/recipes/bioconductor-receptloss/meta.yaml b/recipes/bioconductor-receptloss/meta.yaml index 55a5cd3f1fc37..1dd994f66fc91 100644 --- a/recipes/bioconductor-receptloss/meta.yaml +++ b/recipes/bioconductor-receptloss/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "receptLoss" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45eb200329852f199e2ccd81408799c5 + md5: 3ccddd0181e8b78b843807d1378f86ef build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-receptloss", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 2.1.0), here requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 - r-magrittr - r-tidyr run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-reconsi/meta.yaml b/recipes/bioconductor-reconsi/meta.yaml index c85ae3b34f3a1..7157b2fd15860 100644 --- a/recipes/bioconductor-reconsi/meta.yaml +++ b/recipes/bioconductor-reconsi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "reconsi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bf6ff0103385ff01c60c0a0267fc24c1 + md5: 884019da85885289094a2aed95d18314 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reconsi", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-ggplot2 - r-ks @@ -29,7 +30,7 @@ requirements: - r-matrixstats - r-reshape2 run: - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-ggplot2 - r-ks diff --git a/recipes/bioconductor-recount/meta.yaml b/recipes/bioconductor-recount/meta.yaml index 020e059f3a9ae..d016fb257b38b 100644 --- a/recipes/bioconductor-recount/meta.yaml +++ b/recipes/bioconductor-recount/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "recount" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7dd19c0ea4ada1a5389c83cd7ad24641 + md5: 80d2f08ec7c30f139b1967db7cd07f7c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-recount", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi, BiocManager, BiocStyle (>= 2.5.19), DESeq2, sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures, knitr (>= 1.6), org.Hs.eg.db, RefManageR, regionReport (>= 1.9.4), rmarkdown (>= 0.9.5), testthat (>= 2.1.0), covr, pheatmap, DT, edgeR, ggplot2, RColorBrewer requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-downloader - r-rcurl - r-rentrez run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-downloader - r-rcurl diff --git a/recipes/bioconductor-recount3/meta.yaml b/recipes/bioconductor-recount3/meta.yaml index f8614bbd6239a..4acc5addbf239 100644 --- a/recipes/bioconductor-recount3/meta.yaml +++ b/recipes/bioconductor-recount3/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.2" %} +{% set version = "1.12.0" %} {% set name = "recount3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e914f149ed1771b7e03d34b66d9379c7 + md5: 0e3b0229faa614fbbc49547e44b342d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-recount3", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, knitcitations, knitr, RefManageR, rmarkdown, testthat, pryr, interactiveDisplayBase, recount requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-httr @@ -33,11 +34,11 @@ requirements: - r-r.utils - r-sessioninfo run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-httr diff --git a/recipes/bioconductor-recountmethylation/meta.yaml b/recipes/bioconductor-recountmethylation/meta.yaml index 190a95ddd4d17..8270e20eb93ab 100644 --- a/recipes/bioconductor-recountmethylation/meta.yaml +++ b/recipes/bioconductor-recountmethylation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "recountmethylation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7d8ce3ec6caee2a883704ba14921a753 + md5: 56d6b1dcb581c96c3ee93c4def178a1c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-recountmethylation", max_pin="x.x") }}' noarch: generic -# Suggests: minfiData, knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub +# Suggests: minfiData, minfiDataEPIC, knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-r.utils - r-rcurl - r-reticulate run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-r.utils - r-rcurl diff --git a/recipes/bioconductor-recoup/meta.yaml b/recipes/bioconductor-recoup/meta.yaml index 7afbda57cf0b1..3d9060186612c 100644 --- a/recipes/bioconductor-recoup/meta.yaml +++ b/recipes/bioconductor-recoup/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "recoup" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 43f3f62872c4b637d75c9ebeb37831b9 + md5: 021e00a6ca090381be16bf88e12eef05 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-recoup", max_pin="x.x") }}' noarch: generic # Suggests: grid, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager, BSgenome, RMySQL requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-circlize - r-ggplot2 @@ -40,18 +41,18 @@ requirements: - r-rsqlite - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-circlize - r-ggplot2 diff --git a/recipes/bioconductor-reder/meta.yaml b/recipes/bioconductor-reder/meta.yaml index 6b1d9b412d1a2..f41f96e824ee1 100644 --- a/recipes/bioconductor-reder/meta.yaml +++ b/recipes/bioconductor-reder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.1" %} +{% set version = "2.6.0" %} {% set name = "RedeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 456d8535d228fd0767c9bcae10dea8c5 + md5: 033b5763d95dc222256a4ef85b7e3a99 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reder", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, markdown, TreeAndLeaf # SystemRequirements: Java Runtime Environment (Java>= 11) diff --git a/recipes/bioconductor-redisparam/meta.yaml b/recipes/bioconductor-redisparam/meta.yaml index e27ff9b17ddc6..1ae122c83be0f 100644 --- a/recipes/bioconductor-redisparam/meta.yaml +++ b/recipes/bioconductor-redisparam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "RedisParam" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5149581ff1eb737d62129ff61417385c + md5: cf24018f96bc9de6286d2806dfd7bfaa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-redisparam", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat, BiocStyle # SystemRequirements: hiredis requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-futile.logger - r-redux - r-withr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-futile.logger - r-redux diff --git a/recipes/bioconductor-redseq/meta.yaml b/recipes/bioconductor-redseq/meta.yaml index aeb8f861a45bb..452649f180224 100644 --- a/recipes/bioconductor-redseq/meta.yaml +++ b/recipes/bioconductor-redseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "REDseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e9534df4cbe43b5e8681406ff2b3e163 + md5: f20e437ad9c48683bdaeda1825f87f85 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-redseq", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.celegans.ucsc.ce2 >=1.4.0,<1.5.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.celegans.ucsc.ce2 >=1.4.0,<1.5.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-regionalpcs/build.sh b/recipes/bioconductor-regionalpcs/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-regionalpcs/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-regionalpcs/meta.yaml b/recipes/bioconductor-regionalpcs/meta.yaml new file mode 100644 index 0000000000000..dfc7d8dcc70b5 --- /dev/null +++ b/recipes/bioconductor-regionalpcs/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.0.0" %} +{% set name = "regionalpcs" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 37f0fc1370efacc719f72b419455096a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-regionalpcs", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, RMTstat, testthat (>= 3.0.0), BiocStyle, tidyr, minfiData, TxDb.Hsapiens.UCSC.hg19.knownGene, IRanges +requirements: + host: + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-pcatools >=2.14.0,<2.15.0' + - r-base + - r-dplyr + - r-tibble + run: + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-pcatools >=2.14.0,<2.15.0' + - r-base + - r-dplyr + - r-tibble +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Summarizing Regional Methylation with Regional Principal Components Analysis' + description: 'Functions to summarize DNA methylation data using regional principal components. Regional principal components are computed using principal components analysis within genomic regions to summarize the variability in methylation levels across CpGs. The number of principal components is chosen using either the Marcenko-Pasteur or Gavish-Donoho method to identify relevant signal in the data.' + license_file: LICENSE + diff --git a/recipes/bioconductor-regionalst/build.sh b/recipes/bioconductor-regionalst/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-regionalst/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-regionalst/meta.yaml b/recipes/bioconductor-regionalst/meta.yaml new file mode 100644 index 0000000000000..014618ed68bf1 --- /dev/null +++ b/recipes/bioconductor-regionalst/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.0.1" %} +{% set name = "RegionalST" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d9589bef7f1408c77dee510baa14b4ad +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-regionalst", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, gplots, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-bayesspace >=1.12.0,<1.13.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-toast >=1.16.0,<1.17.0' + - r-assertthat + - r-base + - r-colorspace + - r-dplyr + - r-ggplot2 + - r-gridextra + - r-magrittr + - r-rcolorbrewer + - r-seurat + - r-shiny + - r-tibble + run: + - 'bioconductor-bayesspace >=1.12.0,<1.13.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-toast >=1.16.0,<1.17.0' + - r-assertthat + - r-base + - r-colorspace + - r-dplyr + - r-ggplot2 + - r-gridextra + - r-magrittr + - r-rcolorbrewer + - r-seurat + - r-shiny + - r-tibble +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Investigating regions of interest and performing cross-regional analysis with spatial transcriptomics data' + description: 'This package analyze spatial transcriptomics data through cross-regional analysis. It selects regions of interest (ROIs) and identifys cross-regional cell type-specific differential signals. The ROIs can be selected using automatic algorithm or through manual selection. It facilitates manual selection of ROIs using a shiny application.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-regioner/meta.yaml b/recipes/bioconductor-regioner/meta.yaml index 266bf8254d054..0b0d546a5ab73 100644 --- a/recipes/bioconductor-regioner/meta.yaml +++ b/recipes/bioconductor-regioner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "regioneR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f7f3f5515755c14cc156c8c3b1e0789 + md5: c2a9b6e46aa1aded948991c482cbf8a1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-regioner", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19.masked, testthat requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-memoise run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-memoise test: diff --git a/recipes/bioconductor-regionereloaded/meta.yaml b/recipes/bioconductor-regionereloaded/meta.yaml index c4e42ad969a11..c7131511ca7c5 100644 --- a/recipes/bioconductor-regionereloaded/meta.yaml +++ b/recipes/bioconductor-regionereloaded/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "regioneReloaded" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a2357349974289f47a26a0d3c30dabb5 + md5: 38175e4bcc9ccb951f79fca8238897b2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-regionereloaded", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, BiocStyle, GenomeInfoDb, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-regioner >=1.32.0,<1.33.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' - r-base - r-cluster - r-ggplot2 @@ -32,7 +33,7 @@ requirements: - r-scales - r-umap run: - - 'bioconductor-regioner >=1.32.0,<1.33.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' - r-base - r-cluster - r-ggplot2 diff --git a/recipes/bioconductor-regionreport/meta.yaml b/recipes/bioconductor-regionreport/meta.yaml index 2a041519f0dd4..2b14e31961044 100644 --- a/recipes/bioconductor-regionreport/meta.yaml +++ b/recipes/bioconductor-regionreport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "regionReport" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3bbf529af46b5340193184f866cb4721 + md5: 8ec5fb1e7db2235d543b2a9a6660a3b3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-regionreport", max_pin="x.x") }}' noarch: generic # Suggests: BiocManager, biovizBase, bumphunter (>= 1.7.6), derfinderPlot (>= 1.29.1), sessioninfo, DT, edgeR, ggbio (>= 1.35.2), ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-deformats >=1.28.0,<1.29.0' - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-deformats >=1.30.0,<1.31.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-knitr >=1.6' - 'r-knitrbootstrap >=0.9.0' - r-refmanager - 'r-rmarkdown >=0.9.5' run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-deformats >=1.28.0,<1.29.0' - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-deformats >=1.30.0,<1.31.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-knitr >=1.6' - 'r-knitrbootstrap >=0.9.0' diff --git a/recipes/bioconductor-regparallel/meta.yaml b/recipes/bioconductor-regparallel/meta.yaml index 64ec9f3fe8745..c057ce329d0b4 100644 --- a/recipes/bioconductor-regparallel/meta.yaml +++ b/recipes/bioconductor-regparallel/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "RegParallel" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ac6ed5e19a8dcfe359e97ccf89949dd1 + md5: 68533561edc82ac22088ffdd6e988aad build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-regparallel", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, DESeq2, airway, magrittr, Biobase, GEOquery, biomaRt, survminer, survey, rmarkdown requirements: @@ -39,7 +40,7 @@ requirements: - r-stringr - r-survival - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-regparallel/post-link.sh b/recipes/bioconductor-regparallel/post-link.sh index 647e5431ffe5e..72bade8afac71 100644 --- a/recipes/bioconductor-regparallel/post-link.sh +++ b/recipes/bioconductor-regparallel/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "regparallel-1.18.0" +installBiocDataPackage.sh "regparallel-1.20.0" diff --git a/recipes/bioconductor-regsplice/meta.yaml b/recipes/bioconductor-regsplice/meta.yaml index 5b0e0e6806a81..4c0ad8ce56a86 100644 --- a/recipes/bioconductor-regsplice/meta.yaml +++ b/recipes/bioconductor-regsplice/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "regsplice" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 710fabf735b71d3a00303d4e53d57ce0 + md5: 3f63d2e93b02aec3ed044e2c56938d12 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-regsplice", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-glmnet - r-pbapply run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-glmnet - r-pbapply diff --git a/recipes/bioconductor-regutools/meta.yaml b/recipes/bioconductor-regutools/meta.yaml index a341f9c3a2139..84af8fe9dc688 100644 --- a/recipes/bioconductor-regutools/meta.yaml +++ b/recipes/bioconductor-regutools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "regutools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0f21e48a748b216be4eb31d3d6646185 + md5: f8b22dfa98af4304de7be1654159626a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-regutools", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 2.1.0), covr requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-rsqlite diff --git a/recipes/bioconductor-remp/meta.yaml b/recipes/bioconductor-remp/meta.yaml index 527302ae3737b..d8706ceaf727c 100644 --- a/recipes/bioconductor-remp/meta.yaml +++ b/recipes/bioconductor-remp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "REMP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f922355791b56e6db96c5fc289f60e76 + md5: ee8e5abfbef5fc5798de790cacbe2cfe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-remp", max_pin="x.x") }}' noarch: generic # Suggests: IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, minfiDataEPIC requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-caret - r-doparallel @@ -45,20 +46,20 @@ requirements: - r-readr - r-settings run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-caret - r-doparallel diff --git a/recipes/bioconductor-repitools/meta.yaml b/recipes/bioconductor-repitools/meta.yaml index 90256ba30f818..c78c6b1bf1018 100644 --- a/recipes/bioconductor-repitools/meta.yaml +++ b/recipes/bioconductor-repitools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "Repitools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 614a2e515290ab172e482b38aefcf07c + md5: 3388cac60efdea157e1975abc5dcccd2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-repitools", max_pin="x.x") }}' # Suggests: ShortRead, BSgenome.Hsapiens.UCSC.hg18 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-ringo >=1.64.0,<1.65.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-ringo >=1.66.0,<1.67.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-gplots @@ -42,19 +43,19 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-ringo >=1.64.0,<1.65.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-ringo >=1.66.0,<1.67.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-gplots diff --git a/recipes/bioconductor-reportingtools/meta.yaml b/recipes/bioconductor-reportingtools/meta.yaml index cd3ada7e1ae4b..c00a0944d468c 100644 --- a/recipes/bioconductor-reportingtools/meta.yaml +++ b/recipes/bioconductor-reportingtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.39.0" %} +{% set version = "2.42.2" %} {% set name = "ReportingTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9d17684737cbd651051b60339872967f + md5: 5f5adbf6b8570e232b9f3e98f75eab59 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reportingtools", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla, org.Sc.sgd.db, rmarkdown, markdown requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pfam.db >=3.17.0,<3.18.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pfam.db >=3.18.0,<3.19.0' - r-base - r-ggplot2 - r-hwriter @@ -42,19 +43,19 @@ requirements: - r-r.utils - r-xml run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pfam.db >=3.17.0,<3.18.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pfam.db >=3.18.0,<3.19.0' - r-base - r-ggplot2 - r-hwriter diff --git a/recipes/bioconductor-repviz/meta.yaml b/recipes/bioconductor-repviz/meta.yaml index 284380aa6d46a..eb6ecad3257e6 100644 --- a/recipes/bioconductor-repviz/meta.yaml +++ b/recipes/bioconductor-repviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "RepViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 299815c83d5eeba7e716951e52b4f767 + md5: a740655d18448d4fb24e37ff1c60820d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-repviz", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-reqon/meta.yaml b/recipes/bioconductor-reqon/meta.yaml index 0c703203847d4..b0abd687e3d96 100644 --- a/recipes/bioconductor-reqon/meta.yaml +++ b/recipes/bioconductor-reqon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "ReQON" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa89144c5794fee3c455972783956d63 + md5: 3940db44a4b48a5b04d87c9466df72c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reqon", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle # SystemRequirements: Java version >= 1.6 requirements: host: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-seqbias >=1.48.0,<1.49.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-seqbias >=1.50.0,<1.51.0' - r-base - r-rjava - openjdk run: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-seqbias >=1.48.0,<1.49.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-seqbias >=1.50.0,<1.51.0' - r-base - r-rjava - openjdk diff --git a/recipes/bioconductor-residualmatrix/meta.yaml b/recipes/bioconductor-residualmatrix/meta.yaml index 9dd8341117bf8..aa7ea294a226e 100644 --- a/recipes/bioconductor-residualmatrix/meta.yaml +++ b/recipes/bioconductor-residualmatrix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ResidualMatrix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7d4291731f44ec7111ac14306ce53f18 + md5: 76eaee4311380f83265d9b5ecacd7e49 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-residualmatrix", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-resolve/meta.yaml b/recipes/bioconductor-resolve/meta.yaml index 353621ed4826b..3f516a9501e1f 100644 --- a/recipes/bioconductor-resolve/meta.yaml +++ b/recipes/bioconductor-resolve/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "RESOLVE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 090d75906aa025a56311fe6092ad8356 + md5: 3dd3a656ed19f5faa759f4b37c459f53 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-resolve", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, testthat, knitr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.1000genomes.hs37d5 >=0.99.0,<0.100.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mutationalpatterns >=3.10.0,<3.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mutationalpatterns >=3.12.0,<3.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-ggplot2 @@ -38,14 +39,14 @@ requirements: - r-nnls - r-reshape2 run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.1000genomes.hs37d5 >=0.99.0,<0.100.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mutationalpatterns >=3.10.0,<3.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mutationalpatterns >=3.12.0,<3.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-restfulse/meta.yaml b/recipes/bioconductor-restfulse/meta.yaml index 7ce223f2c7b79..952a18777ff3c 100644 --- a/recipes/bioconductor-restfulse/meta.yaml +++ b/recipes/bioconductor-restfulse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "restfulSE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b746d7b3033fbb1c539462dfb1a5981a + md5: 80c91d615f5ff4997fce69087d3ea106 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-restfulse", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, Rtsne, org.Mm.eg.db, org.Hs.eg.db, BiocStyle, restfulSEData, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-rhdf5client >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-rhdf5client >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bigrquery - r-dbi @@ -38,15 +39,15 @@ requirements: - r-reshape2 - r-rlang run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-rhdf5client >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-rhdf5client >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bigrquery - r-dbi diff --git a/recipes/bioconductor-restfulsedata/meta.yaml b/recipes/bioconductor-restfulsedata/meta.yaml index ea8b5003020a0..8e3b21dac9c8d 100644 --- a/recipes/bioconductor-restfulsedata/meta.yaml +++ b/recipes/bioconductor-restfulsedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "restfulSEData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e92deb8a55a329887e87c9d4520e4b9e + md5: c69fe04b8675edd0faa593fb5ffc72c8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-restfulsedata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, rhdf5client requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-restfulsedata/post-link.sh b/recipes/bioconductor-restfulsedata/post-link.sh index 4242d77395d84..08150a2be497b 100644 --- a/recipes/bioconductor-restfulsedata/post-link.sh +++ b/recipes/bioconductor-restfulsedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "restfulsedata-1.22.1" +installBiocDataPackage.sh "restfulsedata-1.24.0" diff --git a/recipes/bioconductor-retrofit/meta.yaml b/recipes/bioconductor-retrofit/meta.yaml index ea56377150869..82688026bb8d0 100644 --- a/recipes/bioconductor-retrofit/meta.yaml +++ b/recipes/bioconductor-retrofit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "retrofit" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5634b1f69b84d0477586d9cda2223903 + md5: 2b804a752a293f14495e94adb39df466 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-retrofit", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat, DescTools, ggplot2, corrplot, cowplot, grid, colorspace, png, reshape2, pals, RCurl requirements: host: diff --git a/recipes/bioconductor-reusedata/build_failure.linux-64.yaml b/recipes/bioconductor-reusedata/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..ecc86f7cff23e --- /dev/null +++ b/recipes/bioconductor-reusedata/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 1370555a597842bfc527b0664421636a289d7b039c85298dda7098e9b36ad0b9 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.0MB/s 0.0s + [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.0MB/s 0.0s + [?25hMamba failed to solve: + - bioconductor-basilisk >=1.14.0,<1.15.0 + - bioconductor-biocfilecache >=2.10.0,<2.11.0 + - bioconductor-rcwl >=1.18.0,<1.19.0 + - r-yaml + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - r-base 4.3.* + - bioconductor-rcwlpipelines >=1.18.0,<1.19.0 + - r-jsonlite + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-rcwlpipelines >=1.18.0,<1.19.0 + - + + Leaving build/test directories: + Work: + /opt/conda/conda-bld/work + Test: + /opt/conda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + Build: + source activate /opt/conda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - bioconductor-basilisk >=1.14.0,<1.15.0 + - bioconductor-biocfilecache >=2.10.0,<2.11.0 + - bioconductor-rcwl >=1.18.0,<1.19.0 + - r-yaml + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - r-base 4.3.* + - bioconductor-rcwlpipelines >=1.18.0,<1.19.0 + - r-jsonlite + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-rcwlpipelines >=1.18.0,<1.19.0 + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rcwlpipelines[version='>=1.18.0,<1.19.0']")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-reusedata/meta.yaml b/recipes/bioconductor-reusedata/meta.yaml index f45c8f9250f15..3e52defa7ad81 100644 --- a/recipes/bioconductor-reusedata/meta.yaml +++ b/recipes/bioconductor-reusedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.2" %} {% set name = "ReUseData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 93524bd7dc0a684ac5e2413f414197bd + md5: c0041ec5d810d0d043c7375e04e78c06 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reusedata", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, testthat (>= 3.0.0) +# Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-rcwl >=1.16.0,<1.17.0' - - 'bioconductor-rcwlpipelines >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-rcwl >=1.18.0,<1.19.0' + - 'bioconductor-rcwlpipelines >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-jsonlite - r-yaml run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-rcwl >=1.16.0,<1.17.0' - - 'bioconductor-rcwlpipelines >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-rcwl >=1.18.0,<1.19.0' + - 'bioconductor-rcwlpipelines >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-jsonlite - r-yaml diff --git a/recipes/bioconductor-rexposome/meta.yaml b/recipes/bioconductor-rexposome/meta.yaml index dbe866c47fb93..83b17e2db684f 100644 --- a/recipes/bioconductor-rexposome/meta.yaml +++ b/recipes/bioconductor-rexposome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.1" %} {% set name = "rexposome" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 46e7c4f67ccb5a1e7fc583d4eb36bb0f + md5: 5dec247e3db216fed87e97cbfbf254cc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rexposome", max_pin="x.x") }}' noarch: generic -# Suggests: mclust, flexmix, testthat, BiocStyle, knitr, rmarkdown +# Suggests: mclust, flexmix, testthat, BiocStyle, knitr, formatR, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-circlize - r-corrplot - r-factominer - r-ggplot2 - r-ggrepel + - r-ggridges - r-glmnet - r-gplots - r-gridextra @@ -44,14 +46,15 @@ requirements: - r-scatterplot3d - r-stringr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-circlize - r-corrplot - r-factominer - r-ggplot2 - r-ggrepel + - r-ggridges - r-glmnet - r-gplots - r-gridextra diff --git a/recipes/bioconductor-rfarm/meta.yaml b/recipes/bioconductor-rfarm/meta.yaml index 988866dc15b2d..0251337690723 100644 --- a/recipes/bioconductor-rfarm/meta.yaml +++ b/recipes/bioconductor-rfarm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.2" %} +{% set version = "1.14.0" %} {% set name = "rfaRm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f9f5b86baf2759fb096e5236b4ecacbd + md5: c12fb6805f6eecba196474a4527f241a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rfarm", max_pin="x.x") }}' noarch: generic -# Suggests: R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics +# Suggests: R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics, RUnit requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-httr + - r-jsonlite - r-magick - r-rsvg - r-rvest - r-stringi - r-xml2 run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-httr + - r-jsonlite - r-magick - r-rsvg - r-rvest diff --git a/recipes/bioconductor-rfastp/meta.yaml b/recipes/bioconductor-rfastp/meta.yaml index 6cd2d96a5df41..8acaaa9125710 100644 --- a/recipes/bioconductor-rfastp/meta.yaml +++ b/recipes/bioconductor-rfastp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "Rfastp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9dfcaf1b205d287c9af287d0b6e86f1b + md5: 9f6903cb485151c4d3c368abf5193309 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rfastp", max_pin="x.x") }}' # Suggests: BiocStyle, testthat, knitr, rmarkdown # SystemRequirements: GNU make requirements: host: - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-ggplot2 - r-rcpp @@ -31,8 +32,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-ggplot2 - r-rcpp diff --git a/recipes/bioconductor-rforproteomics/meta.yaml b/recipes/bioconductor-rforproteomics/meta.yaml index 258d0fdab9cb3..4a0c7b03f4d54 100644 --- a/recipes/bioconductor-rforproteomics/meta.yaml +++ b/recipes/bioconductor-rforproteomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.1" %} +{% set version = "1.40.0" %} {% set name = "RforProteomics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2dbad7c535bf6a39299cad51ede9aafd + md5: 6d75aedb5902ea26a18e39da6848db4c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rforproteomics", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi, rpx (>= 2.0.3), DT, knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData, Rdisop, OrgMassSpecR, SummarizedExperiment, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, e1071, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, MSnID, msmsTests, msmsEDA, DEP, corrplot, beanplot, Heatplus, gplots, VennDiagram, protViz, genefilter, plotly, gridExtra, dplyr, lubridate, magick, cleaver requirements: host: - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - r-biocmanager - r-r.utils run: - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - r-biocmanager - r-r.utils - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rforproteomics/post-link.sh b/recipes/bioconductor-rforproteomics/post-link.sh index a5c4558d939da..8efbae4b8ad53 100644 --- a/recipes/bioconductor-rforproteomics/post-link.sh +++ b/recipes/bioconductor-rforproteomics/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rforproteomics-1.38.1" +installBiocDataPackage.sh "rforproteomics-1.40.0" diff --git a/recipes/bioconductor-rfpred/meta.yaml b/recipes/bioconductor-rfpred/meta.yaml index 465baae9b458d..3c6bb3e73f786 100644 --- a/recipes/bioconductor-rfpred/meta.yaml +++ b/recipes/bioconductor-rfpred/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "rfPred" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 579bec97ce1052f870abdf8255c098b8 + md5: 125e88d593749d17979dfd08a67ea330 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rfpred", max_pin="x.x") }}' # Suggests: BiocStyle requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-data.table - libblas - liblapack run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-data.table build: diff --git a/recipes/bioconductor-rgadem/meta.yaml b/recipes/bioconductor-rgadem/meta.yaml index 0a01ce8e67e15..9ea5c84cd97c1 100644 --- a/recipes/bioconductor-rgadem/meta.yaml +++ b/recipes/bioconductor-rgadem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.48.0" %} +{% set version = "2.50.0" %} {% set name = "rGADEM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2cdce4776f91cfd938ce4930774c4b8a + md5: 17a121fa91f30cba09ed9dbb6b318555 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgadem", max_pin="x.x") }}' # Suggests: BSgenome.Hsapiens.UCSC.hg19, rtracklayer requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-rgenometracks/meta.yaml b/recipes/bioconductor-rgenometracks/meta.yaml index bfd570946be6d..56ab97b269241 100644 --- a/recipes/bioconductor-rgenometracks/meta.yaml +++ b/recipes/bioconductor-rgenometracks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "rGenomeTracks" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfd465d74676896a9198011488d2f167 + md5: 860c81f62e3abf51de44d4dcdcdbfeef build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgenometracks", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat (>= 3.0.0) # SystemRequirements: pyGenomeTracks (prefered to use install_pyGenomeTracks()) diff --git a/recipes/bioconductor-rgenometracksdata/meta.yaml b/recipes/bioconductor-rgenometracksdata/meta.yaml index a2e79700c4baa..f99c1c756acc0 100644 --- a/recipes/bioconductor-rgenometracksdata/meta.yaml +++ b/recipes/bioconductor-rgenometracksdata/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.0" %} {% set name = "rGenomeTracksData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 713103a8b4b4e48fa762ef589a43ffb8 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgenometracksdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocManager, devtools requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgmql/meta.yaml b/recipes/bioconductor-rgmql/meta.yaml index 94c7ab649c2b7..661ae8f96255e 100644 --- a/recipes/bioconductor-rgmql/meta.yaml +++ b/recipes/bioconductor-rgmql/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RGMQL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b8c068a6ec053a10f5651e97f405dd41 + md5: 78de1ecefadf0a7729bf7b62b50a2c1b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgmql", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rgmqllib >=1.20.0,<1.21.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rgmqllib >=1.22.0,<1.23.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr @@ -35,11 +36,11 @@ requirements: - r-rjava - r-xml2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rgmqllib >=1.20.0,<1.21.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rgmqllib >=1.22.0,<1.23.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-rgmqllib/meta.yaml b/recipes/bioconductor-rgmqllib/meta.yaml index d9b7f55fe7321..8807cc1353fdd 100644 --- a/recipes/bioconductor-rgmqllib/meta.yaml +++ b/recipes/bioconductor-rgmqllib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RGMQLlib" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a9153c4ade0f2149a136bdaefb123f6d + md5: d8ad27b1fe0c5eff6135285db972cab2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgmqllib", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgmqllib/post-link.sh b/recipes/bioconductor-rgmqllib/post-link.sh index d86d102653d10..1b73edc0605c1 100644 --- a/recipes/bioconductor-rgmqllib/post-link.sh +++ b/recipes/bioconductor-rgmqllib/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rgmqllib-1.20.0" +installBiocDataPackage.sh "rgmqllib-1.22.0" diff --git a/recipes/bioconductor-rgntx/meta.yaml b/recipes/bioconductor-rgntx/meta.yaml index db65eb48352f6..265575b96ae87 100644 --- a/recipes/bioconductor-rgntx/meta.yaml +++ b/recipes/bioconductor-rgntx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "RgnTX" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a49f7294a76c9678e892b9f575c9efd + md5: 4ce438a2822a6541467c9781a3c48b26 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgntx", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - r-ggplot2 run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - r-ggplot2 diff --git a/recipes/bioconductor-rgoslin/meta.yaml b/recipes/bioconductor-rgoslin/meta.yaml index 861b06ce8fdb8..ed8b1ed6bb203 100644 --- a/recipes/bioconductor-rgoslin/meta.yaml +++ b/recipes/bioconductor-rgoslin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "rgoslin" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5835d13bddd6f4b07f4f41da411bec20 + md5: 211ef77e63cc8394ebc5eee33328cd08 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgoslin", max_pin="x.x") }}' # Suggests: testthat (>= 2.1.0), BiocStyle, knitr, rmarkdown, kableExtra, BiocManager, stringr, stringi, ggplot2, tibble, lipidr requirements: host: diff --git a/recipes/bioconductor-rgraph2js/meta.yaml b/recipes/bioconductor-rgraph2js/meta.yaml index 6f0f850f1a585..0212b86e5dd86 100644 --- a/recipes/bioconductor-rgraph2js/meta.yaml +++ b/recipes/bioconductor-rgraph2js/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RGraph2js" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54578f3d4a51613dbc158bd4fafc3377 + md5: ccb2f26623270911ba855aa97e1269e1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgraph2js", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, BiocGenerics, xtable, sna # SystemRequirements: jQuery, jQueryUI, qTip2, D3js and Raphael are required Javascript libraries made available via the online CDNJS service (http://cdnjs.cloudflare.com). requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-digest - r-rjson - r-whisker - jquery run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-digest - r-rjson diff --git a/recipes/bioconductor-rgraphviz/meta.yaml b/recipes/bioconductor-rgraphviz/meta.yaml index b9045b863c929..d28bc09c5210b 100644 --- a/recipes/bioconductor-rgraphviz/meta.yaml +++ b/recipes/bioconductor-rgraphviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.44.0" %} +{% set version = "2.46.0" %} {% set name = "Rgraphviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d75a9db059a381ad08e88bf396be9e0 + md5: b93e5d1c383b1e5cd06e4dec89a43ce8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgraphviz", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics, XML # SystemRequirements: optionally Graphviz (>= 2.16) requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - libblas - liblapack run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-rgreat/meta.yaml b/recipes/bioconductor-rgreat/meta.yaml index 97c18c4b4c2a8..607172e832e2e 100644 --- a/recipes/bioconductor-rgreat/meta.yaml +++ b/recipes/bioconductor-rgreat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "rGREAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c4dba74b97e8ebb8e34ba72ae35e48dc + md5: 89ee57f3429887678846bba965ce84dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgreat", max_pin="x.x") }}' # Suggests: testthat (>= 0.3), knitr, rmarkdown, BiocManager, org.Mm.eg.db, msigdbr, KEGGREST, reactome.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-circlize - r-digest @@ -47,16 +48,16 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-circlize - r-digest diff --git a/recipes/bioconductor-rgsea/meta.yaml b/recipes/bioconductor-rgsea/meta.yaml index f31a86d27a77d..9042f59b32251 100644 --- a/recipes/bioconductor-rgsea/meta.yaml +++ b/recipes/bioconductor-rgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "RGSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3038e7d2181e5ece758f5f98a877c15 + md5: 426ab6d4dc463399d014c6e76c3f8c75 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgsea", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, GEOquery, knitr, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-rgsepd/meta.yaml b/recipes/bioconductor-rgsepd/meta.yaml index 3ede6367c46d0..c3b4954bb93cf 100644 --- a/recipes/bioconductor-rgsepd/meta.yaml +++ b/recipes/bioconductor-rgsepd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "rgsepd" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8ccc8627b86ca25b735319429fd56c2c + md5: 0ca30d2f68c98bcc24cc5c5fbc5951b3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgsepd", max_pin="x.x") }}' noarch: generic # Suggests: boot, tools, BiocGenerics, knitr, xtable requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-goseq >=1.52.0,<1.53.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-goseq >=1.54.0,<1.55.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-gplots run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-goseq >=1.52.0,<1.53.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-goseq >=1.54.0,<1.55.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-gplots test: diff --git a/recipes/bioconductor-rgu34a.db/meta.yaml b/recipes/bioconductor-rgu34a.db/meta.yaml index eeb53355f2cb0..460be188747cf 100644 --- a/recipes/bioconductor-rgu34a.db/meta.yaml +++ b/recipes/bioconductor-rgu34a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "rgu34a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e99dc4c05360b49a2249cb5de0b1dd4e build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgu34a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34acdf/meta.yaml b/recipes/bioconductor-rgu34acdf/meta.yaml index 28cf17672e23e..195b7856cd031 100644 --- a/recipes/bioconductor-rgu34acdf/meta.yaml +++ b/recipes/bioconductor-rgu34acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rgu34acdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dcfa7ecce00e529f93809759ed837b8d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgu34acdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34aprobe/meta.yaml b/recipes/bioconductor-rgu34aprobe/meta.yaml index 7e74747aa85c4..2e3ca3c13f057 100644 --- a/recipes/bioconductor-rgu34aprobe/meta.yaml +++ b/recipes/bioconductor-rgu34aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rgu34aprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 902aee259a2894fa8713c4bf9266c0e2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgu34aprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34b.db/meta.yaml b/recipes/bioconductor-rgu34b.db/meta.yaml index dfa15c3c3da20..2be3c456f72de 100644 --- a/recipes/bioconductor-rgu34b.db/meta.yaml +++ b/recipes/bioconductor-rgu34b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "rgu34b.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5aeb80d5190bf2dcffa6b9264d3db33f build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgu34b.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34bcdf/meta.yaml b/recipes/bioconductor-rgu34bcdf/meta.yaml index 8b4984130ab18..c49a72cd0134b 100644 --- a/recipes/bioconductor-rgu34bcdf/meta.yaml +++ b/recipes/bioconductor-rgu34bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rgu34bcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 428b3a39f0d8addd7d863539b8cda6ea build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgu34bcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34bprobe/meta.yaml b/recipes/bioconductor-rgu34bprobe/meta.yaml index f4e8278899c40..01e2a8f025744 100644 --- a/recipes/bioconductor-rgu34bprobe/meta.yaml +++ b/recipes/bioconductor-rgu34bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rgu34bprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2d6488309c5e54231a18e2ecf5608bb1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgu34bprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34c.db/meta.yaml b/recipes/bioconductor-rgu34c.db/meta.yaml index e558c4807edf5..61199d1900ac5 100644 --- a/recipes/bioconductor-rgu34c.db/meta.yaml +++ b/recipes/bioconductor-rgu34c.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "rgu34c.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e19f250869a9894bc9d069a4baf39a3c build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgu34c.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34ccdf/meta.yaml b/recipes/bioconductor-rgu34ccdf/meta.yaml index ba71a4c1c16f8..8360de7865875 100644 --- a/recipes/bioconductor-rgu34ccdf/meta.yaml +++ b/recipes/bioconductor-rgu34ccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rgu34ccdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 556a7130086004d26095594da31c6410 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgu34ccdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34cprobe/meta.yaml b/recipes/bioconductor-rgu34cprobe/meta.yaml index 32165588998fb..1d514934bc4ab 100644 --- a/recipes/bioconductor-rgu34cprobe/meta.yaml +++ b/recipes/bioconductor-rgu34cprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rgu34cprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d1a6c433acd30b95fa7be89147105b74 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgu34cprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rguatlas4k.db/meta.yaml b/recipes/bioconductor-rguatlas4k.db/meta.yaml index 620f460bdb39c..e8a0ab33ef629 100644 --- a/recipes/bioconductor-rguatlas4k.db/meta.yaml +++ b/recipes/bioconductor-rguatlas4k.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rguatlas4k.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6a360676e08319ec5465c47c758110bd build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rguatlas4k.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgug4105a.db/meta.yaml b/recipes/bioconductor-rgug4105a.db/meta.yaml index 3348d296af03d..856bf606c03aa 100644 --- a/recipes/bioconductor-rgug4105a.db/meta.yaml +++ b/recipes/bioconductor-rgug4105a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rgug4105a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3ccf354083ae36a7ae687fb8209c4e5b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgug4105a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgug4130a.db/meta.yaml b/recipes/bioconductor-rgug4130a.db/meta.yaml index 6440322352513..29321c986ab3a 100644 --- a/recipes/bioconductor-rgug4130a.db/meta.yaml +++ b/recipes/bioconductor-rgug4130a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rgug4130a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 13643ac109aaf12590a5b6e379609b79 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgug4130a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgug4131a.db/meta.yaml b/recipes/bioconductor-rgug4131a.db/meta.yaml index 22167eb35715e..1c64418da6bcc 100644 --- a/recipes/bioconductor-rgug4131a.db/meta.yaml +++ b/recipes/bioconductor-rgug4131a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rgug4131a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1168d4906fb8ce60cbc0fa6cfa3b8ec6 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgug4131a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index 22e76300066cf..7e644a64ce038 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -1,49 +1,43 @@ -{% set version = "2.44.0" %} +{% set version = "2.46.1" %} {% set name = "rhdf5" %} -{% set full_name = "bioconductor-" ~ name|lower %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: - name: '{{ full_name }}' + name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ full_name }}/{{ full_name }}_{{ version }}_src_all.tar.gz' - md5: 19c8340a70f1ce28043ba56bb9da1238 + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 947e662fe5f427ed0cc839e8049b431e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - run_exports: - # This pinning is preliminary. It should be changed if either: - # * a general policy for pinning bioconductor packages is decided and differs: - # https://github.com/bioconda/bioconda-recipes/issues/43905 - # * the author of this package assures us that he adheres to semantic - # versioning, in which case we can unpin the minor version, see: - # https://github.com/grimbough/rhdf5/issues/131#issuecomment-1782567153 - - {{ pin_subpackage(full_name, max_pin="x.x") }} + run_exports: '{{ pin_subpackage("bioconductor-rhdf5", max_pin="x.x") }}' # Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr, ggplot2, mockery, BiocParallel # SystemRequirements: GNU make requirements: - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make host: - - 'bioconductor-rhdf5filters >=1.12.0,<1.13.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' + - 'bioconductor-rhdf5filters >=1.14.0,<1.15.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - libblas - liblapack run: - - 'bioconductor-rhdf5filters >=1.12.0,<1.13.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' + - 'bioconductor-rhdf5filters >=1.14.0,<1.15.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -56,7 +50,7 @@ extra: identifiers: - biotools:rhdf5 parent_recipe: - name: '{{ full_name }}' - path: 'recipes/{{ full_name }}' + name: bioconductor-rhdf5 + path: recipes/bioconductor-rhdf5 version: 2.24.0 diff --git a/recipes/bioconductor-rhdf5client/meta.yaml b/recipes/bioconductor-rhdf5client/meta.yaml index 986ec5a995fa4..e9c92f1d8f081 100644 --- a/recipes/bioconductor-rhdf5client/meta.yaml +++ b/recipes/bioconductor-rhdf5client/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "rhdf5client" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fa6adb48f0ca8e63d458da7f96ae3a97 + md5: 9205b30177d59d75b7e544f795a90de5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rhdf5client", max_pin="x.x") }}' # Suggests: knitr, testthat, BiocStyle, DT, rmarkdown requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - r-base - r-data.table - r-httr @@ -28,7 +29,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - r-base - r-data.table - r-httr diff --git a/recipes/bioconductor-rhdf5filters/meta.yaml b/recipes/bioconductor-rhdf5filters/meta.yaml index 5b9f894ca93e7..8d776ef525662 100644 --- a/recipes/bioconductor-rhdf5filters/meta.yaml +++ b/recipes/bioconductor-rhdf5filters/meta.yaml @@ -1,47 +1,39 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.1" %} {% set name = "rhdf5filters" %} -{% set full_name = "bioconductor-" ~ name|lower %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: - name: '{{ full_name }}' + name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ full_name }}/{{ full_name }}_{{ version }}_src_all.tar.gz' - md5: 8cef74eea9c788b536c4561603f265b4 + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3ecb2d30759fee6bde37bbb1f90fbf79 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - run_exports: - # This pinning is preliminary. It should be changed if either: - # * a general policy for pinning bioconductor packages is decided and differs: - # https://github.com/bioconda/bioconda-recipes/issues/43905 - # * the author of this package assures us that he adheres to semantic - # versioning, in which case we can unpin the minor version, see: - # https://github.com/grimbough/rhdf5/issues/131#issuecomment-1782567153 - - {{ pin_subpackage(full_name, max_pin="x.x") }} + run_exports: '{{ pin_subpackage("bioconductor-rhdf5filters", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, tinytest, rhdf5 (>= 2.34.0) # SystemRequirements: GNU make requirements: - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make host: - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - r-base - libblas - liblapack run: - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rhdf5lib/meta.yaml b/recipes/bioconductor-rhdf5lib/meta.yaml index 16d7c44733a9d..0909d78d3986e 100644 --- a/recipes/bioconductor-rhdf5lib/meta.yaml +++ b/recipes/bioconductor-rhdf5lib/meta.yaml @@ -1,45 +1,36 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "Rhdf5lib" %} -{% set full_name = "bioconductor-" ~ name|lower %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: - name: '{{ full_name }}' + name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ full_name }}/{{ full_name }}_{{ version }}_src_all.tar.gz' - md5: 27c19bd24858ba26ff4762d41f3b2a16 + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 722160d55897324217ba8dc2cb60f3cd build: number: 1 rpaths: - lib/R/lib/ - lib/ - run_exports: - # This pinning is preliminary. It should be changed if either: - # * a general policy for pinning bioconductor packages is decided and differs: - # https://github.com/bioconda/bioconda-recipes/issues/43905 - # * the author of this package assures us that he adheres to semantic - # versioning, in which case we can unpin the minor version, see: - # https://github.com/grimbough/rhdf5/issues/131#issuecomment-1782567153 - - {{ pin_subpackage(full_name, max_pin="x.x") }} + run_exports: '{{ pin_subpackage("bioconductor-rhdf5lib", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, tinytest, mockery # SystemRequirements: GNU make requirements: - build: - - {{ compiler('c') }} - - automake - - make host: - r-base - libblas - liblapack - - libcurl run: - r-base + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -50,7 +41,7 @@ about: description: 'Provides C and C++ hdf5 libraries.' extra: parent_recipe: - name: '{{ full_name }}' - path: 'recipes/{{ full_name }}' + name: bioconductor-rhdf5lib + path: recipes/bioconductor-rhdf5lib version: 1.2.1 diff --git a/recipes/bioconductor-rhesus.db0/meta.yaml b/recipes/bioconductor-rhesus.db0/meta.yaml index c44f1b4b386d8..72604a3cbf18b 100644 --- a/recipes/bioconductor-rhesus.db0/meta.yaml +++ b/recipes/bioconductor-rhesus.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "rhesus.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 16b4999171a6b36e72c19b3f15b46354 + md5: 26d7aa426d23f0c64cb0918f90c32314 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rhesus.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rhesus.db0/post-link.sh b/recipes/bioconductor-rhesus.db0/post-link.sh index 4d13d03af1f40..ff96f3afab411 100644 --- a/recipes/bioconductor-rhesus.db0/post-link.sh +++ b/recipes/bioconductor-rhesus.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rhesus.db0-3.17.0" +installBiocDataPackage.sh "rhesus.db0-3.18.0" diff --git a/recipes/bioconductor-rhesuscdf/meta.yaml b/recipes/bioconductor-rhesuscdf/meta.yaml index cc7dff4a990b5..5551420081edf 100644 --- a/recipes/bioconductor-rhesuscdf/meta.yaml +++ b/recipes/bioconductor-rhesuscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rhesuscdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 994e16da5dd31bc2796d0da40aa2634f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rhesuscdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rhesusprobe/meta.yaml b/recipes/bioconductor-rhesusprobe/meta.yaml index 4410c54c821e3..f06026d876a7c 100644 --- a/recipes/bioconductor-rhesusprobe/meta.yaml +++ b/recipes/bioconductor-rhesusprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rhesusprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4169c1c997c4c08b027bc7489533e11e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rhesusprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml b/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml index 27e070df145eb..52618980dd6d5 100644 --- a/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml +++ b/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "rheumaticConditionWOLLBOLD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 58d7b58e54ba5cbd75fafa85aa09f476 + md5: 8c8a5f56b923fe79c4a4902028d6fc5c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rheumaticconditionwollbold", max_pin="x.x") }}' noarch: generic # Suggests: genefilter, Biobase, hgu133plus2.db requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh b/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh index 658d350311901..72f477eba6f72 100644 --- a/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh +++ b/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rheumaticconditionwollbold-1.38.0" +installBiocDataPackage.sh "rheumaticconditionwollbold-1.40.0" diff --git a/recipes/bioconductor-rhisat2/meta.yaml b/recipes/bioconductor-rhisat2/meta.yaml index eea04e8b05160..9bb4b0181af5c 100644 --- a/recipes/bioconductor-rhisat2/meta.yaml +++ b/recipes/bioconductor-rhisat2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Rhisat2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7075cf678dc031a22f157fcf950a7e64 + md5: bcfb03ad1e10fa471b46f2b214ddbb2a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rhisat2", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, BiocStyle # SystemRequirements: GNU make requirements: host: - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-sgseq >=1.34.0,<1.35.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-sgseq >=1.36.0,<1.37.0' - r-base - libblas - liblapack run: - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-sgseq >=1.34.0,<1.35.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-sgseq >=1.36.0,<1.37.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-rhtslib/meta.yaml b/recipes/bioconductor-rhtslib/meta.yaml index 061b2f2176c4e..52867f4d7faa2 100644 --- a/recipes/bioconductor-rhtslib/meta.yaml +++ b/recipes/bioconductor-rhtslib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "Rhtslib" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 862d4cd4c10064f45fc69c63969a4881 + md5: 8aa7fa3050a484702c3065c797948ba8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rhtslib", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle # SystemRequirements: libbz2 & liblzma & libcurl (with header files), GNU make requirements: host: - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-ri16cod.db/meta.yaml b/recipes/bioconductor-ri16cod.db/meta.yaml index 809b448fabd35..8bd8e75824883 100644 --- a/recipes/bioconductor-ri16cod.db/meta.yaml +++ b/recipes/bioconductor-ri16cod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "ri16cod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: cd01b429295fdbba21dbe566effacbdd build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ri16cod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ribocrypt/meta.yaml b/recipes/bioconductor-ribocrypt/meta.yaml index 397596bcce7f1..88ff4d20e3b05 100644 --- a/recipes/bioconductor-ribocrypt/meta.yaml +++ b/recipes/bioconductor-ribocrypt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "RiboCrypt" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 77955ef06f1325b0e0b63971e7ae2aee + md5: b5551bc35ad9798b4b1b401f7a08b280 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ribocrypt", max_pin="x.x") }}' noarch: generic # Suggests: testthat, rmarkdown, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-orfik >=1.20.0,<1.21.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-orfik >=1.22.0,<1.23.0' - r-base - r-bslib - r-data.table @@ -49,14 +50,14 @@ requirements: - r-shinyjqui - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-orfik >=1.20.0,<1.21.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-orfik >=1.22.0,<1.23.0' - r-base - r-bslib - r-data.table diff --git a/recipes/bioconductor-ribodipa/meta.yaml b/recipes/bioconductor-ribodipa/meta.yaml index bc9d90f73db21..e581d9847010c 100644 --- a/recipes/bioconductor-ribodipa/meta.yaml +++ b/recipes/bioconductor-ribodipa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "RiboDiPA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 05d7eabe7434b8191f138d0bea0bef29 + md5: 0aab649d27962694300a1e3b42b9417d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ribodipa", max_pin="x.x") }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-doparallel @@ -42,16 +43,16 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-riboprofiling/meta.yaml b/recipes/bioconductor-riboprofiling/meta.yaml index a9d839aa7db0a..51945ec4291e6 100644 --- a/recipes/bioconductor-riboprofiling/meta.yaml +++ b/recipes/bioconductor-riboprofiling/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "RiboProfiling" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf30f41d5ac40e786a37ea0becb370d7 + md5: ec32fb1993efa63a677422612e03ded7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-riboprofiling", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-ggplot2 @@ -39,17 +40,17 @@ requirements: - r-reshape2 - r-sqldf run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-ribor/meta.yaml b/recipes/bioconductor-ribor/meta.yaml index fc43ff4e568ce..d88e8a7571a55 100644 --- a/recipes/bioconductor-ribor/meta.yaml +++ b/recipes/bioconductor-ribor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ribor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 62847bbc0483e71852fda8fd089729d0 + md5: 6d86ac039324d8fa1b6c708f42da44e2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ribor", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ggplot2 @@ -31,8 +32,8 @@ requirements: - r-tidyr - r-yaml run: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-riboseqr/build.sh b/recipes/bioconductor-riboseqr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-riboseqr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-riboseqr/meta.yaml b/recipes/bioconductor-riboseqr/meta.yaml new file mode 100644 index 0000000000000..548f9398d22d6 --- /dev/null +++ b/recipes/bioconductor-riboseqr/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.36.0" %} +{% set name = "riboSeqR" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: eb9c84e564128ad11960fac5955c4d2f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-riboseqr", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - r-abind + - r-base + run: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - r-abind + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Analysis of sequencing data from ribosome profiling experiments' + description: 'Plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-ribosomeprofilingqc/meta.yaml b/recipes/bioconductor-ribosomeprofilingqc/meta.yaml index df277d3caf594..a96b273f005a2 100644 --- a/recipes/bioconductor-ribosomeprofilingqc/meta.yaml +++ b/recipes/bioconductor-ribosomeprofilingqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ribosomeProfilingQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c9cafb9bd9b9816cc073d7da37b1b4c + md5: f26a7222a62ed0c3462336d1c945cea6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ribosomeprofilingqc", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, edgeR, limma, testthat, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-cluster - r-ggfittext @@ -45,23 +46,23 @@ requirements: - r-ggrepel - r-scales run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-cluster - r-ggfittext diff --git a/recipes/bioconductor-ricecdf/meta.yaml b/recipes/bioconductor-ricecdf/meta.yaml index a93eb09926db1..f47b3ea6adb91 100644 --- a/recipes/bioconductor-ricecdf/meta.yaml +++ b/recipes/bioconductor-ricecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ricecdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 51db6f51f4adcfb7f4940d07668db8b8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ricecdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-riceprobe/meta.yaml b/recipes/bioconductor-riceprobe/meta.yaml index 63f1d8d7cf35c..297a6847aeceb 100644 --- a/recipes/bioconductor-riceprobe/meta.yaml +++ b/recipes/bioconductor-riceprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "riceprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2fac7746c343546cf30e6d54bc1e2019 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-riceprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rifi/meta.yaml b/recipes/bioconductor-rifi/meta.yaml index 374b3a83ddb43..05ed25ea6941c 100644 --- a/recipes/bioconductor-rifi/meta.yaml +++ b/recipes/bioconductor-rifi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "rifi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 40bcaaa842e5f3d40b4da6e31ac73996 + md5: 5d070b26ca40e04e4e3f9851853caa48 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rifi", max_pin="x.x") }}' noarch: generic # Suggests: DescTools, devtools, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-car - r-cowplot @@ -40,9 +41,9 @@ requirements: - r-stringr - r-tibble run: - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-car - r-cowplot diff --git a/recipes/bioconductor-rificomparative/meta.yaml b/recipes/bioconductor-rificomparative/meta.yaml index f4846e577662c..fd8f33a8cb823 100644 --- a/recipes/bioconductor-rificomparative/meta.yaml +++ b/recipes/bioconductor-rificomparative/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "rifiComparative" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e82d286dbce65abb273d2c7107d0ed87 + md5: d371dc0f2b156f4565b09b7cfa5406e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rificomparative", max_pin="x.x") }}' noarch: generic -# Suggests: DescTools, devtools, knitr, rmarkdown, BiocStyle +# Suggests: DescTools, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-dta >=2.46.0,<2.47.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-dta >=2.48.0,<2.49.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-devtools @@ -43,10 +44,10 @@ requirements: - r-tibble - r-writexl run: - - 'bioconductor-dta >=2.46.0,<2.47.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-dta >=2.48.0,<2.49.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-devtools @@ -70,7 +71,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 + file LICENSE' - summary: '''rifiComparative'' compares the outputs of ''rifi'' under two different conditions.' - description: '''rifiComparative'' is an extension of the ''rifi'' package. It is designed to compare the outputs of ''rifi'' under two different conditions by utilizing the half-life and mRNA at time 0 segments. To perform the segmentation, it takes into account the difference in half-life between the two conditions and the log2FC (fold change) of the mRNA at time 0. This package offers various functionalities such as segmentation, statistical analysis, summary tables, visualization of fragments, and additional plots that can be helpful for further analysis.' + summary: '''rifiComparative'' compares the output of rifi from two different conditions.' + description: '''rifiComparative'' is a continuation of rifi package. It compares two conditions output of rifi using half-life and mRNA at time 0 segments. As an input for the segmentation, the difference between half-life of both condtions and log2FC of the mRNA at time 0 are used. The package provides segmentation, statistics, summary table, fragments visualization and some additional useful plots for further anaylsis.' license_file: LICENSE diff --git a/recipes/bioconductor-rimmport/meta.yaml b/recipes/bioconductor-rimmport/meta.yaml index 9c9a4be1b3071..b64ed9ed2061d 100644 --- a/recipes/bioconductor-rimmport/meta.yaml +++ b/recipes/bioconductor-rimmport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RImmPort" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4586b7b4e16bfbfe7437943b0f33b892 + md5: 9a35da0a38439eee55d04ff8321ff09d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rimmport", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: diff --git a/recipes/bioconductor-ringo/meta.yaml b/recipes/bioconductor-ringo/meta.yaml index 8120d86801dc5..a2308eca149c4 100644 --- a/recipes/bioconductor-ringo/meta.yaml +++ b/recipes/bioconductor-ringo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "Ringo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 091ac77889415d4c7f2a018c2aef8ffd + md5: 2aa9ffb65c3d24fed5141f139f8721ab build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ringo", max_pin="x.x") }}' # Suggests: rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-lattice - r-matrix @@ -32,11 +33,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-lattice - r-matrix diff --git a/recipes/bioconductor-risa/meta.yaml b/recipes/bioconductor-risa/meta.yaml index f7c42e97b03be..f7e20d8c31a4e 100644 --- a/recipes/bioconductor-risa/meta.yaml +++ b/recipes/bioconductor-risa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "Risa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ba3487e592132bda3e87cb245b057fb1 + md5: 3d0fb12044023bc34defac509b8b4ab6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-risa", max_pin="x.x") }}' # Suggests: faahKO (>= 1.2.11) requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - 'r-rcpp >=0.9.13' - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - 'r-rcpp >=0.9.13' build: diff --git a/recipes/bioconductor-ritan/meta.yaml b/recipes/bioconductor-ritan/meta.yaml index e4ce931394e66..3b41d1b6ab646 100644 --- a/recipes/bioconductor-ritan/meta.yaml +++ b/recipes/bioconductor-ritan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "RITAN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3aada1fd1d9ff040f43ff6fd6e8be55d + md5: d9b8cf771e70cd374ba72e63aa439865 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ritan", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, BgeeDB requirements: host: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-bgeedb >=2.26.0,<2.27.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-bgeedb >=2.28.0,<2.29.0' - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-ritandata >=1.24.0,<1.25.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-ritandata >=1.26.0,<1.27.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' - r-base - r-dynamictreecut - r-ggplot2 @@ -45,13 +46,13 @@ requirements: - r-reshape2 - r-sqldf run: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-bgeedb >=2.26.0,<2.27.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-bgeedb >=2.28.0,<2.29.0' - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-ritandata >=1.24.0,<1.25.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-ritandata >=1.26.0,<1.27.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' - r-base - r-dynamictreecut - r-ggplot2 diff --git a/recipes/bioconductor-ritandata/meta.yaml b/recipes/bioconductor-ritandata/meta.yaml index 1204ac1b5ac42..5ca38c3c23f92 100644 --- a/recipes/bioconductor-ritandata/meta.yaml +++ b/recipes/bioconductor-ritandata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "RITANdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee9657a5c821eb892c79ef6a1ee4c5e5 + md5: 12987879ef374ad399dd440a058b9a47 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ritandata", max_pin="x.x") }}' noarch: generic +# Suggests: knitr requirements: host: - r-base run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'file LICENSE' - summary: 'This package contains the annotation and network data sets' - description: 'Data such as is contained in these two R data files in this package are required for the RITAN package examples. Users may use their own or additional resources in conjunction with RITANdata. See the RITAN vignettes for more information, such as gathering more up-to-date annotation data.' + summary: 'This package contains reference annotation and network data sets' + description: 'Data such as is contained in the two R data files in this package are required for the RITAN package examples. Users are highly encouraged to use their own or additional resources in conjunction with RITANdata. See the RITAN vignettes and RITAN.md for more information, such as gathering more up-to-date annotation data.' license_file: LICENSE diff --git a/recipes/bioconductor-ritandata/post-link.sh b/recipes/bioconductor-ritandata/post-link.sh index 2f95569f41478..41e2751e05e13 100644 --- a/recipes/bioconductor-ritandata/post-link.sh +++ b/recipes/bioconductor-ritandata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ritandata-1.24.0" +installBiocDataPackage.sh "ritandata-1.26.0" diff --git a/recipes/bioconductor-river/meta.yaml b/recipes/bioconductor-river/meta.yaml index 1f09b68b21b10..cf84189dac66b 100644 --- a/recipes/bioconductor-river/meta.yaml +++ b/recipes/bioconductor-river/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "RIVER" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea28b47a8fe878e4abf8e3cf1b673037 + md5: 7b8f82011a163ae4f4a31f2172d49124 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-river", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-ggplot2 - r-glmnet - r-proc run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-ggplot2 - r-glmnet diff --git a/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml b/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml index 8300621962a83..4c214aee9eaf1 100644 --- a/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml +++ b/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "RJMCMCNucleosomes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f88945884d72fdd6ee15d6008afc07a5 + md5: cec0a46571d187963e019f18fff144f1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rjmcmcnucleosomes", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, nucleoSim, RUnit -# SystemRequirements: Rcpp +# SystemRequirements: Rcpp, gsl requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-consensusseeker >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-consensusseeker >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-rcpp >=0.12.5' - libblas - liblapack + - gsl run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-consensusseeker >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-consensusseeker >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-rcpp >=0.12.5' + - gsl build: - {{ compiler('c') }} - {{ compiler('cxx') }} @@ -54,4 +57,3 @@ about: license: Artistic-2.0 summary: 'Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)' description: 'This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.' - diff --git a/recipes/bioconductor-rlassocox/meta.yaml b/recipes/bioconductor-rlassocox/meta.yaml index 7a9ab1a25b16f..18539199c38bb 100644 --- a/recipes/bioconductor-rlassocox/meta.yaml +++ b/recipes/bioconductor-rlassocox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "RLassoCox" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8cc79742a37f2121756c4ac8897025a4 + md5: 3f92bc442df2edc28546415bc716123b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rlassocox", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: diff --git a/recipes/bioconductor-rlhub/meta.yaml b/recipes/bioconductor-rlhub/meta.yaml index d176101ac3623..9001fbc96cb20 100644 --- a/recipes/bioconductor-rlhub/meta.yaml +++ b/recipes/bioconductor-rlhub/meta.yaml @@ -29,7 +29,7 @@ requirements: - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20230706 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rlmm/meta.yaml b/recipes/bioconductor-rlmm/meta.yaml index fc040d60e4170..f42b4445d98c7 100644 --- a/recipes/bioconductor-rlmm/meta.yaml +++ b/recipes/bioconductor-rlmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "RLMM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4f30cfdb4cb3043dc8dfd8018b7850ab + md5: 7c43c967fab2a5e90059b26e46de345b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rlmm", max_pin="x.x") }}' noarch: generic # SystemRequirements: Internal files Xba.CQV, Xba.regions (or other regions file) requirements: diff --git a/recipes/bioconductor-rlseq/build_failure.linux-64.yaml b/recipes/bioconductor-rlseq/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..b874c0e162bfb --- /dev/null +++ b/recipes/bioconductor-rlseq/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: b7a51b994b018dcebdb6ac934d67a24cdfdf07103b98b0c4084cfbaab5d97155 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-rlhub is stuck at BioC 3.17 because of a build error on their side +category: |- + dependency issue +log: |2- + - bioconductor-regioner >=1.34.0,<1.35.0 + - bioconductor-annotationhub >=3.10.0,<3.11.0 + - bioconductor-genomeinfodb >=1.38.0,<1.39.0 + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-rlhub >=1.8.0,<1.9.0 + - + + Leaving build/test directories: + Work: + /opt/conda/conda-bld/work + Test: + /opt/conda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + Build: + source activate /opt/conda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - r-callr + - bioconductor-complexheatmap >=2.18.0,<2.19.0 + - bioconductor-genomicfeatures >=1.54.0,<1.55.0 + - r-aws.s3 + - r-ggplotify + - r-rcolorbrewer + - r-valr + - r-caretensemble + - bioconductor-rtracklayer >=1.62.0,<1.63.0 + - r-venndiagram + - r-ggprism + - r-circlize + - bioconductor-rlhub >=1.8.0,<1.9.0 + - r-base 4.3.* + - r-ggplot2 + - r-dplyr + - bioconductor-genomicranges >=1.54.0,<1.55.0 + - r-pheatmap + - bioconductor-regioner >=1.34.0,<1.35.0 + - bioconductor-annotationhub >=3.10.0,<3.11.0 + - bioconductor-genomeinfodb >=1.38.0,<1.39.0 + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-rlhub >=1.8.0,<1.9.0 + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rlhub[version='>=1.8.0,<1.9.0']")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-rlseq/meta.yaml b/recipes/bioconductor-rlseq/meta.yaml index 539401a044180..3bdc73c481a19 100644 --- a/recipes/bioconductor-rlseq/meta.yaml +++ b/recipes/bioconductor-rlseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.5.2" %} {% set name = "RLSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11778a7b1e74c4332c8e5db472e3443d + md5: fefe852714378d866e0209fbe48fcf21 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rlseq", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi, BiocStyle, covr, lintr, rcmdcheck, DT, httr, jsonlite, kableExtra, kernlab, knitr, magick, MASS, org.Hs.eg.db, R.utils, randomForest, readr, rmarkdown, rpart, testthat (>= 3.0.0), tibble, tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, futile.logger requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rlhub >=1.6.0,<1.7.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rlhub >=1.8.0,<1.9.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-aws.s3 - r-base - r-callr @@ -43,14 +44,14 @@ requirements: - r-valr - r-venndiagram run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rlhub >=1.6.0,<1.7.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rlhub >=1.8.0,<1.9.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-aws.s3 - r-base - r-callr diff --git a/recipes/bioconductor-rmagpie/meta.yaml b/recipes/bioconductor-rmagpie/meta.yaml index e9c9eae1d81c7..dbd9d4ffce38e 100644 --- a/recipes/bioconductor-rmagpie/meta.yaml +++ b/recipes/bioconductor-rmagpie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "Rmagpie" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 468886302bd604ea3fab549eebd6554a + md5: 939fbdcb38d890daf9880baea89c8685 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rmagpie", max_pin="x.x") }}' noarch: generic # Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-e1071 - r-kernlab - r-pamr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-e1071 - r-kernlab diff --git a/recipes/bioconductor-rmassbank/meta.yaml b/recipes/bioconductor-rmassbank/meta.yaml index b21127ce6a9f3..b45501cfdd4e3 100644 --- a/recipes/bioconductor-rmassbank/meta.yaml +++ b/recipes/bioconductor-rmassbank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.10.0" %} +{% set version = "3.12.0" %} {% set name = "RMassBank" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d1f67c8b225b67387d68ace4243102d + md5: 59330cd723448b79eb751c6864e3dfbf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rmassbank", max_pin="x.x") }}' # Suggests: BiocStyle,gplots,RMassBankData (>= 1.33.1), xcms (>= 1.37.1), CAMERA, RUnit, knitr, rmarkdown # SystemRequirements: OpenBabel requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-chemmineob >=1.38.0,<1.39.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-chemmineob >=1.40.0,<1.41.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - r-data.table - r-digest - r-envipat + - r-glue - r-httr - r-logger - r-r.utils - r-rcdk - r-rcpp - - r-rcurl - r-readjdx - r-rjson - r-webchem @@ -47,23 +48,23 @@ requirements: - liblapack - openbabel run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-chemmineob >=1.38.0,<1.39.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-chemmineob >=1.40.0,<1.41.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - r-data.table - r-digest - r-envipat + - r-glue - r-httr - r-logger - r-r.utils - r-rcdk - r-rcpp - - r-rcurl - r-readjdx - r-rjson - r-webchem diff --git a/recipes/bioconductor-rmassbankdata/meta.yaml b/recipes/bioconductor-rmassbankdata/meta.yaml index c0e415f6acd0f..add2a5313260a 100644 --- a/recipes/bioconductor-rmassbankdata/meta.yaml +++ b/recipes/bioconductor-rmassbankdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "RMassBankData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea11a54b5f2465431c43bb8edde6a112 + md5: ac6f883e962890eebb03c2368be8bcdc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rmassbankdata", max_pin="x.x") }}' noarch: generic # Suggests: RMassBank requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rmassbankdata/post-link.sh b/recipes/bioconductor-rmassbankdata/post-link.sh index 3a9811ab26de7..fa1e79222fceb 100644 --- a/recipes/bioconductor-rmassbankdata/post-link.sh +++ b/recipes/bioconductor-rmassbankdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rmassbankdata-1.38.0" +installBiocDataPackage.sh "rmassbankdata-1.40.0" diff --git a/recipes/bioconductor-rmelting/meta.yaml b/recipes/bioconductor-rmelting/meta.yaml index 94265e7c9ff25..d3b27ada7ef61 100644 --- a/recipes/bioconductor-rmelting/meta.yaml +++ b/recipes/bioconductor-rmelting/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "rmelting" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 42f9700727064207960dab9d71653652 + md5: a73d7dd41b3d77dce067644b04412e9d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rmelting", max_pin="x.x") }}' noarch: generic # Suggests: readxl, knitr, rmarkdown, reshape2, pander, testthat # SystemRequirements: Java diff --git a/recipes/bioconductor-rmir.hs.mirna/meta.yaml b/recipes/bioconductor-rmir.hs.mirna/meta.yaml index 12100652f5496..f38de5714e0ba 100644 --- a/recipes/bioconductor-rmir.hs.mirna/meta.yaml +++ b/recipes/bioconductor-rmir.hs.mirna/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.7" %} {% set name = "RmiR.Hs.miRNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4aedac188382447d9907d2617aa2e8e6 build: - number: 14 + number: 15 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rmir.hs.mirna", max_pin="x.x") }}' noarch: generic # Suggests: methods, hgug4112a.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rmir.hsa/meta.yaml b/recipes/bioconductor-rmir.hsa/meta.yaml index 09617d6a7c380..0f5eb625023cc 100644 --- a/recipes/bioconductor-rmir.hsa/meta.yaml +++ b/recipes/bioconductor-rmir.hsa/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.5" %} {% set name = "RmiR.hsa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f22a18d1a34d12f8fc4ba3daaf1379fd build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rmir.hsa", max_pin="x.x") }}' noarch: generic # Suggests: methods, hgug4112a.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rmmquant/meta.yaml b/recipes/bioconductor-rmmquant/meta.yaml index 938579ddf4d18..5091be475916f 100644 --- a/recipes/bioconductor-rmmquant/meta.yaml +++ b/recipes/bioconductor-rmmquant/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "Rmmquant" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e67a9d31d1acf84a37e1edc3c778d432 + md5: 8f12574d12fdfbb3ef7407666fb22a7b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rmmquant", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat # SystemRequirements: C++11 requirements: host: - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tbx20bamsubset >=1.36.0,<1.37.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tbx20bamsubset >=1.38.0,<1.39.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base - r-devtools @@ -36,14 +37,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tbx20bamsubset >=1.36.0,<1.37.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tbx20bamsubset >=1.38.0,<1.39.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base - r-devtools diff --git a/recipes/bioconductor-rmspc/meta.yaml b/recipes/bioconductor-rmspc/meta.yaml index 4709a931c1529..58eec5b7e1658 100644 --- a/recipes/bioconductor-rmspc/meta.yaml +++ b/recipes/bioconductor-rmspc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "rmspc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7f21760a50ad227a597419cc10c26f10 + md5: fd5ce900bcff0c0a4b4423a7cc261aec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rmspc", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) # SystemRequirements: .NET 6.0 requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-biocmanager - r-processx - r-stringr run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-biocmanager - r-processx diff --git a/recipes/bioconductor-rnaagecalc/meta.yaml b/recipes/bioconductor-rnaagecalc/meta.yaml index d0b26aa2751a5..dee8249e03b08 100644 --- a/recipes/bioconductor-rnaagecalc/meta.yaml +++ b/recipes/bioconductor-rnaagecalc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "RNAAgeCalc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 467f0ca987822c00d042b03c1c7fe382 + md5: 8601edc9bd38ec2387cd9cd9a78b0da8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnaagecalc", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-recount >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-recount >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-recount >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-recount >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-rnaeditr/meta.yaml b/recipes/bioconductor-rnaeditr/meta.yaml index a9c58c91a11ba..cbbbde1bbbebf 100644 --- a/recipes/bioconductor-rnaeditr/meta.yaml +++ b/recipes/bioconductor-rnaeditr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "rnaEditr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 47abbe2ca055d268e3c5a03635549268 + md5: fb5365c7d12dcdc26838f4824e70a00d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnaeditr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-corrplot - r-logistf - r-plyr - r-survival run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-corrplot - r-logistf diff --git a/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml b/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml index 05f72360ba0f3..3fae561ac4294 100644 --- a/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml +++ b/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "RnAgilentDesign028282.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 72cafb0f7514a81f462acb3248e21aa9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnagilentdesign028282.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnainteract/meta.yaml b/recipes/bioconductor-rnainteract/meta.yaml index 6a6592e48526e..a1bd4cfd25c05 100644 --- a/recipes/bioconductor-rnainteract/meta.yaml +++ b/recipes/bioconductor-rnainteract/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "RNAinteract" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b789fe4d04a6fba019a3aaf8ff61646b + md5: 571d13067f2afebde4247de5571e1086 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnainteract", max_pin="x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cellhts2 >=2.64.0,<2.65.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-splots >=1.66.0,<1.67.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cellhts2 >=2.66.0,<2.67.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-splots >=1.68.0,<1.69.0' - r-abind - r-base - r-gplots @@ -36,11 +37,11 @@ requirements: - r-locfit - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cellhts2 >=2.64.0,<2.65.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-splots >=1.66.0,<1.67.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cellhts2 >=2.66.0,<2.67.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-splots >=1.68.0,<1.69.0' - r-abind - r-base - r-gplots diff --git a/recipes/bioconductor-rnainteractmapk/meta.yaml b/recipes/bioconductor-rnainteractmapk/meta.yaml index e34bf3486e80c..47e1b53a2be90 100644 --- a/recipes/bioconductor-rnainteractmapk/meta.yaml +++ b/recipes/bioconductor-rnainteractmapk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "RNAinteractMAPK" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed5fd6239416fbacc80a8995c6e13fb7 + md5: c60bb748ed7dc37d409f5dde69354074 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnainteractmapk", max_pin="x.x") }}' noarch: generic # Suggests: qvalue requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-rnainteract >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-rnainteract >=1.50.0,<1.51.0' - r-base - r-fields - r-gdata @@ -31,9 +32,9 @@ requirements: - r-mass - r-sparselda run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-rnainteract >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-rnainteract >=1.50.0,<1.51.0' - r-base - r-fields - r-gdata @@ -41,7 +42,7 @@ requirements: - r-mass - r-sparselda - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnainteractmapk/post-link.sh b/recipes/bioconductor-rnainteractmapk/post-link.sh index 9e394a3288ff2..d87f516db77a0 100644 --- a/recipes/bioconductor-rnainteractmapk/post-link.sh +++ b/recipes/bioconductor-rnainteractmapk/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnainteractmapk-1.38.0" +installBiocDataPackage.sh "rnainteractmapk-1.40.0" diff --git a/recipes/bioconductor-rnamodr.alkanilineseq/meta.yaml b/recipes/bioconductor-rnamodr.alkanilineseq/meta.yaml index ab88f1c02fb0c..93407ca9b47f1 100644 --- a/recipes/bioconductor-rnamodr.alkanilineseq/meta.yaml +++ b/recipes/bioconductor-rnamodr.alkanilineseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RNAmodR.AlkAnilineSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de1fd6898807bda24c85bea3b82ba655 + md5: a8d93c4a0a55346a6d47edb5f4c4438e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnamodr.alkanilineseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, Biostrings, RNAmodR.Data requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rnamodr >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rnamodr >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rnamodr >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rnamodr >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-rnamodr.data/meta.yaml b/recipes/bioconductor-rnamodr.data/meta.yaml index 772d4123cb9ef..beb72c08bfd72 100644 --- a/recipes/bioconductor-rnamodr.data/meta.yaml +++ b/recipes/bioconductor-rnamodr.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RNAmodR.Data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1299a93be9ed1090e5890741cebde152 + md5: cd4851e2f0c0a93c6d5a9163f542b07f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnamodr.data", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, sessioninfo, testthat requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-experimenthubdata >=1.26.0,<1.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-experimenthubdata >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-experimenthubdata >=1.26.0,<1.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-experimenthubdata >=1.28.0,<1.29.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnamodr.data/post-link.sh b/recipes/bioconductor-rnamodr.data/post-link.sh index 35a51256142a0..7991a62b289cf 100644 --- a/recipes/bioconductor-rnamodr.data/post-link.sh +++ b/recipes/bioconductor-rnamodr.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnamodr.data-1.14.0" +installBiocDataPackage.sh "rnamodr.data-1.16.0" diff --git a/recipes/bioconductor-rnamodr.ml/meta.yaml b/recipes/bioconductor-rnamodr.ml/meta.yaml index 95059b708a6c3..1508ede453dec 100644 --- a/recipes/bioconductor-rnamodr.ml/meta.yaml +++ b/recipes/bioconductor-rnamodr.ml/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RNAmodR.ML" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef2e4335b21c319d46453cc8dd1dd2f4 + md5: b82e119e7d8c2387b22f4b38d0985970 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnamodr.ml", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data, RNAmodR.AlkAnilineSeq, GenomicFeatures, Rsamtools, rtracklayer, keras requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rnamodr >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rnamodr >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ranger run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rnamodr >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rnamodr >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ranger test: diff --git a/recipes/bioconductor-rnamodr.ribomethseq/meta.yaml b/recipes/bioconductor-rnamodr.ribomethseq/meta.yaml index 1e051d06e76b0..a6f3883a418a5 100644 --- a/recipes/bioconductor-rnamodr.ribomethseq/meta.yaml +++ b/recipes/bioconductor-rnamodr.ribomethseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RNAmodR.RiboMethSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c10bb4524dada400d7e9e6fdb6fcafd + md5: fc22b6332a4e89e33ff8921d9e54aac7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnamodr.ribomethseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, RNAmodR.Data requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rnamodr >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rnamodr >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rnamodr >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rnamodr >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-rnamodr/meta.yaml b/recipes/bioconductor-rnamodr/meta.yaml index 9c834d67d273b..78ce0c695332d 100644 --- a/recipes/bioconductor-rnamodr/meta.yaml +++ b/recipes/bioconductor-rnamodr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RNAmodR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: abd9121f4f35d864be10cac6bf1c0d9c + md5: ece4ec8fc16a95ec2ee8d9506283c57e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnamodr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-modstrings >=1.16.0,<1.17.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-modstrings >=1.18.0,<1.19.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-colorramps - r-ggplot2 @@ -43,20 +44,20 @@ requirements: - r-reshape2 - r-rocr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-modstrings >=1.16.0,<1.17.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-modstrings >=1.18.0,<1.19.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-colorramps - r-ggplot2 diff --git a/recipes/bioconductor-rnasense/meta.yaml b/recipes/bioconductor-rnasense/meta.yaml index fd03499b2d792..f75925da2198c 100644 --- a/recipes/bioconductor-rnasense/meta.yaml +++ b/recipes/bioconductor-rnasense/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RNAsense" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b29a1e11b8c90a33aa7ad1885a81b458 + md5: 514e6c09019b7f9116ddbedbdf514a5a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnasense", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-nbpseq run: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-nbpseq diff --git a/recipes/bioconductor-rnaseqcomp/meta.yaml b/recipes/bioconductor-rnaseqcomp/meta.yaml index 1ae3f6bd5d654..874a5325d2799 100644 --- a/recipes/bioconductor-rnaseqcomp/meta.yaml +++ b/recipes/bioconductor-rnaseqcomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "rnaseqcomp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 093b21b510a3c3dbe2652b8c97b10391 + md5: 2d0e9f4dd34f6746ff48994f8067f6f6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnaseqcomp", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-rnaseqcovarimpute/build.sh b/recipes/bioconductor-rnaseqcovarimpute/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rnaseqcovarimpute/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rnaseqcovarimpute/meta.yaml b/recipes/bioconductor-rnaseqcovarimpute/meta.yaml new file mode 100644 index 0000000000000..21a2e0ab62a71 --- /dev/null +++ b/recipes/bioconductor-rnaseqcovarimpute/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.0.2" %} +{% set name = "RNAseqCovarImpute" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 17d14273ae359562d3f0cbf1c45b10a7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnaseqcovarimpute", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, tidyr, stringr, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - r-base + - r-dplyr + - r-foreach + - r-magrittr + - r-mice + - r-rlang + run: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - r-base + - r-dplyr + - r-foreach + - r-magrittr + - r-mice + - r-rlang +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Impute Covariate Data in RNA Sequencing Studies' + description: 'The RNAseqCovarImpute package implements multiple imputation of missing covariates and differential gene expression analysis by: 1) Randomly binning genes into smaller groups, 2) Creating M imputed datasets separately within each bin, where the imputation predictor matrix includes all covariates and the log counts per million (CPM) for the genes within each bin, 3) Estimating gene expression changes using voom followed by lmFit functions, separately on each M imputed dataset within each gene bin, 4) Un-binning the gene sets and stacking the M sets of model results before applying the squeezeVar function to apply a variance shrinking Bayesian procedure to each M set of model results, 5) Pooling the results with Rubins’ rules to produce combined coefficients, standard errors, and P-values, and 6) Adjusting P-values for multiplicity to account for false discovery rate (FDR).' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml index 8c3c00c1f2177..b3e826c19752f 100644 --- a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml +++ b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "RNAseqData.HNRNPC.bam.chr14" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c39f3f2306bb10cb47a97b1d2c893ad + md5: 9bfb7faf3c8770b15f3cf15bb670162d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnaseqdata.hnrnpc.bam.chr14", max_pin="x.x") }}' noarch: generic # Suggests: GenomicAlignments, BiocManager requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh index 0e253883cfc15..02be065d14f92 100644 --- a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh +++ b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnaseqdata.hnrnpc.bam.chr14-0.38.0" +installBiocDataPackage.sh "rnaseqdata.hnrnpc.bam.chr14-0.40.0" diff --git a/recipes/bioconductor-rnaseqpower/meta.yaml b/recipes/bioconductor-rnaseqpower/meta.yaml index eb6b3310173ed..50beb5be190ca 100644 --- a/recipes/bioconductor-rnaseqpower/meta.yaml +++ b/recipes/bioconductor-rnaseqpower/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "RNASeqPower" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8ed9fb060724ab44d75be435f10eceeb + md5: 38da142eb3ee64f2e7684ead27e4520f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnaseqpower", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-rnaseqsamplesize/meta.yaml b/recipes/bioconductor-rnaseqsamplesize/meta.yaml index 4fc692cb5bd46..470e4efabe95e 100644 --- a/recipes/bioconductor-rnaseqsamplesize/meta.yaml +++ b/recipes/bioconductor-rnaseqsamplesize/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "RnaSeqSampleSize" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 99e670bb27777288f4c42bdb45964a89 + md5: faa40e62b53c345d9298c32310e6488c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnaseqsamplesize", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-recount >=1.26.0,<1.27.0' - - 'bioconductor-rnaseqsamplesizedata >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-recount >=1.28.0,<1.29.0' + - 'bioconductor-rnaseqsamplesizedata >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -38,12 +39,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-recount >=1.26.0,<1.27.0' - - 'bioconductor-rnaseqsamplesizedata >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-recount >=1.28.0,<1.29.0' + - 'bioconductor-rnaseqsamplesizedata >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml b/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml index 8fd742f290e66..d6d8fc2ab7470 100644 --- a/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml +++ b/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "RnaSeqSampleSizeData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 415e0dc4f463089c632c9106f6df7d89 + md5: a4edc47422b0be1d83521282c0599440 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnaseqsamplesizedata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base run: - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh b/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh index 538ec6640b572..0b665148a7ee6 100644 --- a/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh +++ b/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnaseqsamplesizedata-1.32.0" +installBiocDataPackage.sh "rnaseqsamplesizedata-1.34.0" diff --git a/recipes/bioconductor-rnbeads.hg19/meta.yaml b/recipes/bioconductor-rnbeads.hg19/meta.yaml index 0287d73aa353c..f712559b76362 100644 --- a/recipes/bioconductor-rnbeads.hg19/meta.yaml +++ b/recipes/bioconductor-rnbeads.hg19/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "RnBeads.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 83a4f81f4c411d8139ba8673687a6a49 + md5: 92612251679ba9c6d2b88b90838edf1c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnbeads.hg19", max_pin="x.x") }}' noarch: generic # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnbeads.hg19/post-link.sh b/recipes/bioconductor-rnbeads.hg19/post-link.sh index a2dd13d8a0453..b7529eae02133 100644 --- a/recipes/bioconductor-rnbeads.hg19/post-link.sh +++ b/recipes/bioconductor-rnbeads.hg19/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnbeads.hg19-1.32.0" +installBiocDataPackage.sh "rnbeads.hg19-1.34.0" diff --git a/recipes/bioconductor-rnbeads.hg38/meta.yaml b/recipes/bioconductor-rnbeads.hg38/meta.yaml index 33af85fcb32ac..8baae260b3c7f 100644 --- a/recipes/bioconductor-rnbeads.hg38/meta.yaml +++ b/recipes/bioconductor-rnbeads.hg38/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "RnBeads.hg38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 87b5a33c515443e05b5ab7cfeb7afa7a + md5: 44dd2d3ae3703e045016a34060a14b0a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnbeads.hg38", max_pin="x.x") }}' noarch: generic # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnbeads.hg38/post-link.sh b/recipes/bioconductor-rnbeads.hg38/post-link.sh index 240286b0e5169..7752ddaad438f 100644 --- a/recipes/bioconductor-rnbeads.hg38/post-link.sh +++ b/recipes/bioconductor-rnbeads.hg38/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnbeads.hg38-1.32.0" +installBiocDataPackage.sh "rnbeads.hg38-1.34.0" diff --git a/recipes/bioconductor-rnbeads.mm10/meta.yaml b/recipes/bioconductor-rnbeads.mm10/meta.yaml index 32cb33a408c62..6b68058cd1575 100644 --- a/recipes/bioconductor-rnbeads.mm10/meta.yaml +++ b/recipes/bioconductor-rnbeads.mm10/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "RnBeads.mm10" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4b25dd4978d2d430192ae93b45945506 + md5: 0c935572ce46183bc5a7aaea31ea2519 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnbeads.mm10", max_pin="x.x") }}' noarch: generic # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnbeads.mm10/post-link.sh b/recipes/bioconductor-rnbeads.mm10/post-link.sh index 8e68b5fa38fc2..f7a47eac3384f 100644 --- a/recipes/bioconductor-rnbeads.mm10/post-link.sh +++ b/recipes/bioconductor-rnbeads.mm10/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnbeads.mm10-2.8.0" +installBiocDataPackage.sh "rnbeads.mm10-2.10.0" diff --git a/recipes/bioconductor-rnbeads.mm9/meta.yaml b/recipes/bioconductor-rnbeads.mm9/meta.yaml index c117153200f26..0788e300ed3ab 100644 --- a/recipes/bioconductor-rnbeads.mm9/meta.yaml +++ b/recipes/bioconductor-rnbeads.mm9/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "RnBeads.mm9" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 83951bafa8f84863f5cdd3e0128c1e0d + md5: 76f271051b1c542e5ac0da492777f933 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnbeads.mm9", max_pin="x.x") }}' noarch: generic # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnbeads.mm9/post-link.sh b/recipes/bioconductor-rnbeads.mm9/post-link.sh index aea69f9cb33bb..6831e4e1b6ab5 100644 --- a/recipes/bioconductor-rnbeads.mm9/post-link.sh +++ b/recipes/bioconductor-rnbeads.mm9/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnbeads.mm9-1.32.0" +installBiocDataPackage.sh "rnbeads.mm9-1.34.0" diff --git a/recipes/bioconductor-rnbeads.rn5/meta.yaml b/recipes/bioconductor-rnbeads.rn5/meta.yaml index 8dbb3257a3563..82d6777b5462e 100644 --- a/recipes/bioconductor-rnbeads.rn5/meta.yaml +++ b/recipes/bioconductor-rnbeads.rn5/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "RnBeads.rn5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 704db9c010242b63f68e02de58b77ee0 + md5: ed075717da62b68e7a9b47a14ac09a35 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnbeads.rn5", max_pin="x.x") }}' noarch: generic # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnbeads.rn5/post-link.sh b/recipes/bioconductor-rnbeads.rn5/post-link.sh index e47bc2c56b22e..a47dfa0ed34b1 100644 --- a/recipes/bioconductor-rnbeads.rn5/post-link.sh +++ b/recipes/bioconductor-rnbeads.rn5/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnbeads.rn5-1.32.0" +installBiocDataPackage.sh "rnbeads.rn5-1.34.0" diff --git a/recipes/bioconductor-rnbeads/meta.yaml b/recipes/bioconductor-rnbeads/meta.yaml index 2f00032bce087..23bf5205b7e61 100644 --- a/recipes/bioconductor-rnbeads/meta.yaml +++ b/recipes/bioconductor-rnbeads/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "RnBeads" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 350ab4afb8a56dce1661f349388f7145 + md5: 40a269bbbddeb407ca5c4545cb6852ff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnbeads", max_pin="x.x") }}' noarch: generic # Suggests: Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RnBeads.hg19, RnBeads.mm9, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit, MethylSeekR, sesame requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-ff @@ -39,13 +40,13 @@ requirements: - r-matrixstats - r-plyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-ff diff --git a/recipes/bioconductor-rnits/meta.yaml b/recipes/bioconductor-rnits/meta.yaml index 4dd15afc090c0..64032849b40f0 100644 --- a/recipes/bioconductor-rnits/meta.yaml +++ b/recipes/bioconductor-rnits/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "Rnits" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9743b9d8fca7c4ae623a115779553815 + md5: 4b767809cee3875eb2f7f991fba83771 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnits", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, GEOquery, stringr requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-boot - r-ggplot2 - r-reshape2 run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-boot - r-ggplot2 diff --git a/recipes/bioconductor-rnu34.db/meta.yaml b/recipes/bioconductor-rnu34.db/meta.yaml index 326295a981604..bda66c2c787a1 100644 --- a/recipes/bioconductor-rnu34.db/meta.yaml +++ b/recipes/bioconductor-rnu34.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "rnu34.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7345817f2f26270779d2409b8a17a5bd build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnu34.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnu34cdf/meta.yaml b/recipes/bioconductor-rnu34cdf/meta.yaml index d0398e2fadfb0..2611cd113cc77 100644 --- a/recipes/bioconductor-rnu34cdf/meta.yaml +++ b/recipes/bioconductor-rnu34cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rnu34cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0f2564fc6ac89de4d779faf253f23ce3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnu34cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnu34probe/meta.yaml b/recipes/bioconductor-rnu34probe/meta.yaml index 6e71cfd8f8834..7c8368ad92536 100644 --- a/recipes/bioconductor-rnu34probe/meta.yaml +++ b/recipes/bioconductor-rnu34probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rnu34probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c5ef9793a437f2bf990f6e84d31da0de build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnu34probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-roar/meta.yaml b/recipes/bioconductor-roar/meta.yaml index c1e9fe04b60a1..3e8eae075f595 100644 --- a/recipes/bioconductor-roar/meta.yaml +++ b/recipes/bioconductor-roar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "roar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1cbb5f5c6c86922f0f97a3c5318d9500 + md5: 563dcc245ffbc288c2e6ec9a9c138faa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-roar", max_pin="x.x") }}' noarch: generic # Suggests: RNAseqData.HNRNPC.bam.chr14, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-roastgsa/build.sh b/recipes/bioconductor-roastgsa/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-roastgsa/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-roastgsa/meta.yaml b/recipes/bioconductor-roastgsa/meta.yaml new file mode 100644 index 0000000000000..0f8d85c23ec25 --- /dev/null +++ b/recipes/bioconductor-roastgsa/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "roastgsa" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 83d20d90ed18c719222042ae3d9f46d3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-roastgsa", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, GSEABenchmarkeR, EnrichmentBrowser, preprocessCore, DESeq2 +requirements: + host: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - r-base + - r-ggplot2 + - r-gplots + - r-rcolorbrewer + run: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - r-base + - r-ggplot2 + - r-gplots + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Rotation based gene set analysis' + description: 'This package implements a variety of functions useful for gene set analysis using rotations to approximate the null distribution. It contributes with the implementation of seven test statistic scores that can be used with different goals and interpretations. Several functions are available to complement the statistical results with graphical representations.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-roberts2005annotation.db/meta.yaml b/recipes/bioconductor-roberts2005annotation.db/meta.yaml index 590ff86933c63..54bd6307c474c 100644 --- a/recipes/bioconductor-roberts2005annotation.db/meta.yaml +++ b/recipes/bioconductor-roberts2005annotation.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "Roberts2005Annotation.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fb28aaf1a1e0c81cf936badc674b754a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-roberts2005annotation.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-roc/meta.yaml b/recipes/bioconductor-roc/meta.yaml index cfe53ee311603..f03479e853006 100644 --- a/recipes/bioconductor-roc/meta.yaml +++ b/recipes/bioconductor-roc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "ROC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5df627cc8040f624fb107b972e9dc12 + md5: 2b84dc68639bbe6dbc5e4b9eeb429dbb build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-roc", max_pin="x.x") }}' # Suggests: rmarkdown, Biobase, BiocStyle requirements: host: diff --git a/recipes/bioconductor-rocpai/meta.yaml b/recipes/bioconductor-rocpai/meta.yaml index 6519f055f9742..f3147e68cacfa 100644 --- a/recipes/bioconductor-rocpai/meta.yaml +++ b/recipes/bioconductor-rocpai/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ROCpAI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3672b1cf97ce197f0f992c5b8fc0d27e + md5: 8d2702c4029efeb23248e107384ffd27 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rocpai", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-fission >=1.20.0,<1.21.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-fission >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-knitr run: - - 'bioconductor-fission >=1.20.0,<1.21.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-fission >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-knitr diff --git a/recipes/bioconductor-rolde/meta.yaml b/recipes/bioconductor-rolde/meta.yaml index 2144127e4bca7..839f45ba07b2e 100644 --- a/recipes/bioconductor-rolde/meta.yaml +++ b/recipes/bioconductor-rolde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "RolDE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c372addd6ebd25bd625bc7c490b3b38d + md5: 12c19e976fa6e9be2e9fa9a433690355 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rolde", max_pin="x.x") }}' noarch: generic # Suggests: knitr, printr, rmarkdown, testthat requirements: host: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rots >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rots >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-dorng @@ -32,9 +33,9 @@ requirements: - r-nlme - r-rngtools run: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rots >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rots >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-dorng diff --git a/recipes/bioconductor-rols/meta.yaml b/recipes/bioconductor-rols/meta.yaml index 8ed0008c17f7d..caf228701c0ba 100644 --- a/recipes/bioconductor-rols/meta.yaml +++ b/recipes/bioconductor-rols/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "rols" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 20398c9ed6df71963c3f186cbb5007d2 + md5: ef7159fc8010e7a7a1c5ecf285b91fc8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rols", max_pin="x.x") }}' noarch: generic # Suggests: GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), testthat, lubridate, DT, rmarkdown, requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-httr - r-jsonlite - r-progress run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-httr - r-jsonlite diff --git a/recipes/bioconductor-rontotools/meta.yaml b/recipes/bioconductor-rontotools/meta.yaml index c9696b3f8fe86..af20e2f7fb71a 100644 --- a/recipes/bioconductor-rontotools/meta.yaml +++ b/recipes/bioconductor-rontotools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "ROntoTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3c0b94ebd7487fcddaa27f914b3cd8c + md5: 11764a125b9411a5b2d2ba20f4c64024 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rontotools", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-boot run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-boot test: diff --git a/recipes/bioconductor-ropls/meta.yaml b/recipes/bioconductor-ropls/meta.yaml index fed107c32ab86..eda59d7bb9280 100644 --- a/recipes/bioconductor-ropls/meta.yaml +++ b/recipes/bioconductor-ropls/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "ropls" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 43cd3622aa3b6632a328590056d0b727 + md5: a1c4a1710eb179bb29f3831a5fe80849 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ropls", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, knitr, multtest, omicade4, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-plotly run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-plotly diff --git a/recipes/bioconductor-roseq/meta.yaml b/recipes/bioconductor-roseq/meta.yaml index b7c8fd1c0f45c..487093f51cc24 100644 --- a/recipes/bioconductor-roseq/meta.yaml +++ b/recipes/bioconductor-roseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ROSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 825b4add5728a53d474403048dbbb8c4 + md5: 9af42531e92f5a535c6a139f0856e6e3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-roseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, RUnit, BiocGenerics requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-pbmcapply run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-pbmcapply test: diff --git a/recipes/bioconductor-rots/meta.yaml b/recipes/bioconductor-rots/meta.yaml index 94fa2835ce543..9ac10605af128 100644 --- a/recipes/bioconductor-rots/meta.yaml +++ b/recipes/bioconductor-rots/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "ROTS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0fe2a766a69ca811fc88c2141b937e4f + md5: 02d51e24e501790ad3049c1bb5b3f90b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rots", max_pin="x.x") }}' # Suggests: testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-rpa/meta.yaml b/recipes/bioconductor-rpa/meta.yaml index 88699561f5d27..f6f0aaf7b94d8 100644 --- a/recipes/bioconductor-rpa/meta.yaml +++ b/recipes/bioconductor-rpa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "RPA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7337a8f9784ebb75d6e058c977717f2 + md5: ea38f5a76b570c091b8f818c48c836cb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rpa", max_pin="x.x") }}' noarch: generic # Suggests: knitr, parallel requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-rmarkdown run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-rmarkdown test: diff --git a/recipes/bioconductor-rprimer/meta.yaml b/recipes/bioconductor-rprimer/meta.yaml index b40f74abaaf73..cf4019c640733 100644 --- a/recipes/bioconductor-rprimer/meta.yaml +++ b/recipes/bioconductor-rprimer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "rprimer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9e05e6e2bf6f84403840fa9654f99a7e + md5: f866266895669cd0e898d1ffb0df86fa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rprimer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, kableExtra, knitr, rmarkdown, styler, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bslib - r-dt @@ -35,9 +36,9 @@ requirements: - r-shinycssloaders - r-shinyfeedback run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bslib - r-dt diff --git a/recipes/bioconductor-rprotobuflib/meta.yaml b/recipes/bioconductor-rprotobuflib/meta.yaml index 887fd41d8f8d0..5b102fbec59c1 100644 --- a/recipes/bioconductor-rprotobuflib/meta.yaml +++ b/recipes/bioconductor-rprotobuflib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "RProtoBufLib" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73ac1a9dd31c1bc83d88a24008beb92b + md5: e7351127e6b19daaae94fcecc970292b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rprotobuflib", max_pin="x.x") }}' # Suggests: knitr, rmarkdown # SystemRequirements: GNU make requirements: diff --git a/recipes/bioconductor-rpx/meta.yaml b/recipes/bioconductor-rpx/meta.yaml index 99d8734560712..95d2c560c7b95 100644 --- a/recipes/bioconductor-rpx/meta.yaml +++ b/recipes/bioconductor-rpx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "rpx" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 39f8bb2ca64ca8cde2630fb139038ea1 + md5: 7e3f2004892b6fb40746c0dcdd990a43 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rpx", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, BiocStyle, testthat, knitr, tibble, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-curl - r-jsonlite - r-rcurl - r-xml2 run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-curl - r-jsonlite diff --git a/recipes/bioconductor-rqc/meta.yaml b/recipes/bioconductor-rqc/meta.yaml index fbb30894aa710..c7e563d22e776 100644 --- a/recipes/bioconductor-rqc/meta.yaml +++ b/recipes/bioconductor-rqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "Rqc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 64ea2b574c7fb886f19aade0f205d697 + md5: 425dbc839b22b6af4d19ca20174c24c1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rqc", max_pin="x.x") }}' # Suggests: rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-ggplot2 - 'r-knitr >=1.7' @@ -42,17 +43,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-ggplot2 - 'r-knitr >=1.7' diff --git a/recipes/bioconductor-rqt/meta.yaml b/recipes/bioconductor-rqt/meta.yaml index 4269eb2172ed2..b028572a28d95 100644 --- a/recipes/bioconductor-rqt/meta.yaml +++ b/recipes/bioconductor-rqt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "rqt" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b9f8ad7ad17223f2fb69df9879e33574 + md5: b6120899c4586c9dcfd093db762af1c8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rqt", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-car - r-compquadform @@ -32,8 +33,8 @@ requirements: - r-pls - r-runit run: - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-car - r-compquadform diff --git a/recipes/bioconductor-rqubic/meta.yaml b/recipes/bioconductor-rqubic/meta.yaml index f7b64a6ae9e77..a7d84df176096 100644 --- a/recipes/bioconductor-rqubic/meta.yaml +++ b/recipes/bioconductor-rqubic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "rqubic" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7cfb52fd500be860a103d30e22ede5e1 + md5: 018144d5ccfbe2df88a79212dedc2066 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rqubic", max_pin="x.x") }}' # Suggests: RColorBrewer requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-biclust - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-biclust build: diff --git a/recipes/bioconductor-rrbsdata/meta.yaml b/recipes/bioconductor-rrbsdata/meta.yaml index 8659e51ec8464..eccd81fafefdc 100644 --- a/recipes/bioconductor-rrbsdata/meta.yaml +++ b/recipes/bioconductor-rrbsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RRBSdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a418c0df3db7d2285a1629bd473129ce + md5: 04bcf0f0348dc54984ca9506773820ec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rrbsdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biseq >=1.40.0,<1.41.0' + - 'bioconductor-biseq >=1.42.0,<1.43.0' - r-base run: - - 'bioconductor-biseq >=1.40.0,<1.41.0' + - 'bioconductor-biseq >=1.42.0,<1.43.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rrbsdata/post-link.sh b/recipes/bioconductor-rrbsdata/post-link.sh index 92dd5a3f08424..9daeae9d07b91 100644 --- a/recipes/bioconductor-rrbsdata/post-link.sh +++ b/recipes/bioconductor-rrbsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rrbsdata-1.20.0" +installBiocDataPackage.sh "rrbsdata-1.22.0" diff --git a/recipes/bioconductor-rrdp/meta.yaml b/recipes/bioconductor-rrdp/meta.yaml index 3652e635a4bac..d4af9718a1b5b 100644 --- a/recipes/bioconductor-rrdp/meta.yaml +++ b/recipes/bioconductor-rrdp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "rRDP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73f762d80ae94c8d655ac6c07ec4c3c0 + md5: 1a6dbbc2c3e31aa382c312202e85ce62 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rrdp", max_pin="x.x") }}' noarch: generic # Suggests: rRDPData -# SystemRequirements: Java +# SystemRequirements: Java JDK 1.4 or higher requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - - openjdk run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - - openjdk test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rrdpdata/meta.yaml b/recipes/bioconductor-rrdpdata/meta.yaml index 43018f4496c03..e76d77d70c8d6 100644 --- a/recipes/bioconductor-rrdpdata/meta.yaml +++ b/recipes/bioconductor-rrdpdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "rRDPData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 81a8cf3a83812318bbacb9cc2503f8d1 + md5: 9ca56f1bf00bfaefb27c351ccc7346ae build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rrdpdata", max_pin="x.x") }}' noarch: generic # SystemRequirements: Java requirements: host: - - 'bioconductor-rrdp >=1.34.0,<1.35.0' + - 'bioconductor-rrdp >=1.36.0,<1.37.0' - r-base - openjdk run: - - 'bioconductor-rrdp >=1.34.0,<1.35.0' + - 'bioconductor-rrdp >=1.36.0,<1.37.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' - openjdk test: commands: diff --git a/recipes/bioconductor-rrdpdata/post-link.sh b/recipes/bioconductor-rrdpdata/post-link.sh index 257b850bd9bad..529c560bd8bc7 100644 --- a/recipes/bioconductor-rrdpdata/post-link.sh +++ b/recipes/bioconductor-rrdpdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rrdpdata-1.20.0" +installBiocDataPackage.sh "rrdpdata-1.22.0" diff --git a/recipes/bioconductor-rrho/meta.yaml b/recipes/bioconductor-rrho/meta.yaml index a588bc711b0b4..7873debb38070 100644 --- a/recipes/bioconductor-rrho/meta.yaml +++ b/recipes/bioconductor-rrho/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "RRHO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1715d1199550801cb72bb4d0077d6c7f + md5: 979e74a493ef06b25a98574facdd4c3f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rrho", max_pin="x.x") }}' noarch: generic # Suggests: lattice requirements: diff --git a/recipes/bioconductor-rrvgo/meta.yaml b/recipes/bioconductor-rrvgo/meta.yaml index 64076753029de..f22c0df7d085d 100644 --- a/recipes/bioconductor-rrvgo/meta.yaml +++ b/recipes/bioconductor-rrvgo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "rrvgo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b877ead2232a39f8df718f2a217968ac + md5: d84378ff00f99dfe761c41763a56315b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rrvgo", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), shinydashboard, DT, plotly, heatmaply, magrittr, utils, clusterProfiler, DOSE, slam, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - r-base - r-ggplot2 - r-ggrepel @@ -34,9 +35,9 @@ requirements: - r-umap - r-wordcloud run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-rsamtools/meta.yaml b/recipes/bioconductor-rsamtools/meta.yaml index 74a81bf5f7acc..6f812efc1e88e 100644 --- a/recipes/bioconductor-rsamtools/meta.yaml +++ b/recipes/bioconductor-rsamtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "Rsamtools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14fcdb18a7da2608dd3325bcd7cf1fc9 + md5: 63af2a7dd2513e992fd78b26ca2b3775 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rsamtools", max_pin="x.x") }}' # Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bitops - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bitops build: diff --git a/recipes/bioconductor-rsbml/meta.yaml b/recipes/bioconductor-rsbml/meta.yaml index 94a4308dbd31c..d79175c91dce7 100644 --- a/recipes/bioconductor-rsbml/meta.yaml +++ b/recipes/bioconductor-rsbml/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.58.0" %} +{% set version = "2.60.0" %} {% set name = "rsbml" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5609d4db75e067a6ca2cead8e06e7d1d + md5: 9e3df3c47a3bbb5b92bf55b478078d1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rsbml", max_pin="x.x") }}' # SystemRequirements: libsbml (==5.10.2) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - libblas - liblapack - 'libsbml >=5.10.2' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - 'libsbml >=5.10.2' build: diff --git a/recipes/bioconductor-rscudo/meta.yaml b/recipes/bioconductor-rscudo/meta.yaml index 1bfe843a4066a..0709bb86099e6 100644 --- a/recipes/bioconductor-rscudo/meta.yaml +++ b/recipes/bioconductor-rscudo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "rScudo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a86ef401d20c50d959c82febca2329be + md5: 2ca44b84bbccb7ffdc9dc082d9a071ad build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rscudo", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret, e1071, parallel, doParallel requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-stringr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-stringr diff --git a/recipes/bioconductor-rsemmed/meta.yaml b/recipes/bioconductor-rsemmed/meta.yaml index 580518cfebf91..1e8115b130485 100644 --- a/recipes/bioconductor-rsemmed/meta.yaml +++ b/recipes/bioconductor-rsemmed/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "rsemmed" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a7d28e150432339925902ebb48d4499e + md5: 379f918582942443c9823373180a9978 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rsemmed", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle, rmarkdown requirements: diff --git a/recipes/bioconductor-rseqan/meta.yaml b/recipes/bioconductor-rseqan/meta.yaml index 6271ff68554e7..47423acccd913 100644 --- a/recipes/bioconductor-rseqan/meta.yaml +++ b/recipes/bioconductor-rseqan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RSeqAn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a456731aa836d8d5d813db5861eb6d31 + md5: 278ce2c8087516d02a4203bdcf9a6b9f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rseqan", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat requirements: host: diff --git a/recipes/bioconductor-rsubread/meta.yaml b/recipes/bioconductor-rsubread/meta.yaml index d59b0076ce4ba..65ccd28a75f2c 100644 --- a/recipes/bioconductor-rsubread/meta.yaml +++ b/recipes/bioconductor-rsubread/meta.yaml @@ -47,4 +47,3 @@ extra: name: bioconductor-rsubread path: recipes/bioconductor-rsubread version: 1.30.9 - diff --git a/recipes/bioconductor-rsvsim/meta.yaml b/recipes/bioconductor-rsvsim/meta.yaml index 0626335630506..8a08b4435d024 100644 --- a/recipes/bioconductor-rsvsim/meta.yaml +++ b/recipes/bioconductor-rsvsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "RSVSim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 58aa1505639580f74acc64c3f641b614 + md5: 0ce59bfd8791d8b1bf0b4fa48ea37e31 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rsvsim", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base test: commands: diff --git a/recipes/bioconductor-rsweep/meta.yaml b/recipes/bioconductor-rsweep/meta.yaml index 56cb2ae8fdb0d..62261663a3374 100644 --- a/recipes/bioconductor-rsweep/meta.yaml +++ b/recipes/bioconductor-rsweep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "rSWeeP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3e60840b337a6d545b79f804ff0730c + md5: 42d80dcf3d267562e175115cdfd4c731 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rsweep", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, methods, knitr, rmarkdown, BiocStyle requirements: diff --git a/recipes/bioconductor-rta10probeset.db/meta.yaml b/recipes/bioconductor-rta10probeset.db/meta.yaml index c93a76873722d..02c8c7bd97fab 100644 --- a/recipes/bioconductor-rta10probeset.db/meta.yaml +++ b/recipes/bioconductor-rta10probeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "rta10probeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ce002623471eef89fb841f0bf3e7c9f8 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rta10probeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml b/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml index 40b33d0356e54..2794ecc9761ab 100644 --- a/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml +++ b/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "rta10transcriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 14ade3f4fca2d1091ccb28e7a777f3e5 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rta10transcriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtca/meta.yaml b/recipes/bioconductor-rtca/meta.yaml index 976aa90b03b01..ab6f863af48a9 100644 --- a/recipes/bioconductor-rtca/meta.yaml +++ b/recipes/bioconductor-rtca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "RTCA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 03617e534844a5f3f0a7af4b9c810ca8 + md5: 8e1039d013ef1d5e08b48003ecffc25a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtca", max_pin="x.x") }}' noarch: generic # Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-gtools - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-gtools - r-rcolorbrewer diff --git a/recipes/bioconductor-rtcga.clinical/meta.yaml b/recipes/bioconductor-rtcga.clinical/meta.yaml index fdaf2a4cc5641..0cbafa6e3191f 100644 --- a/recipes/bioconductor-rtcga.clinical/meta.yaml +++ b/recipes/bioconductor-rtcga.clinical/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "20151101.30.0" %} +{% set version = "20151101.32.0" %} {% set name = "RTCGA.clinical" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 772ed6b2aafe700536b01d9b4c55dfef + md5: 9c32b8aef86c9ad34ea8c3672575d724 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga.clinical", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr requirements: host: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.clinical/post-link.sh b/recipes/bioconductor-rtcga.clinical/post-link.sh index 65dba96a8e66c..a682ce0470fa4 100644 --- a/recipes/bioconductor-rtcga.clinical/post-link.sh +++ b/recipes/bioconductor-rtcga.clinical/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.clinical-20151101.30.0" +installBiocDataPackage.sh "rtcga.clinical-20151101.32.0" diff --git a/recipes/bioconductor-rtcga.cnv/meta.yaml b/recipes/bioconductor-rtcga.cnv/meta.yaml index 4c5be8f8b8803..2b0f7466f8e32 100644 --- a/recipes/bioconductor-rtcga.cnv/meta.yaml +++ b/recipes/bioconductor-rtcga.cnv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RTCGA.CNV" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4c2f73f6edefa0ca82b7c6f9add37156 + md5: 15267c2322da59ccd344657a28d2ba6a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga.cnv", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.cnv/post-link.sh b/recipes/bioconductor-rtcga.cnv/post-link.sh index 09dfafdfe1a37..046dd8d84df82 100644 --- a/recipes/bioconductor-rtcga.cnv/post-link.sh +++ b/recipes/bioconductor-rtcga.cnv/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.cnv-1.28.0" +installBiocDataPackage.sh "rtcga.cnv-1.30.0" diff --git a/recipes/bioconductor-rtcga.methylation/meta.yaml b/recipes/bioconductor-rtcga.methylation/meta.yaml index 4b33e944578bd..60cb29db9aef4 100644 --- a/recipes/bioconductor-rtcga.methylation/meta.yaml +++ b/recipes/bioconductor-rtcga.methylation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RTCGA.methylation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1aff8900c676eb32d9655b0d4fbf834e + md5: 9d90704cb34a57878ef719348489c702 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga.methylation", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.methylation/post-link.sh b/recipes/bioconductor-rtcga.methylation/post-link.sh index 4e1d367fc2b38..0149be259586a 100644 --- a/recipes/bioconductor-rtcga.methylation/post-link.sh +++ b/recipes/bioconductor-rtcga.methylation/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.methylation-1.28.0" +installBiocDataPackage.sh "rtcga.methylation-1.30.0" diff --git a/recipes/bioconductor-rtcga.mirnaseq/meta.yaml b/recipes/bioconductor-rtcga.mirnaseq/meta.yaml index 5060dc87de4be..b3bc9acfe4918 100644 --- a/recipes/bioconductor-rtcga.mirnaseq/meta.yaml +++ b/recipes/bioconductor-rtcga.mirnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RTCGA.miRNASeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61a11184082b390c05d74b660d06635d + md5: 744062c2f0db68a88e27db9d61929a79 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga.mirnaseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.mirnaseq/post-link.sh b/recipes/bioconductor-rtcga.mirnaseq/post-link.sh index eca1a892dd0ca..4553a7939d834 100644 --- a/recipes/bioconductor-rtcga.mirnaseq/post-link.sh +++ b/recipes/bioconductor-rtcga.mirnaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.mirnaseq-1.28.0" +installBiocDataPackage.sh "rtcga.mirnaseq-1.30.0" diff --git a/recipes/bioconductor-rtcga.mrna/meta.yaml b/recipes/bioconductor-rtcga.mrna/meta.yaml index f9aa8092374df..0fd9e1c2bc703 100644 --- a/recipes/bioconductor-rtcga.mrna/meta.yaml +++ b/recipes/bioconductor-rtcga.mrna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RTCGA.mRNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 63adca06a76cfc761b88b853a34580d1 + md5: c9774207df355ef5945677d36e915103 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga.mrna", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.mrna/post-link.sh b/recipes/bioconductor-rtcga.mrna/post-link.sh index f0495038ac542..75fe3ba6ceb43 100644 --- a/recipes/bioconductor-rtcga.mrna/post-link.sh +++ b/recipes/bioconductor-rtcga.mrna/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.mrna-1.28.0" +installBiocDataPackage.sh "rtcga.mrna-1.30.0" diff --git a/recipes/bioconductor-rtcga.mutations/meta.yaml b/recipes/bioconductor-rtcga.mutations/meta.yaml index bfa83041ff12b..dc0d506bc3755 100644 --- a/recipes/bioconductor-rtcga.mutations/meta.yaml +++ b/recipes/bioconductor-rtcga.mutations/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "20151101.30.0" %} +{% set version = "20151101.32.0" %} {% set name = "RTCGA.mutations" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d1f7686f0203ccdffd3c0d903947ffbb + md5: 0740acb5a6a47fd9d1281ccaf80bafed build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga.mutations", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.mutations/post-link.sh b/recipes/bioconductor-rtcga.mutations/post-link.sh index 7c0a1251f3c7f..82133986d47de 100644 --- a/recipes/bioconductor-rtcga.mutations/post-link.sh +++ b/recipes/bioconductor-rtcga.mutations/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.mutations-20151101.30.0" +installBiocDataPackage.sh "rtcga.mutations-20151101.32.0" diff --git a/recipes/bioconductor-rtcga.pancan12/meta.yaml b/recipes/bioconductor-rtcga.pancan12/meta.yaml index 196c2545fba7a..fed3714cbbb38 100644 --- a/recipes/bioconductor-rtcga.pancan12/meta.yaml +++ b/recipes/bioconductor-rtcga.pancan12/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RTCGA.PANCAN12" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c4fcdde44501b93a022b8b1fe3abf96 + md5: 8b0742d189afe05f47a2656556d85d0b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga.pancan12", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.pancan12/post-link.sh b/recipes/bioconductor-rtcga.pancan12/post-link.sh index 60c525c0a3a63..a5698c90619ab 100644 --- a/recipes/bioconductor-rtcga.pancan12/post-link.sh +++ b/recipes/bioconductor-rtcga.pancan12/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.pancan12-1.28.0" +installBiocDataPackage.sh "rtcga.pancan12-1.30.0" diff --git a/recipes/bioconductor-rtcga.rnaseq/meta.yaml b/recipes/bioconductor-rtcga.rnaseq/meta.yaml index 1fab0e5b25a53..8d5fa4f1313d2 100644 --- a/recipes/bioconductor-rtcga.rnaseq/meta.yaml +++ b/recipes/bioconductor-rtcga.rnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "20151101.30.0" %} +{% set version = "20151101.32.0" %} {% set name = "RTCGA.rnaseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df65c9add93e3fa3f2f321442057c807 + md5: 47bee14c68ff4d1014677eca0ed969a9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga.rnaseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.rnaseq/post-link.sh b/recipes/bioconductor-rtcga.rnaseq/post-link.sh index 55c6465239030..50935322d590a 100644 --- a/recipes/bioconductor-rtcga.rnaseq/post-link.sh +++ b/recipes/bioconductor-rtcga.rnaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.rnaseq-20151101.30.0" +installBiocDataPackage.sh "rtcga.rnaseq-20151101.32.0" diff --git a/recipes/bioconductor-rtcga.rppa/meta.yaml b/recipes/bioconductor-rtcga.rppa/meta.yaml index e84e52e6ee075..62d36b44246ca 100644 --- a/recipes/bioconductor-rtcga.rppa/meta.yaml +++ b/recipes/bioconductor-rtcga.rppa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RTCGA.RPPA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: caff1ad6b62dbd868be8cf6452cc4312 + md5: 5eccece412039d43cdf74aec284fa0d9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga.rppa", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.rppa/post-link.sh b/recipes/bioconductor-rtcga.rppa/post-link.sh index 529c9967d90f1..382ca3c6abed1 100644 --- a/recipes/bioconductor-rtcga.rppa/post-link.sh +++ b/recipes/bioconductor-rtcga.rppa/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.rppa-1.28.0" +installBiocDataPackage.sh "rtcga.rppa-1.30.0" diff --git a/recipes/bioconductor-rtcga/meta.yaml b/recipes/bioconductor-rtcga/meta.yaml index 988503b8e726c..84fabac1dc0ff 100644 --- a/recipes/bioconductor-rtcga/meta.yaml +++ b/recipes/bioconductor-rtcga/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "RTCGA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b3e0d94c8945799da632011ed8db9c34 + md5: 97f413704d77f40ecbe00a1e0d25602d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga", max_pin="x.x") }}' noarch: generic # Suggests: devtools, testthat, pander, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, magrittr, tidyr requirements: diff --git a/recipes/bioconductor-rtcgatoolbox/meta.yaml b/recipes/bioconductor-rtcgatoolbox/meta.yaml index 6300eefa7e782..22e51db05ee47 100644 --- a/recipes/bioconductor-rtcgatoolbox/meta.yaml +++ b/recipes/bioconductor-rtcgatoolbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.1" %} {% set name = "RTCGAToolbox" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,44 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9a4dce01f2ceec3f3881c02b9bd0b5f7 + md5: 002662ddf44b6ca3e771db3adcbda6d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcgatoolbox", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgautils >=1.20.0,<1.21.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgautils >=1.22.0,<1.23.0' - r-base - r-data.table - r-httr - - r-rcircos - r-rcurl - r-rjsonio - r-rvest - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgautils >=1.20.0,<1.21.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgautils >=1.22.0,<1.23.0' - r-base - r-data.table - r-httr - - r-rcircos - r-rcurl - r-rjsonio - r-rvest diff --git a/recipes/bioconductor-rtn/meta.yaml b/recipes/bioconductor-rtn/meta.yaml index e222318b7961b..31510ebec49e0 100644 --- a/recipes/bioconductor-rtn/meta.yaml +++ b/recipes/bioconductor-rtn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "RTN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 486eee6f562b159c0d54c65a4bd957d4 + md5: 3e79f58bcc4f0ac95a48819a0027028e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtn", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-reder >=2.4.0,<2.5.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base - r-car - r-data.table @@ -37,13 +38,13 @@ requirements: - r-pwr - r-snow run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-reder >=2.4.0,<2.5.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base - r-car - r-data.table diff --git a/recipes/bioconductor-rtnduals/meta.yaml b/recipes/bioconductor-rtnduals/meta.yaml index 1596d9b351656..b9f3b2044cd8e 100644 --- a/recipes/bioconductor-rtnduals/meta.yaml +++ b/recipes/bioconductor-rtnduals/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "RTNduals" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95497f3821f66f3cd274745614587884 + md5: 5a4f986eb1a34493a1a577ea3546fe92 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtnduals", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics requirements: host: - - 'bioconductor-rtn >=2.24.0,<2.25.0' + - 'bioconductor-rtn >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-rtn >=2.24.0,<2.25.0' + - 'bioconductor-rtn >=2.26.0,<2.27.0' - r-base test: commands: diff --git a/recipes/bioconductor-rtnsurvival/meta.yaml b/recipes/bioconductor-rtnsurvival/meta.yaml index 71d2686f5b910..42c05a101eef4 100644 --- a/recipes/bioconductor-rtnsurvival/meta.yaml +++ b/recipes/bioconductor-rtnsurvival/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "RTNsurvival" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7f61ac2a0851b96b39fef5a9b4299e20 + md5: db9d03eee81fed17fae3acb66a07893f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtnsurvival", max_pin="x.x") }}' noarch: generic # Suggests: Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics requirements: host: - - 'bioconductor-rtn >=2.24.0,<2.25.0' - - 'bioconductor-rtnduals >=1.24.0,<1.25.0' + - 'bioconductor-rtn >=2.26.0,<2.27.0' + - 'bioconductor-rtnduals >=1.26.0,<1.27.0' - r-base - r-data.table - r-dunn.test @@ -33,8 +34,8 @@ requirements: - r-scales - r-survival run: - - 'bioconductor-rtn >=2.24.0,<2.25.0' - - 'bioconductor-rtnduals >=1.24.0,<1.25.0' + - 'bioconductor-rtn >=2.26.0,<2.27.0' + - 'bioconductor-rtnduals >=1.26.0,<1.27.0' - r-base - r-data.table - r-dunn.test diff --git a/recipes/bioconductor-rtopper/meta.yaml b/recipes/bioconductor-rtopper/meta.yaml index f3de0abc3850e..70748cb77078b 100644 --- a/recipes/bioconductor-rtopper/meta.yaml +++ b/recipes/bioconductor-rtopper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "RTopper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 05f914a8fec4de3ad0769d298e50719e + md5: e551ec836b4c0743feabbd2deff66cb8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtopper", max_pin="x.x") }}' noarch: generic # Suggests: org.Hs.eg.db, KEGGREST, GO.db requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-rtpca/meta.yaml b/recipes/bioconductor-rtpca/meta.yaml index 6ca2b8c374d97..dc314446feed5 100644 --- a/recipes/bioconductor-rtpca/meta.yaml +++ b/recipes/bioconductor-rtpca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "Rtpca" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 92e3001dc980973d8a33bc0a8310d99c + md5: 671f34f1c510812fc37d66ed50378d75 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtpca", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, TPP, testthat, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-dplyr - r-fdrtool @@ -30,7 +31,7 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-dplyr - r-fdrtool diff --git a/recipes/bioconductor-rtracklayer/meta.yaml b/recipes/bioconductor-rtracklayer/meta.yaml index 967607fc68109..e278e9ce8f4ea 100644 --- a/recipes/bioconductor-rtracklayer/meta.yaml +++ b/recipes/bioconductor-rtracklayer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "rtracklayer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ea85a15c469bbc3b7c909fee857b02bc + md5: a16a9ca02e49808b38823899860abdb6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtracklayer", max_pin="x.x") }}' # Suggests: BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - 'r-rcurl >=1.4-2' - 'r-restfulr >=0.0.13' @@ -38,17 +39,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - 'r-rcurl >=1.4-2' - 'r-restfulr >=0.0.13' diff --git a/recipes/bioconductor-rtreemix/meta.yaml b/recipes/bioconductor-rtreemix/meta.yaml index c454a93b616db..3fcbf4f2015c1 100644 --- a/recipes/bioconductor-rtreemix/meta.yaml +++ b/recipes/bioconductor-rtreemix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "Rtreemix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d05f9b9b4dce2e4a90fd273abcee669 + md5: 3a9bda84ad8cd784165f1b8ce1a43af7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtreemix", max_pin="x.x") }}' # Suggests: Rgraphviz requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-hmisc - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-hmisc build: diff --git a/recipes/bioconductor-rtrm/meta.yaml b/recipes/bioconductor-rtrm/meta.yaml index a0eff930f80c6..e12f221409eeb 100644 --- a/recipes/bioconductor-rtrm/meta.yaml +++ b/recipes/bioconductor-rtrm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "rTRM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6284b5e947d0c1b087ed858e85a80b11 + md5: 2804488949a044166efe737d4e25d9ac build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtrm", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-igraph >=1.0' - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-igraph >=1.0' diff --git a/recipes/bioconductor-rtrmui/meta.yaml b/recipes/bioconductor-rtrmui/meta.yaml index eb45f8922de4a..c92d5cb854754 100644 --- a/recipes/bioconductor-rtrmui/meta.yaml +++ b/recipes/bioconductor-rtrmui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "rTRMui" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9255a3ec1721743cb12a993094fe52bb + md5: 6e1589a0f3e51870f4eb71a0eb56d915 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtrmui", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-motifdb >=1.42.0,<1.43.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtrm >=1.38.0,<1.39.0' + - 'bioconductor-motifdb >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtrm >=1.40.0,<1.41.0' - r-base - 'r-shiny >=0.9' run: - - 'bioconductor-motifdb >=1.42.0,<1.43.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtrm >=1.38.0,<1.39.0' + - 'bioconductor-motifdb >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtrm >=1.40.0,<1.41.0' - r-base - 'r-shiny >=0.9' test: diff --git a/recipes/bioconductor-rtu34.db/meta.yaml b/recipes/bioconductor-rtu34.db/meta.yaml index 3746466128099..fc5ff8cdaf925 100644 --- a/recipes/bioconductor-rtu34.db/meta.yaml +++ b/recipes/bioconductor-rtu34.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "rtu34.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f46c4763627f1a9e00cdc9d0af8c5f2e build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtu34.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtu34cdf/meta.yaml b/recipes/bioconductor-rtu34cdf/meta.yaml index 687bfa4f11997..4c46f39a9d9c1 100644 --- a/recipes/bioconductor-rtu34cdf/meta.yaml +++ b/recipes/bioconductor-rtu34cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rtu34cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 317abfcca319d01eb14f16efa6d91da1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtu34cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtu34probe/meta.yaml b/recipes/bioconductor-rtu34probe/meta.yaml index 6e82cebf7cdfb..85fe1dcc09abf 100644 --- a/recipes/bioconductor-rtu34probe/meta.yaml +++ b/recipes/bioconductor-rtu34probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rtu34probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1778d857a61bf181b80b9fcf46ebd2c3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtu34probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-runibic/meta.yaml b/recipes/bioconductor-runibic/meta.yaml index 7cca70531af16..2880440cd9bb6 100644 --- a/recipes/bioconductor-runibic/meta.yaml +++ b/recipes/bioconductor-runibic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "runibic" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a1dab58d1c0b9f7eab2bb787dcf09486 + md5: e67e1067d80c06f72208fca94d7a2e52 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-runibic", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, GEOquery, affy, airway, QUBIC # SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biclust - 'r-rcpp >=0.12.12' @@ -29,7 +30,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biclust - 'r-rcpp >=0.12.12' diff --git a/recipes/bioconductor-ruvcorr/meta.yaml b/recipes/bioconductor-ruvcorr/meta.yaml index ea463f3c08a89..2579d63c4c8d9 100644 --- a/recipes/bioconductor-ruvcorr/meta.yaml +++ b/recipes/bioconductor-ruvcorr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "RUVcorr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dcabc6f20ae34007170c74c3687438f0 + md5: cfc2e185bc7d37f264843a6fa5ed7c6d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ruvcorr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, hgu133a2.db, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bladderbatch >=1.38.0,<1.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bladderbatch >=1.40.0,<1.41.0' - r-base - r-corrplot - r-gridextra @@ -32,8 +33,8 @@ requirements: - r-reshape2 - r-snowfall run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bladderbatch >=1.38.0,<1.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bladderbatch >=1.40.0,<1.41.0' - r-base - r-corrplot - r-gridextra diff --git a/recipes/bioconductor-ruvnormalize/meta.yaml b/recipes/bioconductor-ruvnormalize/meta.yaml index b4dec3a853f92..7c155c7112009 100644 --- a/recipes/bioconductor-ruvnormalize/meta.yaml +++ b/recipes/bioconductor-ruvnormalize/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "RUVnormalize" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c1c1270e40710ca88df4cd06f7b83436 + md5: 2d5d0d40d8720734dee3f8dc437c0756 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ruvnormalize", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ruvnormalizedata >=1.20.0,<1.21.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ruvnormalizedata >=1.22.0,<1.23.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ruvnormalizedata >=1.20.0,<1.21.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ruvnormalizedata >=1.22.0,<1.23.0' - r-base test: commands: diff --git a/recipes/bioconductor-ruvnormalizedata/meta.yaml b/recipes/bioconductor-ruvnormalizedata/meta.yaml index 84738d3293026..b4d2035842550 100644 --- a/recipes/bioconductor-ruvnormalizedata/meta.yaml +++ b/recipes/bioconductor-ruvnormalizedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RUVnormalizeData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 138ed1f796a9967fce840e1f751769a2 + md5: 5d7104746a5cac16500870312dd769a6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ruvnormalizedata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ruvnormalizedata/post-link.sh b/recipes/bioconductor-ruvnormalizedata/post-link.sh index c3960ee3ad193..3d7a877bdd836 100644 --- a/recipes/bioconductor-ruvnormalizedata/post-link.sh +++ b/recipes/bioconductor-ruvnormalizedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ruvnormalizedata-1.20.0" +installBiocDataPackage.sh "ruvnormalizedata-1.22.0" diff --git a/recipes/bioconductor-ruvseq/meta.yaml b/recipes/bioconductor-ruvseq/meta.yaml index c8fc15fd77d19..2f25bffb6074b 100644 --- a/recipes/bioconductor-ruvseq/meta.yaml +++ b/recipes/bioconductor-ruvseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "RUVSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: da6483e460647efa6a7f5754661e6254 + md5: eebbc7e6520dc1fb18f5d8f66de7b739 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ruvseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-rvisdiff/build.sh b/recipes/bioconductor-rvisdiff/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rvisdiff/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rvisdiff/meta.yaml b/recipes/bioconductor-rvisdiff/meta.yaml new file mode 100644 index 0000000000000..5b328f86ae0db --- /dev/null +++ b/recipes/bioconductor-rvisdiff/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.0" %} +{% set name = "Rvisdiff" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3e3b8ccc9cb71388e2e7c17d60995cbe +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rvisdiff", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, DESeq2, limma, SummarizedExperiment, airway, BiocStyle, matrixTests, BiocManager +requirements: + host: + - 'bioconductor-edger >=4.0.0,<4.1.0' + - r-base + run: + - 'bioconductor-edger >=4.0.0,<4.1.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-2 | GPL-3' + summary: 'Interactive Graphs for Differential Expression' + description: 'Creates a muti-graph web page which allows the interactive exploration of differential expression results. The graphical web interface presents results as a table which is integrated with five interactive graphs: MA-plot, volcano plot, box plot, lines plot and cluster heatmap. Graphical aspect and information represented in the graphs can be customized by means of user controls. Final graphics can be exported as PNG format.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-rvs/meta.yaml b/recipes/bioconductor-rvs/meta.yaml index d01234acfc8da..0439a11c2393c 100644 --- a/recipes/bioconductor-rvs/meta.yaml +++ b/recipes/bioconductor-rvs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "RVS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0c73fd33ebe8620d49b052656faf3988 + md5: 209870dca9bf6ebc9831014045ddbd42 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rvs", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation requirements: host: - - 'bioconductor-snpstats >=1.50.0,<1.51.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' - r-base - r-genlib - r-grain - r-kinship2 run: - - 'bioconductor-snpstats >=1.50.0,<1.51.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' - r-base - r-genlib - r-grain diff --git a/recipes/bioconductor-rwgcod.db/meta.yaml b/recipes/bioconductor-rwgcod.db/meta.yaml index 59dede08fe2de..0fc2b8cb3aa76 100644 --- a/recipes/bioconductor-rwgcod.db/meta.yaml +++ b/recipes/bioconductor-rwgcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "rwgcod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c8d2fa81b6f03c4ee629a0883431e5fd build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rwgcod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rwikipathways/meta.yaml b/recipes/bioconductor-rwikipathways/meta.yaml index 36c370f0c00b4..f038e83886397 100644 --- a/recipes/bioconductor-rwikipathways/meta.yaml +++ b/recipes/bioconductor-rwikipathways/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.1" %} {% set name = "rWikiPathways" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bdab499f36c3811aaf36347c445bab3e + md5: 4a836092dcb14297a316efeb45de307d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rwikipathways", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - r-base - r-data.table + - r-dplyr - r-httr + - r-lubridate + - r-purrr - r-rcurl + - r-readr - r-rjson + - r-stringr - r-tidyr - r-xml run: - r-base - r-data.table + - r-dplyr - r-httr + - r-lubridate + - r-purrr - r-rcurl + - r-readr - r-rjson + - r-stringr - r-tidyr - r-xml test: diff --git a/recipes/bioconductor-s4arrays/meta.yaml b/recipes/bioconductor-s4arrays/meta.yaml index bd3614bd01d98..67a951397a9aa 100644 --- a/recipes/bioconductor-s4arrays/meta.yaml +++ b/recipes/bioconductor-s4arrays/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.4" %} +{% set version = "1.2.0" %} {% set name = "S4Arrays" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 60786b2573cb89bad3f57e4e9bb1e530 + md5: c77474b839251d19d31708831de3c1bf build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-s4arrays", max_pin="x.x") }}' # Suggests: BiocParallel, SparseArray (>= 0.0.4), DelayedArray, testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-abind - r-base - r-crayon - r-matrix - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-abind - r-base - r-crayon - r-matrix diff --git a/recipes/bioconductor-s4vectors/meta.yaml b/recipes/bioconductor-s4vectors/meta.yaml index fd70918e733e3..5f22a031ef513 100644 --- a/recipes/bioconductor-s4vectors/meta.yaml +++ b/recipes/bioconductor-s4vectors/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.1" %} +{% set version = "0.40.2" %} {% set name = "S4Vectors" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 683b1d01ccff0bb1c60087b4cb82f656 + md5: ee94f4f6c25dcaf7a50f5814495310e3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-s4vectors", max_pin="x.x") }}' # Suggests: IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-safe/meta.yaml b/recipes/bioconductor-safe/meta.yaml index b7c5e1e2201ac..628005304fbab 100644 --- a/recipes/bioconductor-safe/meta.yaml +++ b/recipes/bioconductor-safe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.40.0" %} +{% set version = "3.42.0" %} {% set name = "safe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3207c6250626853ac244f56091f6b419 + md5: 70cc344ddfe65a9d0f3a021c565a1e8e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-safe", max_pin="x.x") }}' noarch: generic # Suggests: GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-sparsem run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-sparsem test: diff --git a/recipes/bioconductor-sagenhaft/meta.yaml b/recipes/bioconductor-sagenhaft/meta.yaml index 561dd90c5992f..678694684b10b 100644 --- a/recipes/bioconductor-sagenhaft/meta.yaml +++ b/recipes/bioconductor-sagenhaft/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "sagenhaft" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c383e7a39b428ad34cf8ed33a4ca599f + md5: 4f27450a0e98b4f0f7396a784eb0e4e3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sagenhaft", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-saigegds/meta.yaml b/recipes/bioconductor-saigegds/meta.yaml index 487a7c010422c..ff7383e3f09cc 100644 --- a/recipes/bioconductor-saigegds/meta.yaml +++ b/recipes/bioconductor-saigegds/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.1" %} +{% set version = "2.2.0" %} {% set name = "SAIGEgds" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0d1a7a33eacf51e2b792ffe48a95a9d8 + md5: d5792543f5eba866f022723bad21b67e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-saigegds", max_pin="x.x") }}' # Suggests: parallel, crayon, CompQuadForm, survey, SNPRelate, RUnit, knitr, markdown, rmarkdown, ggmanh, BiocGenerics # SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' - r-base - r-matrix - r-rcpp @@ -31,8 +32,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-sampleclassifier/meta.yaml b/recipes/bioconductor-sampleclassifier/meta.yaml index 3ad85e51aa5cc..f2f2a849ce0a0 100644 --- a/recipes/bioconductor-sampleclassifier/meta.yaml +++ b/recipes/bioconductor-sampleclassifier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "sampleClassifier" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a2381e59b5ff80cd0f74a56ae644ca25 + md5: 7f17cc7eb566dcd27148ee400491b6c7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sampleclassifier", max_pin="x.x") }}' noarch: generic # Suggests: sampleClassifierData, BiocStyle, hgu133a.db, hgu133plus2.db requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-mgfm >=1.34.0,<1.35.0' - - 'bioconductor-mgfr >=1.26.0,<1.27.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-mgfm >=1.36.0,<1.37.0' + - 'bioconductor-mgfr >=1.28.0,<1.29.0' - r-base - r-e1071 - r-ggplot2 run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-mgfm >=1.34.0,<1.35.0' - - 'bioconductor-mgfr >=1.26.0,<1.27.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-mgfm >=1.36.0,<1.37.0' + - 'bioconductor-mgfr >=1.28.0,<1.29.0' - r-base - r-e1071 - r-ggplot2 diff --git a/recipes/bioconductor-sampleclassifierdata/meta.yaml b/recipes/bioconductor-sampleclassifierdata/meta.yaml index 89ea031921117..a1b9746040b66 100644 --- a/recipes/bioconductor-sampleclassifierdata/meta.yaml +++ b/recipes/bioconductor-sampleclassifierdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "sampleClassifierData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4b0d64737358fad818a4a1cc71a27c8 + md5: 941790a92cde9051601206ed162f4151 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sampleclassifierdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sampleclassifierdata/post-link.sh b/recipes/bioconductor-sampleclassifierdata/post-link.sh index c6a957c0a883c..9b49079caf80f 100644 --- a/recipes/bioconductor-sampleclassifierdata/post-link.sh +++ b/recipes/bioconductor-sampleclassifierdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "sampleclassifierdata-1.24.0" +installBiocDataPackage.sh "sampleclassifierdata-1.26.0" diff --git a/recipes/bioconductor-samspectral/meta.yaml b/recipes/bioconductor-samspectral/meta.yaml index 555bf904ed589..54499b23d8f09 100644 --- a/recipes/bioconductor-samspectral/meta.yaml +++ b/recipes/bioconductor-samspectral/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "SamSPECTRAL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5c1cee5d6e3e0c2a3792b274772d14eb + md5: 2724bc54054c093fac88a672a6b173d6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-samspectral", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-sangeranalyser/meta.yaml b/recipes/bioconductor-sangeranalyser/meta.yaml index 3b1e01b66590c..3b746fd6bf70d 100644 --- a/recipes/bioconductor-sangeranalyser/meta.yaml +++ b/recipes/bioconductor-sangeranalyser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "sangeranalyseR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 320b2dd2f4c63054bebd0a4c48dfd488 + md5: da4a748e4e8a1eaba322abafbd7aedad build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sangeranalyser", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0) requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-sangerseqr >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-sangerseqr >=1.38.0,<1.39.0' - r-ape - r-base - r-data.table @@ -48,10 +49,10 @@ requirements: - r-stringr - r-zeallot run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-sangerseqr >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-sangerseqr >=1.38.0,<1.39.0' - r-ape - r-base - r-data.table diff --git a/recipes/bioconductor-sangerseqr/meta.yaml b/recipes/bioconductor-sangerseqr/meta.yaml index ecac53a019305..adeddccc55773 100644 --- a/recipes/bioconductor-sangerseqr/meta.yaml +++ b/recipes/bioconductor-sangerseqr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "sangerseqR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c1fd0d600e418cf0e841f7aeb0cc70e0 + md5: efc55dbe39324b21b62910684962b86b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sangerseqr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-shiny - r-stringr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-shiny - r-stringr diff --git a/recipes/bioconductor-santa/meta.yaml b/recipes/bioconductor-santa/meta.yaml index 4c98dae1098bd..5c73501ad8a78 100644 --- a/recipes/bioconductor-santa/meta.yaml +++ b/recipes/bioconductor-santa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.36.0" %} +{% set version = "2.38.0" %} {% set name = "SANTA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 30c6e9de6ec8283380f691f2f2037378 + md5: 1b2b87312bb663905abbc444be13a056 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-santa", max_pin="x.x") }}' # Suggests: BiocGenerics, BioNet, DLBCL, formatR, knitr, msm, org.Sc.sgd.db, markdown, rmarkdown, RUnit requirements: host: diff --git a/recipes/bioconductor-sarc/build.sh b/recipes/bioconductor-sarc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sarc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sarc/meta.yaml b/recipes/bioconductor-sarc/meta.yaml new file mode 100644 index 0000000000000..168d1508d39d2 --- /dev/null +++ b/recipes/bioconductor-sarc/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.0.0" %} +{% set name = "SARC" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b3ccd1bbc820bc93c4b13ec4e3ec9705 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sarc", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, kableExtra, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, Homo.sapiens, TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus, GenomicAlignments +requirements: + host: + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - r-base + - r-data.table + - r-desctools + - r-ggplot2 + - r-gridextra + - r-gtable + - r-metap + - r-plotly + - r-rcolorbrewer + - r-reshape2 + - r-scales + - r-tidyverse + run: + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - r-base + - r-data.table + - r-desctools + - r-ggplot2 + - r-gridextra + - r-gtable + - r-metap + - r-plotly + - r-rcolorbrewer + - r-reshape2 + - r-scales + - r-tidyverse +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Statistical Analysis of Regions with CNVs' + description: 'Imports a cov/coverage file (normalised read coverages from BAM files) and a cnv file (list of CNVs - similiar to a BED file) from WES/ WGS CNV (copy number variation) detection pipelines and utilises several metrics to weigh the likelihood of a sample containing a detected CNV being a true CNV or a false positive. Highly useful for diagnostic testing to filter out false positives to provide clinicians with fewer variants to interpret. SARC uniquely only used cov and csv (similiar to BED file) files which are the common CNV pipeline calling filetypes, and can be used as to supplement the Interactive Genome Browser (IGV) to generate many figures automatedly, which can be especially helpful in large cohorts with 100s-1000s of patients.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-sarks/meta.yaml b/recipes/bioconductor-sarks/meta.yaml index c5a227bf63b65..632d42d45814e 100644 --- a/recipes/bioconductor-sarks/meta.yaml +++ b/recipes/bioconductor-sarks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "sarks" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0c3c63006f7a3850821e4d2bbbcffe77 + md5: b6fc7553269237bea782582b858aaee5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sarks", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, ggplot2 # SystemRequirements: Java (>= 1.8) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-binom - r-cluster - r-rjava - openjdk run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-binom - r-cluster diff --git a/recipes/bioconductor-saturn/meta.yaml b/recipes/bioconductor-saturn/meta.yaml index 115cb8599eb59..56ea686073d4f 100644 --- a/recipes/bioconductor-saturn/meta.yaml +++ b/recipes/bioconductor-saturn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "satuRn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 89d8bb9ce1b8397fba9a9ded087cd0a6 + md5: a0826944ab0aee6ff42127fa7eebf43c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-saturn", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub, ensembldb, edgeR, DEXSeq, stageR, DelayedArray requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-ggplot2 @@ -31,9 +32,9 @@ requirements: - r-matrix - r-pbapply run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-ggplot2 diff --git a/recipes/bioconductor-saureuscdf/meta.yaml b/recipes/bioconductor-saureuscdf/meta.yaml index 193995bd07b86..63b9008ca29cf 100644 --- a/recipes/bioconductor-saureuscdf/meta.yaml +++ b/recipes/bioconductor-saureuscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "saureuscdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d01883e4c3dd99f32012e6dbab8cdb8b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-saureuscdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-saureusprobe/meta.yaml b/recipes/bioconductor-saureusprobe/meta.yaml index 207987f0e84d0..7346b9ecb2da6 100644 --- a/recipes/bioconductor-saureusprobe/meta.yaml +++ b/recipes/bioconductor-saureusprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "saureusprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: eb4e91b10a536cbde4ecc08951ddf4d3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-saureusprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sbgnview.data/meta.yaml b/recipes/bioconductor-sbgnview.data/meta.yaml index c96698e9c9057..aba842e7df3b8 100644 --- a/recipes/bioconductor-sbgnview.data/meta.yaml +++ b/recipes/bioconductor-sbgnview.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SBGNview.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ab6acd3a8b3411fcba1cf7ab1bbbd370 + md5: 7e1bce0dfbc48b3cdc023d88e2ea7d9a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sbgnview.data", max_pin="x.x") }}' noarch: generic # Suggests: SummarizedExperiment requirements: @@ -31,7 +32,7 @@ requirements: - r-knitr - r-rmarkdown - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sbgnview.data/post-link.sh b/recipes/bioconductor-sbgnview.data/post-link.sh index e1f08a4c01f3d..b736f2bdd3bfd 100644 --- a/recipes/bioconductor-sbgnview.data/post-link.sh +++ b/recipes/bioconductor-sbgnview.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "sbgnview.data-1.14.0" +installBiocDataPackage.sh "sbgnview.data-1.16.0" diff --git a/recipes/bioconductor-sbgnview/meta.yaml b/recipes/bioconductor-sbgnview/meta.yaml index 8f354e0856fdb..8c50f540bbd86 100644 --- a/recipes/bioconductor-sbgnview/meta.yaml +++ b/recipes/bioconductor-sbgnview/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SBGNview" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e069957bf05ad05540c11fc90360a2cb + md5: 785b51f08ce7b40f23b6e9168ce1d1af build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sbgnview", max_pin="x.x") }}' noarch: generic # Suggests: testthat, gage requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' - - 'bioconductor-sbgnview.data >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' + - 'bioconductor-sbgnview.data >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bookdown - r-httr @@ -36,11 +37,11 @@ requirements: - r-rsvg - r-xml2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' - - 'bioconductor-sbgnview.data >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' + - 'bioconductor-sbgnview.data >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bookdown - r-httr diff --git a/recipes/bioconductor-sbmlr/meta.yaml b/recipes/bioconductor-sbmlr/meta.yaml index 09aed6b74a822..2c7a8f8515985 100644 --- a/recipes/bioconductor-sbmlr/meta.yaml +++ b/recipes/bioconductor-sbmlr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.96.0" %} +{% set version = "1.98.0" %} {% set name = "SBMLR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4fe40b590e4bfdb241a89787f0475ce7 + md5: 36433007d11730737942753523a9d91e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sbmlr", max_pin="x.x") }}' noarch: generic # Suggests: rsbml requirements: diff --git a/recipes/bioconductor-sc3/meta.yaml b/recipes/bioconductor-sc3/meta.yaml index bee00ba007ab8..87691107738fc 100644 --- a/recipes/bioconductor-sc3/meta.yaml +++ b/recipes/bioconductor-sc3/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.3" %} +{% set version = "1.30.0" %} {% set name = "SC3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3621e7e5933a11aea8306f53389c85d4 + md5: c61e14eaf22ab5535ff11763d97e8c96 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sc3", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, mclust, scater, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-doparallel @@ -42,10 +43,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-doparallel diff --git a/recipes/bioconductor-scale4c/meta.yaml b/recipes/bioconductor-scale4c/meta.yaml index 46a8eca886c47..114860f5f9880 100644 --- a/recipes/bioconductor-scale4c/meta.yaml +++ b/recipes/bioconductor-scale4c/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "Scale4C" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 762ef20a76782aaf8526f4e4575b8188 + md5: 7897932085759a05ad185eaec2afcd13 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scale4c", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-smoothie run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-smoothie test: diff --git a/recipes/bioconductor-scaledmatrix/meta.yaml b/recipes/bioconductor-scaledmatrix/meta.yaml index 3055cb3574f0e..2c06205107872 100644 --- a/recipes/bioconductor-scaledmatrix/meta.yaml +++ b/recipes/bioconductor-scaledmatrix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "ScaledMatrix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 259cee9d8c815fc9760fa68a997fd12c + md5: 337f2af494241ac5def9fcae4dc12313 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scaledmatrix", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular, DelayedMatrixStats requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-scan.upc/meta.yaml b/recipes/bioconductor-scan.upc/meta.yaml index 66c8fd0a58c4a..bc6fddb7ec4c6 100644 --- a/recipes/bioconductor-scan.upc/meta.yaml +++ b/recipes/bioconductor-scan.upc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.42.0" %} +{% set version = "2.44.0" %} {% set name = "SCAN.UPC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ae3e59735107bb06928ac081fa52b308 + md5: 9da1b69c833d18db111112370bfe15ae build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scan.upc", max_pin="x.x") }}' noarch: generic # Suggests: pd.hg.u95a requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-foreach - r-mass run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-foreach - r-mass diff --git a/recipes/bioconductor-scanmir/meta.yaml b/recipes/bioconductor-scanmir/meta.yaml index e6d5d8f303248..97c1cf26883e9 100644 --- a/recipes/bioconductor-scanmir/meta.yaml +++ b/recipes/bioconductor-scanmir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scanMiR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 043184d2269eeba5b620b4c97af9f33c + md5: a08199f29933bb3b0d1e9336b1b46a76 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scanmir", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-data.table @@ -34,12 +35,12 @@ requirements: - r-ggseqlogo - r-stringi run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-data.table diff --git a/recipes/bioconductor-scanmirapp/meta.yaml b/recipes/bioconductor-scanmirapp/meta.yaml index 760d5e52a1240..247186ca2ad89 100644 --- a/recipes/bioconductor-scanmirapp/meta.yaml +++ b/recipes/bioconductor-scanmirapp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scanMiRApp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 396fd2bf8dfcf6fc2a801c5ccaa0e3b0 + md5: 637ec69edde646093548d190325738fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scanmirapp", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn6 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scanmir >=1.6.0,<1.7.0' - - 'bioconductor-scanmirdata >=1.6.0,<1.7.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scanmir >=1.8.0,<1.9.0' + - 'bioconductor-scanmirdata >=1.8.0,<1.9.0' - r-base - r-data.table - r-digest @@ -51,20 +52,20 @@ requirements: - r-shinyjqui - r-waiter run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scanmir >=1.6.0,<1.7.0' - - 'bioconductor-scanmirdata >=1.6.0,<1.7.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scanmir >=1.8.0,<1.9.0' + - 'bioconductor-scanmirdata >=1.8.0,<1.9.0' - r-base - r-data.table - r-digest diff --git a/recipes/bioconductor-scanmirdata/meta.yaml b/recipes/bioconductor-scanmirdata/meta.yaml index 85e026948f7e0..0deef63b6ab5b 100644 --- a/recipes/bioconductor-scanmirdata/meta.yaml +++ b/recipes/bioconductor-scanmirdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scanMiRData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 163f0250a82df0c4fb402b756a3010d7 + md5: 4c717492a3c85bbcf199873e35190219 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scanmirdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-scanmir >=1.6.0,<1.7.0' + - 'bioconductor-scanmir >=1.8.0,<1.9.0' - r-base run: - - 'bioconductor-scanmir >=1.6.0,<1.7.0' + - 'bioconductor-scanmir >=1.8.0,<1.9.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-scanmirdata/post-link.sh b/recipes/bioconductor-scanmirdata/post-link.sh index ef71048d18442..38be41e8fc92c 100644 --- a/recipes/bioconductor-scanmirdata/post-link.sh +++ b/recipes/bioconductor-scanmirdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "scanmirdata-1.6.0" +installBiocDataPackage.sh "scanmirdata-1.8.0" diff --git a/recipes/bioconductor-scannotatr.models/meta.yaml b/recipes/bioconductor-scannotatr.models/meta.yaml index 5fa07ac9d2496..6f96a2629007b 100644 --- a/recipes/bioconductor-scannotatr.models/meta.yaml +++ b/recipes/bioconductor-scannotatr.models/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.10" %} {% set name = "scAnnotatR.models" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 77c6e16382645164d6413356c5ab52c5 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scannotatr.models", max_pin="x.x") }}' noarch: generic # Suggests: scAnnotatR, knitr requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-scannotatr/meta.yaml b/recipes/bioconductor-scannotatr/meta.yaml index 939cb6786b62e..cf184bb7c972c 100644 --- a/recipes/bioconductor-scannotatr/meta.yaml +++ b/recipes/bioconductor-scannotatr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scAnnotatR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f99427ba417fd087195f719f781d499 + md5: 5474e416000bda50dc8273a09b41a54b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scannotatr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, scRNAseq, testthat requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-base - r-caret @@ -36,9 +37,9 @@ requirements: - r-rocr - r-seurat run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-base - r-caret diff --git a/recipes/bioconductor-scanvis/meta.yaml b/recipes/bioconductor-scanvis/meta.yaml index 1a5a2a0f2c982..507c7fb6aedb7 100644 --- a/recipes/bioconductor-scanvis/meta.yaml +++ b/recipes/bioconductor-scanvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SCANVIS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef9110c213faf5e20efba42cf2d7f3ae + md5: 36977f903eb019d8171d60519360cd9e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scanvis", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-plotrix - r-rcurl run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-plotrix - r-rcurl diff --git a/recipes/bioconductor-scarray.sat/meta.yaml b/recipes/bioconductor-scarray.sat/meta.yaml index d7f2b2408acbb..b1f611aef2382 100644 --- a/recipes/bioconductor-scarray.sat/meta.yaml +++ b/recipes/bioconductor-scarray.sat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.2" %} +{% set version = "1.2.0" %} {% set name = "SCArray.sat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7e9d968f47394b45250bbfdd798e2a7 + md5: da0366cd6f3cc83e7acc0a45bf2d2389 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scarray.sat", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, knitr, markdown, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scarray >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scarray >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-seurat >=4.0' - 'r-seuratobject >=4.0' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scarray >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scarray >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-seurat >=4.0' - 'r-seuratobject >=4.0' diff --git a/recipes/bioconductor-scarray/meta.yaml b/recipes/bioconductor-scarray/meta.yaml index 141ecd2dc248e..2253c7eb3d251 100644 --- a/recipes/bioconductor-scarray/meta.yaml +++ b/recipes/bioconductor-scarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.2" %} +{% set version = "1.10.0" %} {% set name = "SCArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c456b74aefd2269839c207b8207bb99 + md5: c777bd1f1f52dd055b83830ed6da1f77 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scarray", max_pin="x.x") }}' # Suggests: BiocGenerics, scater, scuttle, uwot, RUnit, knitr, markdown, rmarkdown, rhdf5, HDF5Array requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix build: diff --git a/recipes/bioconductor-scatac.explorer/meta.yaml b/recipes/bioconductor-scatac.explorer/meta.yaml index 988544a3cc48c..dc04d869c90f5 100644 --- a/recipes/bioconductor-scatac.explorer/meta.yaml +++ b/recipes/bioconductor-scatac.explorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scATAC.Explorer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 74c840082c522937d200169fcb963f71 + md5: 80927899a83bb06d19b0f9800c183b36 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scatac.explorer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-data.table - r-matrix run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-data.table - r-matrix - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-scatac.explorer/post-link.sh b/recipes/bioconductor-scatac.explorer/post-link.sh index 9ae3e68b76fb3..e9ece7245fbbd 100644 --- a/recipes/bioconductor-scatac.explorer/post-link.sh +++ b/recipes/bioconductor-scatac.explorer/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "scatac.explorer-1.6.0" +installBiocDataPackage.sh "scatac.explorer-1.8.0" diff --git a/recipes/bioconductor-scatedata/meta.yaml b/recipes/bioconductor-scatedata/meta.yaml index 811edf8de2da5..4682d43f3bac4 100644 --- a/recipes/bioconductor-scatedata/meta.yaml +++ b/recipes/bioconductor-scatedata/meta.yaml @@ -31,7 +31,7 @@ requirements: - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20230706 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-scater/meta.yaml b/recipes/bioconductor-scater/meta.yaml index 876940f11b334..06196151e19c6 100644 --- a/recipes/bioconductor-scater/meta.yaml +++ b/recipes/bioconductor-scater/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.1" %} {% set name = "scater" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f90f3937e49253c9abc23e88a0b65b8b + md5: c161043392323318c01792e2de828ad5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scater", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, snifter, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore +# Suggests: BiocStyle, snifter, densvis, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-densvis >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggbeeswarm - r-ggplot2 @@ -47,18 +47,17 @@ requirements: - r-uwot - r-viridis run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-densvis >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggbeeswarm - r-ggplot2 diff --git a/recipes/bioconductor-scatterhatch/meta.yaml b/recipes/bioconductor-scatterhatch/meta.yaml index b2c98f3629e72..7d4048dd2cdaa 100644 --- a/recipes/bioconductor-scatterhatch/meta.yaml +++ b/recipes/bioconductor-scatterhatch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scatterHatch" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d4e9a2d3f03e6a797fb2e5185083adfb + md5: d86cfd4fa0820f65efd6085edc997eed build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scatterhatch", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-scbfa/meta.yaml b/recipes/bioconductor-scbfa/meta.yaml index 18ef2f29a014d..9ab87c6d31b44 100644 --- a/recipes/bioconductor-scbfa/meta.yaml +++ b/recipes/bioconductor-scbfa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "scBFA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0be803eb4149ba1c7b717bbcc44d5f5d + md5: 7729a460da97e96d4da3957b959149db build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scbfa", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, Rtsne requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zinbwave >=1.22.0,<1.23.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zinbwave >=1.24.0,<1.25.0' - r-base - r-copula - r-ggplot2 @@ -32,10 +33,10 @@ requirements: - r-matrix - r-seurat run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zinbwave >=1.22.0,<1.23.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zinbwave >=1.24.0,<1.25.0' - r-base - r-copula - r-ggplot2 diff --git a/recipes/bioconductor-scbn/meta.yaml b/recipes/bioconductor-scbn/meta.yaml index 8fc71321208ce..7da3092848b1b 100644 --- a/recipes/bioconductor-scbn/meta.yaml +++ b/recipes/bioconductor-scbn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "SCBN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9b458b6eb2e4734d08c20d943eb8d591 + md5: c58ee707d9418bd3374773e2675efad7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scbn", max_pin="x.x") }}' noarch: generic # Suggests: knitr,rmarkdown,BiocStyle,BiocManager requirements: diff --git a/recipes/bioconductor-scbubbletree/meta.yaml b/recipes/bioconductor-scbubbletree/meta.yaml index 21887483a2ea6..785fc8a629766 100644 --- a/recipes/bioconductor-scbubbletree/meta.yaml +++ b/recipes/bioconductor-scbubbletree/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "scBubbletree" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 38f21dcba3b6a83f95b6aa770117b5fa + md5: d64f38622d8aec6ebb23e81231710134 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scbubbletree", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat, cluster, SingleCellExperiment # SystemRequirements: Python (>= 3.6), leidenalg (>= 0.8.2) requirements: host: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-ape - r-base - r-future @@ -34,7 +35,7 @@ requirements: - r-scales - r-seurat run: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-ape - r-base - r-future diff --git a/recipes/bioconductor-sccb2/meta.yaml b/recipes/bioconductor-sccb2/meta.yaml index 3de70972b457e..50528ac515db8 100644 --- a/recipes/bioconductor-sccb2/meta.yaml +++ b/recipes/bioconductor-sccb2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "scCB2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c89162a3736d26d21f71934c6cfe782e + md5: aaa88ac58fbc1b32bfc514cc72109ada build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sccb2", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle, rmarkdown # SystemRequirements: C++11 requirements: host: - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-foreach @@ -34,11 +35,11 @@ requirements: - r-matrix - r-seurat run: - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-scclassify/build_failure.linux-64.yaml b/recipes/bioconductor-scclassify/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0c17e3a10137a --- /dev/null +++ b/recipes/bioconductor-scclassify/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5d9ecd6df4ab307246d9923f365939c559cf85122664ccc27d4a9200bf32c6b7 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - r-ggraph + - r-ggplot2 + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - r-cluster + - r-base 4.3.* + - r-matrix + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-cepo >=1.8.0,<1.9.0 + - + + Leaving build/test directories: + Work: + /opt/conda/conda-bld/work + Test: + /opt/conda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + Build: + source activate /opt/conda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - bioconductor-cepo >=1.8.0,<1.9.0 + - r-mixtools + - r-igraph + - r-proxyc + - bioconductor-limma >=3.58.0,<3.59.0 + - r-minpack.lm + - r-diptest + - r-mgcv + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - r-statmod + - bioconductor-hopach >=2.62.0,<2.63.0 + - r-proxy + - r-ggraph + - r-ggplot2 + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - r-cluster + - r-base 4.3.* + - r-matrix + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-cepo >=1.8.0,<1.9.0 + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-cepo[version='>=1.8.0,<1.9.0']")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-scclassify/meta.yaml b/recipes/bioconductor-scclassify/meta.yaml index b4a37a58ae136..c466f33922a97 100644 --- a/recipes/bioconductor-scclassify/meta.yaml +++ b/recipes/bioconductor-scclassify/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "scClassify" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4885483f204e79d0dc8b226030c92ec2 + md5: 6268da69185981088025702610fd424c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scclassify", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, pkgdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-cepo >=1.6.0,<1.7.0' - - 'bioconductor-hopach >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-cepo >=1.8.0,<1.9.0' + - 'bioconductor-hopach >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-diptest @@ -40,11 +41,11 @@ requirements: - r-proxyc - r-statmod run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-cepo >=1.6.0,<1.7.0' - - 'bioconductor-hopach >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-cepo >=1.8.0,<1.9.0' + - 'bioconductor-hopach >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-diptest diff --git a/recipes/bioconductor-sccomp/build_failure.linux-64.yaml b/recipes/bioconductor-sccomp/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..f18015f5e5ff0 --- /dev/null +++ b/recipes/bioconductor-sccomp/build_failure.linux-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: c6c86a551617ab192acea3543c4da0aa9ddee063ff6e7204b82211c508530538 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + package r-rstan-2.32.3-r43h884c59f_0 is excluded by strict repo priority +category: |- + dependency issue diff --git a/recipes/bioconductor-sccomp/build_failure.osx-64.yaml b/recipes/bioconductor-sccomp/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..2b6541107a2bf --- /dev/null +++ b/recipes/bioconductor-sccomp/build_failure.osx-64.yaml @@ -0,0 +1,7 @@ +recipe_sha: c6c86a551617ab192acea3543c4da0aa9ddee063ff6e7204b82211c508530538 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + nothing provides requested r-rstan >=2.26.0 +category: |- + dependency issue + diff --git a/recipes/bioconductor-sccomp/meta.yaml b/recipes/bioconductor-sccomp/meta.yaml index c48f9559a8aa2..60929b0dd67fd 100644 --- a/recipes/bioconductor-sccomp/meta.yaml +++ b/recipes/bioconductor-sccomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "sccomp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 583e84778aab5f72817a07565eab2b4c + md5: 8a24adb07d155b94645a5f684e1455f6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sccomp", max_pin="x.x") }}' # Suggests: BiocStyle, testthat (>= 3.0.0), markdown, knitr, tidyseurat, tidySingleCellExperiment, loo # SystemRequirements: GNU make requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - 'r-bh >=1.66.0' - r-boot @@ -39,11 +40,11 @@ requirements: - 'r-rcppparallel >=5.0.1' - r-readr - r-rlang - - 'r-rstan >=2.18.1' + - 'r-rstan >=2.26.0' - 'r-rstantools >=2.1.1' - r-scales - r-seuratobject - - 'r-stanheaders >=2.18.0' + - 'r-stanheaders >=2.26.0' - r-stringr - r-tibble - r-tidyr @@ -51,7 +52,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - 'r-bh >=1.66.0' - r-boot @@ -69,11 +70,11 @@ requirements: - 'r-rcppparallel >=5.0.1' - r-readr - r-rlang - - 'r-rstan >=2.18.1' + - 'r-rstan >=2.26.0' - 'r-rstantools >=2.1.1' - r-scales - r-seuratobject - - 'r-stanheaders >=2.18.0' + - 'r-stanheaders >=2.26.0' - r-stringr - r-tibble - r-tidyr diff --git a/recipes/bioconductor-scdataviz/meta.yaml b/recipes/bioconductor-scdataviz/meta.yaml index fd5e523561ea4..655232cf0f529 100644 --- a/recipes/bioconductor-scdataviz/meta.yaml +++ b/recipes/bioconductor-scdataviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "scDataviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4970752cedf1f045d1c9e71ec15ae69f + md5: 71744390661cb39c6c12d920e7861d7f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scdataviz", max_pin="x.x") }}' noarch: generic # Suggests: PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra, rmarkdown requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-corrplot - r-ggplot2 @@ -36,9 +37,9 @@ requirements: - r-seurat - r-umap run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-corrplot - r-ggplot2 diff --git a/recipes/bioconductor-scdblfinder/meta.yaml b/recipes/bioconductor-scdblfinder/meta.yaml index c45f71e9d8e46..42aaa31be2a5c 100644 --- a/recipes/bioconductor-scdblfinder/meta.yaml +++ b/recipes/bioconductor-scdblfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "scDblFinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,56 +11,57 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b69060db20baad2947be59b016056069 + md5: b833caa7cf87c1fb4cf9bf599f750ffa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scdblfinder", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-bluster >=1.10.0,<1.11.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-bluster >=1.12.0,<1.13.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-mass - r-matrix - r-xgboost run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-bluster >=1.10.0,<1.11.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-bluster >=1.12.0,<1.13.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-mass diff --git a/recipes/bioconductor-scdd/meta.yaml b/recipes/bioconductor-scdd/meta.yaml index 68ccda52d32b3..417177257b74a 100644 --- a/recipes/bioconductor-scdd/meta.yaml +++ b/recipes/bioconductor-scdd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "scDD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0020a2f90b2264d58527a49f0c467b02 + md5: 3c95209683b09f0584ab315a6fc1e779 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scdd", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, gridExtra requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebseq >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-arm - r-base - r-fields @@ -34,12 +35,12 @@ requirements: - r-mclust - r-outliers run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebseq >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-arm - r-base - r-fields diff --git a/recipes/bioconductor-scddboost/meta.yaml b/recipes/bioconductor-scddboost/meta.yaml index ba0f4ac4f8dfb..5268eed04fe71 100644 --- a/recipes/bioconductor-scddboost/meta.yaml +++ b/recipes/bioconductor-scddboost/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "scDDboost" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45a9eceba86f71915cb4f21a233a86f1 + md5: ac0cac5975ebe4025ea07ad00e132847 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scddboost", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, testthat # SystemRequirements: c++11 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebseq >=1.40.0,<1.41.0' - - 'bioconductor-oscope >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' + - 'bioconductor-oscope >=1.32.0,<1.33.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-cluster @@ -36,11 +37,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebseq >=1.40.0,<1.41.0' - - 'bioconductor-oscope >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' + - 'bioconductor-oscope >=1.32.0,<1.33.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-cluster diff --git a/recipes/bioconductor-scde/meta.yaml b/recipes/bioconductor-scde/meta.yaml index 738ebdeee2379..f4b90ef2f8f2c 100644 --- a/recipes/bioconductor-scde/meta.yaml +++ b/recipes/bioconductor-scde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.2" %} +{% set version = "2.30.0" %} {% set name = "scde" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 46139e017c4865f6976c4ffd576f5c33 + md5: ee4cb04c3a1431fb088d8681ff950d49 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scde", max_pin="x.x") }}' # Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - r-base - r-cairo - r-extremes @@ -40,9 +41,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - r-base - r-cairo - r-extremes diff --git a/recipes/bioconductor-scdesign3/build.sh b/recipes/bioconductor-scdesign3/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scdesign3/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scdesign3/meta.yaml b/recipes/bioconductor-scdesign3/meta.yaml new file mode 100644 index 0000000000000..a5b20677348d3 --- /dev/null +++ b/recipes/bioconductor-scdesign3/meta.yaml @@ -0,0 +1,73 @@ +{% set version = "1.0.0" %} +{% set name = "scDesign3" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 84c2f07635607b2167f24750f952745a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scdesign3", max_pin="x.x") }}' + noarch: generic +# Suggests: mvnfast, igraph, knitr, rmarkdown, testthat (>= 3.0.0), RefManageR, sessioninfo, BiocStyle +requirements: + host: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-dplyr + - r-gamlss + - r-gamlss.dist + - r-ggplot2 + - r-irlba + - r-matrix + - r-matrixstats + - r-mclust + - r-mgcv + - r-mvtnorm + - r-pbmcapply + - r-rvinecopulib + - r-tibble + - r-umap + - r-viridis + run: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-dplyr + - r-gamlss + - r-gamlss.dist + - r-ggplot2 + - r-irlba + - r-matrix + - r-matrixstats + - r-mclust + - r-mgcv + - r-mvtnorm + - r-pbmcapply + - r-rvinecopulib + - r-tibble + - r-umap + - r-viridis +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics' + description: 'We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning interpretable parameters from real data. Using a unified probabilistic model for single-cell and spatial omics data, scDesign3 infers biologically meaningful parameters; assesses the goodness-of-fit of inferred cell clusters, trajectories, and spatial locations; and generates in silico negative and positive controls for benchmarking computational tools.' + license_file: LICENSE + diff --git a/recipes/bioconductor-scds/meta.yaml b/recipes/bioconductor-scds/meta.yaml index 9eb5e24d3a2a2..58c835c7336f2 100644 --- a/recipes/bioconductor-scds/meta.yaml +++ b/recipes/bioconductor-scds/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "scds" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 604b9f1136e4d2cfa79cc1ea1776e194 + md5: df6bd91f4acdd6ea2e54d2f20f632cbf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scds", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-matrix - r-proc - r-xgboost run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-matrix diff --git a/recipes/bioconductor-scfa/meta.yaml b/recipes/bioconductor-scfa/meta.yaml index 2aa546f1a74e0..1980760f8cd2b 100644 --- a/recipes/bioconductor-scfa/meta.yaml +++ b/recipes/bioconductor-scfa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "SCFA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c694613f0dc42e223334903db005fcae + md5: c4e7d00ff20faff6a8a14eddde8e7a84 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scfa", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-cluster - r-coro @@ -34,7 +35,7 @@ requirements: - r-survival - 'r-torch >=0.3.0' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-cluster - r-coro diff --git a/recipes/bioconductor-scfeaturefilter/meta.yaml b/recipes/bioconductor-scfeaturefilter/meta.yaml index 7dbd32013e28f..ce5324266d06b 100644 --- a/recipes/bioconductor-scfeaturefilter/meta.yaml +++ b/recipes/bioconductor-scfeaturefilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "scFeatureFilter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2bd744106dbac3e5ea1b17cdc17db357 + md5: f642025d766eb2cd17f406126e6fe0ba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scfeaturefilter", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot requirements: diff --git a/recipes/bioconductor-scfeatures/meta.yaml b/recipes/bioconductor-scfeatures/meta.yaml index 2bcef4fd2f796..1b4a39426bc3a 100644 --- a/recipes/bioconductor-scfeatures/meta.yaml +++ b/recipes/bioconductor-scfeatures/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "scFeatures" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eaf120744a2b4c979aaf8ef6a0b56179 + md5: 00b3e1296507cdf60879fd6d112c1e53 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scfeatures", max_pin="x.x") }}' noarch: generic # Suggests: knitr, S4Vectors, survival, survminer, BiocStyle, ClassifyR, org.Hs.eg.db, clusterProfiler requirements: host: - - 'bioconductor-aucell >=1.22.0,<1.23.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' + - 'bioconductor-aucell >=1.24.0,<1.25.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - 'bioconductor-ensdb.hsapiens.v79 >=2.99.0,<2.100.0' - 'bioconductor-ensdb.mmusculus.v79 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-singlecellsignalr >=1.12.0,<1.13.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-singlecellsignalr >=1.14.0,<1.15.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-base - r-cli @@ -49,18 +50,18 @@ requirements: - r-spatstat.geom - r-tidyr run: - - 'bioconductor-aucell >=1.22.0,<1.23.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' + - 'bioconductor-aucell >=1.24.0,<1.25.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - 'bioconductor-ensdb.hsapiens.v79 >=2.99.0,<2.100.0' - 'bioconductor-ensdb.mmusculus.v79 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-singlecellsignalr >=1.12.0,<1.13.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-singlecellsignalr >=1.14.0,<1.15.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-base - r-cli diff --git a/recipes/bioconductor-scgps/meta.yaml b/recipes/bioconductor-scgps/meta.yaml index 64fd1c2a66667..c5ced940c31bd 100644 --- a/recipes/bioconductor-scgps/meta.yaml +++ b/recipes/bioconductor-scgps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "scGPS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5470238c90cb59ccf891bd93de16774c + md5: 5d11fe3a4af0d56d3028d97c6090ccfb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scgps", max_pin="x.x") }}' # Suggests: Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown, RColorBrewer, ReactomePA, clusterProfiler, cowplot, org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne, BiocParallel, e1071, WGCNA, devtools, DOSE # SystemRequirements: GNU make requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-caret >=6.0' - r-dplyr @@ -38,9 +39,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-caret >=6.0' - r-dplyr diff --git a/recipes/bioconductor-schex/meta.yaml b/recipes/bioconductor-schex/meta.yaml index 540fadf7b9012..c1c3dd9dbf16f 100644 --- a/recipes/bioconductor-schex/meta.yaml +++ b/recipes/bioconductor-schex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "schex" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ed1bc17ff4de0560d1d36821b72b7ca2 + md5: 5be5dd9c76b2ee49cc894a728b08e2e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-schex", max_pin="x.x") }}' noarch: generic # Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, shinydashboard, iSEE, igraph, scran requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-cluster - r-concaveman @@ -34,7 +35,7 @@ requirements: - r-seurat - r-shiny run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-cluster - r-concaveman diff --git a/recipes/bioconductor-schot/meta.yaml b/recipes/bioconductor-schot/meta.yaml index 40e0dc7962bde..c35c587215b4b 100644 --- a/recipes/bioconductor-schot/meta.yaml +++ b/recipes/bioconductor-schot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "scHOT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 22cc889e9d524a0744ac6477d9e7dac9 + md5: 75f460d2a6c2d8bee223b64a05eb6224 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-schot", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown, rmarkdown, scater, scattermore, scales, matrixStats, deldir requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggforce - r-ggplot2 @@ -33,11 +34,11 @@ requirements: - r-matrix - r-reshape run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggforce - r-ggplot2 diff --git a/recipes/bioconductor-scider/build.sh b/recipes/bioconductor-scider/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scider/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scider/meta.yaml b/recipes/bioconductor-scider/meta.yaml new file mode 100644 index 0000000000000..2dae5324cfcfe --- /dev/null +++ b/recipes/bioconductor-scider/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.0.0" %} +{% set name = "scider" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d20e0e846be7368da2613650b3834957 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scider", max_pin="x.x") }}' + noarch: generic +# Suggests: edgeR, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-ggplot2 + - r-igraph + - r-isoband + - r-janitor + - r-knitr + - r-lwgeom + - r-pheatmap + - r-plotly + - r-rlang + - r-sf + - r-shiny + - r-spatstat.explore + - r-spatstat.geom + run: + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-ggplot2 + - r-igraph + - r-isoband + - r-janitor + - r-knitr + - r-lwgeom + - r-pheatmap + - r-plotly + - r-rlang + - r-sf + - r-shiny + - r-spatstat.explore + - r-spatstat.geom +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'Spatial cell-type inter-correlation by density in R' + description: 'scider is an user-friendly R package providing functions to model the global density of cells in a slide of spatial transcriptomics data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. After modelling density, the package allows for serveral downstream analysis, including colocalization analysis, boundary detection analysis and differential density analysis.' + license_file: LICENSE + diff --git a/recipes/bioconductor-scifer/meta.yaml b/recipes/bioconductor-scifer/meta.yaml index 58e0dc58589ef..6f53163b0a43b 100644 --- a/recipes/bioconductor-scifer/meta.yaml +++ b/recipes/bioconductor-scifer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "scifer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e39ab9c9a71dd10992aedf09000f9848 + md5: 82fb184bec0c09d5f7067baf81f8fee1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scifer", max_pin="x.x") }}' noarch: generic # Suggests: fs, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-sangerseqr >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-sangerseqr >=1.38.0,<1.39.0' - r-base - r-data.table - r-dplyr @@ -39,10 +40,10 @@ requirements: - r-stringr - r-tibble run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-sangerseqr >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-sangerseqr >=1.38.0,<1.39.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-sclcbam/meta.yaml b/recipes/bioconductor-sclcbam/meta.yaml index 407bca15aae77..974fda737ce12 100644 --- a/recipes/bioconductor-sclcbam/meta.yaml +++ b/recipes/bioconductor-sclcbam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "SCLCBam" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ca48c42a5e16460f72eb8bfbc697258f + md5: 660f11c1751b54cc942e91045884bfe6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sclcbam", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sclcbam/post-link.sh b/recipes/bioconductor-sclcbam/post-link.sh index bb942bfa1cea4..ebe08391743a4 100644 --- a/recipes/bioconductor-sclcbam/post-link.sh +++ b/recipes/bioconductor-sclcbam/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "sclcbam-1.32.0" +installBiocDataPackage.sh "sclcbam-1.34.0" diff --git a/recipes/bioconductor-scmap/meta.yaml b/recipes/bioconductor-scmap/meta.yaml index 931d39e162095..747a349f39a63 100644 --- a/recipes/bioconductor-scmap/meta.yaml +++ b/recipes/bioconductor-scmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.3" %} +{% set version = "1.24.0" %} {% set name = "scmap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a58a3a176f62d952dcd685a9027459bf + md5: de159d16de109a02a1c7cb3c85418b58 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scmap", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-e1071 @@ -39,11 +40,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-e1071 diff --git a/recipes/bioconductor-scmerge/meta.yaml b/recipes/bioconductor-scmerge/meta.yaml index 8387100c27930..e33892f3dba5d 100644 --- a/recipes/bioconductor-scmerge/meta.yaml +++ b/recipes/bioconductor-scmerge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "scMerge" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cee90634720dffc0c35a55bb3b6cb95b + md5: d5b285890500ad5c781d33ab45282aca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scmerge", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, proxy, testthat, badger requirements: host: - - 'bioconductor-batchelor >=1.16.0,<1.17.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-m3drop >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-batchelor >=1.18.0,<1.19.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-m3drop >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-cvtools @@ -41,18 +42,18 @@ requirements: - r-proxyc - r-ruv run: - - 'bioconductor-batchelor >=1.16.0,<1.17.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-m3drop >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-batchelor >=1.18.0,<1.19.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-m3drop >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-cvtools diff --git a/recipes/bioconductor-scmet/meta.yaml b/recipes/bioconductor-scmet/meta.yaml index c8f7b35e4d3a1..9a2d2fce9889a 100644 --- a/recipes/bioconductor-scmet/meta.yaml +++ b/recipes/bioconductor-scmet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "scMET" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ade04cb98f2b5a74bdab738295cfabb + md5: 6420a2af7464f67eb676f06d20f9d5a6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scmet", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - 'r-bh >=1.66.0' @@ -48,10 +49,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - 'r-bh >=1.66.0' diff --git a/recipes/bioconductor-scmeth/meta.yaml b/recipes/bioconductor-scmeth/meta.yaml index 4502f17020d8e..97b16204b19f5 100644 --- a/recipes/bioconductor-scmeth/meta.yaml +++ b/recipes/bioconductor-scmeth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "scmeth" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,42 +11,43 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f3e27676cdd8c4eda10fd5004329a574 + md5: 52beac81d58da27e01cc5e1a0b6584b2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scmeth", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-annotatr >=1.26.0,<1.27.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-annotatr >=1.28.0,<1.29.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dt - r-knitr - r-reshape2 - r-rmarkdown run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-annotatr >=1.26.0,<1.27.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-annotatr >=1.28.0,<1.29.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dt - r-knitr diff --git a/recipes/bioconductor-scmultiome/build_failure.linux-64.yaml b/recipes/bioconductor-scmultiome/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..3225ddc538d53 --- /dev/null +++ b/recipes/bioconductor-scmultiome/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 6724b9796e501ce375d77f605eb535671bf9bee68ee4a9d1873f64c6432b2905 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + dependency issue +log: |2- + - bioconductor-genomicranges >=1.52.0,<1.53.0 + - r-base 4.3.* + - bioconductor-multiassayexperiment >=1.26.0,<1.27.0 + - bioconductor-experimenthub >=2.8.0,<2.9.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - r-checkmate + - bioconductor-hdf5array >=1.28.0,<1.29.0 + - bioconductor-singlecellexperiment >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.26.0,<0.27.0 + - bioconductor-rhdf5 >=2.44.0,<2.45.0 + - bioconductor-annotationhub >=3.8.0,<3.9.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - r-azurestor + + with channels: + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested r-azurestor + - + + Leaving build/test directories: + Work: + /opt/conda/conda-bld/work + Test: + /opt/conda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + Build: + source activate /opt/conda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - bioconductor-genomicranges >=1.52.0,<1.53.0 + - r-base 4.3.* + - bioconductor-multiassayexperiment >=1.26.0,<1.27.0 + - bioconductor-experimenthub >=2.8.0,<2.9.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - r-checkmate + - bioconductor-hdf5array >=1.28.0,<1.29.0 + - bioconductor-singlecellexperiment >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.26.0,<0.27.0 + - bioconductor-rhdf5 >=2.44.0,<2.45.0 + - bioconductor-annotationhub >=3.8.0,<3.9.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - r-azurestor + + with channels: + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested r-azurestor + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-azurestor")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-scmultiome/meta.yaml b/recipes/bioconductor-scmultiome/meta.yaml index 4439589f6fb34..eaa4577ecd304 100644 --- a/recipes/bioconductor-scmultiome/meta.yaml +++ b/recipes/bioconductor-scmultiome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "scMultiome" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 22aceaa129afbecd400b2d16b6333d43 + md5: db13145ffc5eb5430eee8ac7212e1b7d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scmultiome", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, IRanges, Matrix, knitr, rmarkdown, rstudioapi, testthat (>= 3.0.0), devtools, BiocStyle, ExperimentHubData requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-azurestor - r-base - r-checkmate run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-azurestor - r-base - r-checkmate - curl - - bioconductor-data-packages >=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-scmultiome/post-link.sh b/recipes/bioconductor-scmultiome/post-link.sh index 3ce950ad4ac67..1324e5cb2e2c7 100644 --- a/recipes/bioconductor-scmultiome/post-link.sh +++ b/recipes/bioconductor-scmultiome/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "scmultiome-1.0.0" +installBiocDataPackage.sh "scmultiome-1.2.0" diff --git a/recipes/bioconductor-scnorm/meta.yaml b/recipes/bioconductor-scnorm/meta.yaml index b9547849c0a78..c4058c473a397 100644 --- a/recipes/bioconductor-scnorm/meta.yaml +++ b/recipes/bioconductor-scnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "SCnorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5901d07a8f6feacfef451fc204de8eed + md5: cfac086eb57336e865c999c4c0b42a0c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scnorm", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, devtools requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-data.table @@ -34,11 +35,11 @@ requirements: - r-moments - r-quantreg run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-data.table diff --git a/recipes/bioconductor-scone/meta.yaml b/recipes/bioconductor-scone/meta.yaml index 7dbfa2a2f2363..07e654e223342 100644 --- a/recipes/bioconductor-scone/meta.yaml +++ b/recipes/bioconductor-scone/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "scone" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 03ca7a497be498bc8ba6ff313d121434 + md5: 0e7dd77999fc8cbf842fee6452c82a1b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scone", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData requirements: host: - - 'bioconductor-aroma.light >=3.30.0,<3.31.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-aroma.light >=3.32.0,<3.33.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-class @@ -44,15 +45,15 @@ requirements: - r-rarpack - r-rcolorbrewer run: - - 'bioconductor-aroma.light >=3.30.0,<3.31.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-aroma.light >=3.32.0,<3.33.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-class diff --git a/recipes/bioconductor-sconify/meta.yaml b/recipes/bioconductor-sconify/meta.yaml index 26161eee8cbc4..c166731eb09ff 100644 --- a/recipes/bioconductor-sconify/meta.yaml +++ b/recipes/bioconductor-sconify/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "Sconify" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 730ac89643009501cab5346657dfe4a8 + md5: 61762bc5d7e8560ae818942a21da33a5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sconify", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-dplyr - r-fnn @@ -31,7 +32,7 @@ requirements: - r-rtsne - r-tibble run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-dplyr - r-fnn diff --git a/recipes/bioconductor-scope/meta.yaml b/recipes/bioconductor-scope/meta.yaml index a631ec984b3ab..3943cc3b77751 100644 --- a/recipes/bioconductor-scope/meta.yaml +++ b/recipes/bioconductor-scope/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "SCOPE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a727431edb54a52f5618b8273c73be24 + md5: b8e4ce76717f217322282d378de1b3bd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scope", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-desctools - r-doparallel @@ -38,16 +39,16 @@ requirements: - r-gplots - r-rcolorbrewer run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-desctools - r-doparallel diff --git a/recipes/bioconductor-scoreinvhap/meta.yaml b/recipes/bioconductor-scoreinvhap/meta.yaml index a0e7f0f0f7dc2..2ce9837a52775 100644 --- a/recipes/bioconductor-scoreinvhap/meta.yaml +++ b/recipes/bioconductor-scoreinvhap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "scoreInvHap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3acda727fc5294ab60fa6badf682b337 + md5: 7505f8161571dcc7b9b752fc62dedce5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scoreinvhap", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-scp/meta.yaml b/recipes/bioconductor-scp/meta.yaml index 914e612750fe1..c349acb3dacba 100644 --- a/recipes/bioconductor-scp/meta.yaml +++ b/recipes/bioconductor-scp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "scp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f16e9ca95ef9a6ff5df7dd223533d987 + md5: c4f759cfb996e6150ecec65b7de3e343 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scp", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, knitr, BiocStyle, rmarkdown, patchwork, ggplot2, impute, scater, sva, preprocessCore, vsn, uwot +# Suggests: scpdata, testthat, knitr, BiocStyle, rmarkdown, ggplot2, patchwork, impute, scater, sva, preprocessCore, vsn, uwot requirements: host: - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-magrittr - r-matrixstats run: - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-magrittr diff --git a/recipes/bioconductor-scpca/meta.yaml b/recipes/bioconductor-scpca/meta.yaml index 0d8b6478fc46d..61a413188a29a 100644 --- a/recipes/bioconductor-scpca/meta.yaml +++ b/recipes/bioconductor-scpca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "scPCA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 573b440af9c8058ea71852420c36c695 + md5: e7058ad8f079f25d21ae55911652d01d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scpca", max_pin="x.x") }}' noarch: generic # Suggests: DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter, SingleCellExperiment, microbenchmark requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-scaledmatrix >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' - r-assertthat - r-base - r-cluster @@ -42,10 +43,10 @@ requirements: - r-stringr - r-tibble run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-scaledmatrix >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' - r-assertthat - r-base - r-cluster diff --git a/recipes/bioconductor-scpdata/meta.yaml b/recipes/bioconductor-scpdata/meta.yaml index 8d5a56ba0bbb4..cf133817eeedf 100644 --- a/recipes/bioconductor-scpdata/meta.yaml +++ b/recipes/bioconductor-scpdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "scpdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0a00beb40a6ae72de0364698c7a0129b + md5: eac9eae58fe9297359188c45a3dabd1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scpdata", max_pin="x.x") }}' noarch: generic # Suggests: scp, magrittr, dplyr, knitr, BiocStyle, BiocCheck, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-scpdata/post-link.sh b/recipes/bioconductor-scpdata/post-link.sh index 25f2c1ee4adfb..6e55327fbf91f 100644 --- a/recipes/bioconductor-scpdata/post-link.sh +++ b/recipes/bioconductor-scpdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "scpdata-1.8.0" +installBiocDataPackage.sh "scpdata-1.10.0" diff --git a/recipes/bioconductor-scpipe/meta.yaml b/recipes/bioconductor-scpipe/meta.yaml index 0b0bb5c2db301..9efcbe7c1cace 100644 --- a/recipes/bioconductor-scpipe/meta.yaml +++ b/recipes/bioconductor-scpipe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.0" %} +{% set version = "2.2.0" %} {% set name = "scPipe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 460d566decff05a6ed6c304b1aa2a9ee + md5: 477ce2b2da9cc1ae5365c3140d6ed566 build: skip: True # [osx] number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scpipe", max_pin="x.x") }}' # Suggests: BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra, knitr, locStra, plotly, rmarkdown, RColorBrewer, readr, reshape2, RANN, shiny, scater (>= 1.11.0), testthat, xml2, umap # SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-data.table - r-dplyr @@ -65,29 +66,30 @@ requirements: - r-testthat - r-tibble - r-tidyr + - 'r-vctrs >=0.5.2' - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-data.table - r-dplyr @@ -111,6 +113,7 @@ requirements: - r-testthat - r-tibble - r-tidyr + - 'r-vctrs >=0.5.2' build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-scran/meta.yaml b/recipes/bioconductor-scran/meta.yaml index 9bff44d2d9e10..e1341546092cc 100644 --- a/recipes/bioconductor-scran/meta.yaml +++ b/recipes/bioconductor-scran/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "scran" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 46f41388ff6b8b0928f012dbf1e962fd + md5: f8cc4c59dde80171927b115dc09592af build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scran", max_pin="x.x") }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, monocle, Biobase, pheatmap, scater # SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-bluster >=1.10.0,<1.11.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-metapod >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-bluster >=1.12.0,<1.13.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-metapod >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-dqrng @@ -45,20 +46,20 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-bluster >=1.10.0,<1.11.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-metapod >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-bluster >=1.12.0,<1.13.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-metapod >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-dqrng diff --git a/recipes/bioconductor-screclassify/meta.yaml b/recipes/bioconductor-screclassify/meta.yaml index a8888b9ef13c0..6ab9c50202c44 100644 --- a/recipes/bioconductor-screclassify/meta.yaml +++ b/recipes/bioconductor-screclassify/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scReClassify" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0b0b6ffa809d9b206a9eecf23e3d4b23 + md5: 722bce944db1f380df35d68a47c4bef7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-screclassify", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-randomforest run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-randomforest diff --git a/recipes/bioconductor-screcover/meta.yaml b/recipes/bioconductor-screcover/meta.yaml index bfb98c8972abd..f0024c38fdf5e 100644 --- a/recipes/bioconductor-screcover/meta.yaml +++ b/recipes/bioconductor-screcover/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "scRecover" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b621333aa197e50352b5e297092ab2bb + md5: ebdc203b50818397a1856fdce417f10e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-screcover", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, SingleCellExperiment, testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - 'r-bbmle >=1.0.18' - r-doparallel @@ -36,7 +37,7 @@ requirements: - r-rsvd - 'r-saver >=1.1.1' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - 'r-bbmle >=1.0.18' - r-doparallel diff --git a/recipes/bioconductor-screencounter/meta.yaml b/recipes/bioconductor-screencounter/meta.yaml index 05d9fc3635670..d706b51cee9f4 100644 --- a/recipes/bioconductor-screencounter/meta.yaml +++ b/recipes/bioconductor-screencounter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "screenCounter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5865a3dafb6a822adc5831b3c1fad028 + md5: 35bb89fb63853645e76facfc72e77522 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: Biostrings, BiocStyle, knitr, rmarkdown, testthat -# SystemRequirements: C++17 + run_exports: '{{ pin_subpackage("bioconductor-screencounter", max_pin="x.x") }}' +# Suggests: BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown, testthat +# SystemRequirements: C++17, GNU make requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-screenr/meta.yaml b/recipes/bioconductor-screenr/meta.yaml index 46671016ada11..34203b1646f65 100644 --- a/recipes/bioconductor-screenr/meta.yaml +++ b/recipes/bioconductor-screenr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ScreenR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 07fa63df60f427c8bacc15777075f113 + md5: bb8bd3276b17f7e0d63de9c19e64473d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-screenr", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown (>= 2.11), knitr (>= 1.37), testthat (>= 3.0.0), BiocStyle (>= 2.22.0), covr (>= 3.5) requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - 'r-dplyr >=1.0' - 'r-ggplot2 >=3.3' @@ -37,8 +38,8 @@ requirements: - 'r-tidyr >=1.2' - 'r-tidyselect >=1.1.2' run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - 'r-dplyr >=1.0' - 'r-ggplot2 >=3.3' diff --git a/recipes/bioconductor-screpertoire/meta.yaml b/recipes/bioconductor-screpertoire/meta.yaml index 9b5a1b165f172..e423553bb5630 100644 --- a/recipes/bioconductor-screpertoire/meta.yaml +++ b/recipes/bioconductor-screpertoire/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "scRepertoire" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d64c8e5caff50abe3de5ddf47f49598 + md5: 3debd173702ebe6c551ba6c572a76c25 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-screpertoire", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, circlize, scales, Seurat, scater requirements: host: - - 'bioconductor-powertcr >=1.20.0,<1.21.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-powertcr >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-dplyr @@ -40,9 +41,9 @@ requirements: - r-tidygraph - r-vegan run: - - 'bioconductor-powertcr >=1.20.0,<1.21.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-powertcr >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-dplyr diff --git a/recipes/bioconductor-scrnaseq/meta.yaml b/recipes/bioconductor-scrnaseq/meta.yaml index 5fe75ed603bb6..8ac4a0edce522 100644 --- a/recipes/bioconductor-scrnaseq/meta.yaml +++ b/recipes/bioconductor-scrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "scRNAseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3adccc738839605191c0eda859e3d7c7 + md5: 55196cb10876aa15733c6a29ffc38100 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scrnaseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, BiocFileCache, testthat, rappdirs, tools requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-scrnaseq/post-link.sh b/recipes/bioconductor-scrnaseq/post-link.sh index 95c672ef7f73a..25b040d1f3d7a 100644 --- a/recipes/bioconductor-scrnaseq/post-link.sh +++ b/recipes/bioconductor-scrnaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "scrnaseq-2.14.0" +installBiocDataPackage.sh "scrnaseq-2.16.0" diff --git a/recipes/bioconductor-scrnaseqapp/meta.yaml b/recipes/bioconductor-scrnaseqapp/meta.yaml index cb79acb7eff21..d31492b6be478 100644 --- a/recipes/bioconductor-scrnaseqapp/meta.yaml +++ b/recipes/bioconductor-scrnaseqapp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.2" %} {% set name = "scRNAseqApp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 831fc1f4ceb49cfe0182b5c22312521f + md5: a9b64e980a9e0acef5ab93a44a35e124 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scrnaseqapp", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat, BiocStyle requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-slingshot >=2.8.0,<2.9.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-slingshot >=2.10.0,<2.11.0' - r-base - r-bibtex - r-bslib @@ -57,18 +58,19 @@ requirements: - r-shiny - r-shinyhelper - r-shinymanager + - r-sortable - r-xfun - r-xml2 run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-slingshot >=2.8.0,<2.9.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-slingshot >=2.10.0,<2.11.0' - r-base - r-bibtex - r-bslib @@ -96,6 +98,7 @@ requirements: - r-shiny - r-shinyhelper - r-shinymanager + - r-sortable - r-xfun - r-xml2 test: diff --git a/recipes/bioconductor-scruff/meta.yaml b/recipes/bioconductor-scruff/meta.yaml index 0c226e6bef9eb..51177f8c27686 100644 --- a/recipes/bioconductor-scruff/meta.yaml +++ b/recipes/bioconductor-scruff/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "scruff" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,60 +11,63 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bad66b3a487c31db11e46744295fb017 + md5: cd21598690887291d1540e0a827fb6cc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scruff", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-ggplot2 - r-ggthemes + - r-parallelly - r-plyr - r-scales - r-stringdist run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-ggplot2 - r-ggthemes + - r-parallelly - r-plyr - r-scales - r-stringdist diff --git a/recipes/bioconductor-scry/meta.yaml b/recipes/bioconductor-scry/meta.yaml index b979189a9b8a4..741c3bb267ea5 100644 --- a/recipes/bioconductor-scry/meta.yaml +++ b/recipes/bioconductor-scry/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "scry" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6887e89a51b1ea222901e82c6ae9c98b + md5: dbdcf37d35f52ba787d1d8d5f21e886e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scry", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, covr, DuoClustering2018, ggplot2, HDF5Array, knitr, markdown, rmarkdown, TENxPBMCData, testthat requirements: host: - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-glmpca >=0.2.0' - r-matrix run: - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-glmpca >=0.2.0' - r-matrix diff --git a/recipes/bioconductor-scshapes/meta.yaml b/recipes/bioconductor-scshapes/meta.yaml index 922a38b33bcd6..d12d4297ae966 100644 --- a/recipes/bioconductor-scshapes/meta.yaml +++ b/recipes/bioconductor-scshapes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scShapes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b5284952d27abe9951426b826927589d + md5: 5a4954c320f7b1f30f8fbff6e9f5ad91 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scshapes", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-dgof - r-emdbook @@ -31,7 +32,7 @@ requirements: - r-pscl - r-vgam run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-dgof - r-emdbook diff --git a/recipes/bioconductor-sctensor/meta.yaml b/recipes/bioconductor-sctensor/meta.yaml index c4d7f96cb801e..a835706474c23 100644 --- a/recipes/bioconductor-sctensor/meta.yaml +++ b/recipes/bioconductor-sctensor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "scTensor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a026dfae8b4238cae3ff79142fc22cdb + md5: cfbb59a88b526fe373aacf4b1b1a5a97 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sctensor", max_pin="x.x") }}' noarch: generic # Suggests: testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-meshdbi >=1.36.0,<1.37.0' - - 'bioconductor-meshr >=2.6.0,<2.7.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-reactomepa >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-schex >=1.14.0,<1.15.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-meshdbi >=1.38.0,<1.39.0' + - 'bioconductor-meshr >=2.8.0,<2.9.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-reactomepa >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-schex >=1.16.0,<1.17.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-biocmanager @@ -55,20 +56,20 @@ requirements: - r-tagcloud - r-visnetwork run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-meshdbi >=1.36.0,<1.37.0' - - 'bioconductor-meshr >=2.6.0,<2.7.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-reactomepa >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-schex >=1.14.0,<1.15.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-meshdbi >=1.38.0,<1.39.0' + - 'bioconductor-meshr >=2.8.0,<2.9.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-reactomepa >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-schex >=1.16.0,<1.17.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-biocmanager diff --git a/recipes/bioconductor-sctgif/meta.yaml b/recipes/bioconductor-sctgif/meta.yaml index 42c82df750628..bc0285138b195 100644 --- a/recipes/bioconductor-sctgif/meta.yaml +++ b/recipes/bioconductor-sctgif/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "scTGIF" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 374dde7d11795e274cfc50aed4fe792d + md5: 7fcf2fd9ff8c1d34aaa64399fa876f3a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sctgif", max_pin="x.x") }}' # Suggests: testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-schex >=1.14.0,<1.15.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-schex >=1.16.0,<1.17.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-igraph @@ -43,13 +44,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-schex >=1.14.0,<1.15.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-schex >=1.16.0,<1.17.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-igraph diff --git a/recipes/bioconductor-scthi.data/meta.yaml b/recipes/bioconductor-scthi.data/meta.yaml index 05d45aa099e78..d2c6c62b7e0c1 100644 --- a/recipes/bioconductor-scthi.data/meta.yaml +++ b/recipes/bioconductor-scthi.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "scTHI.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 28e55c6ba60cb8527c376ca87993c95c + md5: 1fd101f8dc30262c323bdfa79810f6f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scthi.data", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-scthi.data/post-link.sh b/recipes/bioconductor-scthi.data/post-link.sh index 16c433ce6a893..7763769e34368 100644 --- a/recipes/bioconductor-scthi.data/post-link.sh +++ b/recipes/bioconductor-scthi.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "scthi.data-1.12.0" +installBiocDataPackage.sh "scthi.data-1.14.0" diff --git a/recipes/bioconductor-scthi/meta.yaml b/recipes/bioconductor-scthi/meta.yaml index b4e4abeceb114..1e0797b2c9961 100644 --- a/recipes/bioconductor-scthi/meta.yaml +++ b/recipes/bioconductor-scthi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "scTHI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ebb6421876980b77128b35e11b44e86 + md5: c90e49b0aaed73dd76437e5236607e06 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scthi", max_pin="x.x") }}' noarch: generic # Suggests: scTHI.data, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-rtsne run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-rtsne test: diff --git a/recipes/bioconductor-sctreeviz/meta.yaml b/recipes/bioconductor-sctreeviz/meta.yaml index 39baa864da5fb..b05fd3b6f86e7 100644 --- a/recipes/bioconductor-sctreeviz/meta.yaml +++ b/recipes/bioconductor-sctreeviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scTreeViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 927a1013984382aa44378cc9c728e2d4 + md5: 9e1a317862ad079f52876f54d7160bde build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sctreeviz", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb requirements: host: - - 'bioconductor-epivizr >=2.30.0,<2.31.0' - - 'bioconductor-epivizrdata >=1.28.0,<1.29.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-epivizr >=2.32.0,<2.33.0' + - 'bioconductor-epivizrdata >=1.30.0,<1.31.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-clustree - r-data.table @@ -42,14 +43,14 @@ requirements: - r-seurat - r-sys run: - - 'bioconductor-epivizr >=2.30.0,<2.31.0' - - 'bioconductor-epivizrdata >=1.28.0,<1.29.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-epivizr >=2.32.0,<2.33.0' + - 'bioconductor-epivizrdata >=1.30.0,<1.31.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-clustree - r-data.table diff --git a/recipes/bioconductor-scuttle/meta.yaml b/recipes/bioconductor-scuttle/meta.yaml index 9ce4f8ac5fa8f..a227c84e0e2c4 100644 --- a/recipes/bioconductor-scuttle/meta.yaml +++ b/recipes/bioconductor-scuttle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "scuttle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 55127c8e30fa4c15da7ba31721165165 + md5: b784ac30ef76b7c0cdac8b79be67b995 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scuttle", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat, scran # SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-scvir/meta.yaml b/recipes/bioconductor-scvir/meta.yaml index 4608eb617c904..1c38e61212da1 100644 --- a/recipes/bioconductor-scvir/meta.yaml +++ b/recipes/bioconductor-scvir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "scviR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a3c949daf08cae151d0ffc4fe6918fb + md5: 71d6c427fcc042ac8b011a31935641df build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scvir", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, reshape2, ggplot2, rhdf5, BiocStyle requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-pheatmap - r-reticulate - r-shiny run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-pheatmap - r-reticulate diff --git a/recipes/bioconductor-sdams/meta.yaml b/recipes/bioconductor-sdams/meta.yaml index 10f1e293bd99c..8ad0a22e4f270 100644 --- a/recipes/bioconductor-sdams/meta.yaml +++ b/recipes/bioconductor-sdams/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "SDAMS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 70ceba01b2d6ce773d03ed13e393ee87 + md5: 27ac3a8046a94bf8473502ee2cd5afe1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sdams", max_pin="x.x") }}' noarch: generic # Suggests: testthat requirements: host: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-trust run: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-trust test: diff --git a/recipes/bioconductor-sechm/meta.yaml b/recipes/bioconductor-sechm/meta.yaml index 14b5526db7524..5d3d35924430b 100644 --- a/recipes/bioconductor-sechm/meta.yaml +++ b/recipes/bioconductor-sechm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "sechm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f1467f46edc1aa8f86c05aae81d2f368 + md5: 6935a759779eaf70e1cbf3f22c7a1358 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sechm", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-matrixstats - r-randomcolor - r-seriation run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-matrixstats diff --git a/recipes/bioconductor-segmenter/meta.yaml b/recipes/bioconductor-segmenter/meta.yaml index c03b8b20a8a21..76cfdd42e39c9 100644 --- a/recipes/bioconductor-segmenter/meta.yaml +++ b/recipes/bioconductor-segmenter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "segmenter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 45997faeb651d2c6d5670b3713a8388d + md5: 8877dce2f35cc59e9c3d8b3fb38bf29e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-segmenter", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz requirements: host: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-chipseeker >=1.36.0,<1.37.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-chipseeker >=1.38.0,<1.39.0' - 'bioconductor-chromhmmdata >=0.99.0,<0.100.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-chipseeker >=1.36.0,<1.37.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-chipseeker >=1.38.0,<1.39.0' - 'bioconductor-chromhmmdata >=0.99.0,<0.100.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-segmentseq/build.sh b/recipes/bioconductor-segmentseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-segmentseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-segmentseq/meta.yaml b/recipes/bioconductor-segmentseq/meta.yaml new file mode 100644 index 0000000000000..e43eace8f35f7 --- /dev/null +++ b/recipes/bioconductor-segmentseq/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "2.36.0" %} +{% set name = "segmentSeq" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f86ecc00eba08e4f13412c624d98697c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-segmentseq", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, BiocGenerics +requirements: + host: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - r-abind + - r-base + run: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - r-abind + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Methods for identifying small RNA loci from high-throughput sequencing data' + description: 'High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-selectksigs/meta.yaml b/recipes/bioconductor-selectksigs/meta.yaml index 3455fc77d0785..15de6e1d4eb79 100644 --- a/recipes/bioconductor-selectksigs/meta.yaml +++ b/recipes/bioconductor-selectksigs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "selectKSigs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 730b7e4439fcf388eb775a220e23213f + md5: 95d84e53b480a52695c40071dfa9be68 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-selectksigs", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr requirements: host: - - 'bioconductor-hilda >=1.14.0,<1.15.0' + - 'bioconductor-hilda >=1.16.0,<1.17.0' - r-base - r-gtools - r-magrittr @@ -28,7 +29,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-hilda >=1.14.0,<1.15.0' + - 'bioconductor-hilda >=1.16.0,<1.17.0' - r-base - r-gtools - r-magrittr diff --git a/recipes/bioconductor-selex/meta.yaml b/recipes/bioconductor-selex/meta.yaml index 51229bf30d096..f722404705424 100644 --- a/recipes/bioconductor-selex/meta.yaml +++ b/recipes/bioconductor-selex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "SELEX" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37f1efe42a0799212df721e13d53dfe9 + md5: fdb39d601a2ce8c882e9a0e822ef014c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-selex", max_pin="x.x") }}' noarch: generic # SystemRequirements: Java (>= 1.5) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - 'r-rjava >=0.5-0' - openjdk run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - 'r-rjava >=0.5-0' - openjdk diff --git a/recipes/bioconductor-semdist/meta.yaml b/recipes/bioconductor-semdist/meta.yaml index 221af1c2a8fe0..4d76de2af60bc 100644 --- a/recipes/bioconductor-semdist/meta.yaml +++ b/recipes/bioconductor-semdist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "SemDist" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2c69ea1b7da63b8c2dc2e99923dba8d3 + md5: b95a04e7daaae24fb22f3b2a40b17f5f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-semdist", max_pin="x.x") }}' noarch: generic # Suggests: GOSemSim requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base test: commands: diff --git a/recipes/bioconductor-semisup/meta.yaml b/recipes/bioconductor-semisup/meta.yaml index b857a81831940..e541f2fdda943 100644 --- a/recipes/bioconductor-semisup/meta.yaml +++ b/recipes/bioconductor-semisup/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "semisup" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2ff384fc0dbca3f33f519a4b8de74167 + md5: fb3d32c07acbfadbbee01f9a6c8333fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-semisup", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, SummarizedExperiment requirements: diff --git a/recipes/bioconductor-seq.hotspot/meta.yaml b/recipes/bioconductor-seq.hotspot/meta.yaml index 2f14c697b4d91..a2ea709167002 100644 --- a/recipes/bioconductor-seq.hotspot/meta.yaml +++ b/recipes/bioconductor-seq.hotspot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "seq.hotSPOT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20614c1b700f6efb77257e9ec89a13fe + md5: 37e04dc7e1bb05af58c50cb7701388c7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seq.hotspot", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) requirements: diff --git a/recipes/bioconductor-seq2pathway.data/meta.yaml b/recipes/bioconductor-seq2pathway.data/meta.yaml index bb203b9c7cc5e..8410739a77c65 100644 --- a/recipes/bioconductor-seq2pathway.data/meta.yaml +++ b/recipes/bioconductor-seq2pathway.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "seq2pathway.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f5b47c139925e607c100f2e3e0292db0 + md5: b0035ff986391159c1329eac9fb96661 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seq2pathway.data", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-seq2pathway.data/post-link.sh b/recipes/bioconductor-seq2pathway.data/post-link.sh index 8d976f432fdf2..30b629ea74cff 100644 --- a/recipes/bioconductor-seq2pathway.data/post-link.sh +++ b/recipes/bioconductor-seq2pathway.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "seq2pathway.data-1.32.0" +installBiocDataPackage.sh "seq2pathway.data-1.34.0" diff --git a/recipes/bioconductor-seq2pathway/meta.yaml b/recipes/bioconductor-seq2pathway/meta.yaml index cd6d03f8af502..4dbc70fe6e390 100644 --- a/recipes/bioconductor-seq2pathway/meta.yaml +++ b/recipes/bioconductor-seq2pathway/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "seq2pathway" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 76098141614149c9fcc18823aeb3e359 + md5: 4aaa34232c40fdc31f493d67c72742c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seq2pathway", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-seq2pathway.data >=1.32.0,<1.33.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-seq2pathway.data >=1.34.0,<1.35.0' - r-base - r-gsa - r-nnet - r-wgcna run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-seq2pathway.data >=1.32.0,<1.33.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-seq2pathway.data >=1.34.0,<1.35.0' - r-base - r-gsa - r-nnet diff --git a/recipes/bioconductor-seqarchr/meta.yaml b/recipes/bioconductor-seqarchr/meta.yaml index b2d195646ee7e..228d43f42052d 100644 --- a/recipes/bioconductor-seqarchr/meta.yaml +++ b/recipes/bioconductor-seqarchr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "seqArchR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fecd57059a333de35b3509909921541c + md5: b991ca99e52e357f8ef95a3a75a1decc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqarchr", max_pin="x.x") }}' noarch: generic # Suggests: cowplot, hopach (>= 2.42.0), BiocStyle, knitr (>= 1.22), rmarkdown (>= 1.12), testthat (>= 3.0.2), covr, vdiffr (>= 0.3.0) # SystemRequirements: Python (>= 3.5), scikit-learn (>= 0.21.2), packaging requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-cli - r-cluster @@ -38,8 +39,8 @@ requirements: - 'r-reshape2 >=1.4.3' - 'r-reticulate >=1.22' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-cli - r-cluster diff --git a/recipes/bioconductor-seqarchrplus/meta.yaml b/recipes/bioconductor-seqarchrplus/meta.yaml index 73dd5f3d2a1b9..9c12d8beb187b 100644 --- a/recipes/bioconductor-seqarchrplus/meta.yaml +++ b/recipes/bioconductor-seqarchrplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "seqArchRplus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,57 +11,60 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 35db67395c9e71a8e40360d5266a8e1f + md5: 9f20e2eed3e5b5a498564ea201b251d9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqarchrplus", max_pin="x.x") }}' noarch: generic -# Suggests: BSgenome.Dmelanogaster.UCSC.dm6, BiocStyle, CAGEr (>= 2.0.2), covr, knitr (>= 1.22), org.Dm.eg.db, rmarkdown (>= 1.12), TxDb.Dmelanogaster.UCSC.dm6.ensGene, xfun +# Suggests: BSgenome.Dmelanogaster.UCSC.dm6, BiocStyle, CAGEr (>= 2.0.2), covr, knitr (>= 1.22), org.Dm.eg.db, pdftools, rmarkdown (>= 1.12), slickR, TxDb.Dmelanogaster.UCSC.dm6.ensGene, xfun requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-chipseeker >=1.36.0,<1.37.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-heatmaps >=1.24.0,<1.25.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarchr >=1.4.0,<1.5.0' - - 'bioconductor-seqpattern >=1.32.0,<1.33.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-chipseeker >=1.38.0,<1.39.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-heatmaps >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarchr >=1.6.0,<1.7.0' + - 'bioconductor-seqpattern >=1.34.0,<1.35.0' - r-base - r-cli - r-cowplot - r-factoextra - - r-forcats + - r-ggimage - r-ggplot2 - r-gridextra + - r-magick - r-rcolorbrewer - r-scales run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-chipseeker >=1.36.0,<1.37.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-heatmaps >=1.24.0,<1.25.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarchr >=1.4.0,<1.5.0' - - 'bioconductor-seqpattern >=1.32.0,<1.33.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-chipseeker >=1.38.0,<1.39.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-heatmaps >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarchr >=1.6.0,<1.7.0' + - 'bioconductor-seqpattern >=1.34.0,<1.35.0' - r-base - r-cli - r-cowplot - r-factoextra - - r-forcats + - r-ggimage - r-ggplot2 - r-gridextra + - r-magick - r-rcolorbrewer - r-scales test: @@ -71,6 +74,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Downstream analyses of promoter sequence architectures and HTML report generation' - description: 'seqArchRplus facilitates downstream analyses of promoter sequence architectures/clusters identified by seqArchR (or any other tool/method). With additional available information such as the TPM values and interquantile widths (IQWs) of the CAGE tag clusters, seqArchRplus can order the input promoter clusters by their shape (IQWs), and write the cluster information as browser/IGV track files. Provided visualizations are of two kind: per sample/stage and per cluster visualizations. Those of the first kind include: plot panels for each sample showing per cluster shape, TPM and other score distributions, sequence logos, and peak annotations. The second include per cluster chromosome-wise and strand distributions, motif occurrence heatmaps and GO term enrichments. Additionally, seqArchRplus can also generate HTML reports for easy viewing and comparison of promoter architectures between samples/stages (future).' + description: 'seqArchRplus facilitates downstream analyses of promoter sequence architectures/clusters identified by seqArchR (or any other tool/method). With additional available information such as the TPM values and interquantile widths (IQWs) of the CAGE tag clusters, seqArchRplus can order the input promoter clusters by their shape (IQWs), and write the cluster information as browser/IGV track files. Provided visualizations are of two kind: per sample/stage and per cluster visualizations. Those of the first kind include: plot panels for each sample showing per cluster shape, TPM and other score distributions, sequence logos, and peak annotations. The second include per cluster chromosome-wise and strand distributions, motif occurrence heatmaps and GO term enrichments. Additionally, seqArchRplus can also generate HTML reports for easy viewing and comparison of promoter architectures between samples/stages.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-seqarray/meta.yaml b/recipes/bioconductor-seqarray/meta.yaml index cfd8a66707fd9..189913b7b1e3e 100644 --- a/recipes/bioconductor-seqarray/meta.yaml +++ b/recipes/bioconductor-seqarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.1" %} +{% set version = "1.42.0" %} {% set name = "SeqArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7fe9f3e22cc01b8c418d18e382b7a1c7 + md5: 9754225574380705e505629db229d41a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqarray", max_pin="x.x") }}' # Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-seqbias/meta.yaml b/recipes/bioconductor-seqbias/meta.yaml index 7ccf27fe16e38..68fec85f215e5 100644 --- a/recipes/bioconductor-seqbias/meta.yaml +++ b/recipes/bioconductor-seqbias/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "seqbias" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0c5d17dfe8932ed8cd03a6b0428a74fd + md5: 0482c079ead497bdddd61be6bac445f7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqbias", max_pin="x.x") }}' # Suggests: Rsamtools, ggplot2 # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-seqc/meta.yaml b/recipes/bioconductor-seqc/meta.yaml index a24dc500afc1a..6da322827d369 100644 --- a/recipes/bioconductor-seqc/meta.yaml +++ b/recipes/bioconductor-seqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "seqc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 834e2a378860f1f6aea76581e87c876f + md5: 105a278c97aca90968641aec403c1219 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqc", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-seqc/post-link.sh b/recipes/bioconductor-seqc/post-link.sh index c4675267b71f1..9d67b6fc469d9 100644 --- a/recipes/bioconductor-seqc/post-link.sh +++ b/recipes/bioconductor-seqc/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "seqc-1.34.0" +installBiocDataPackage.sh "seqc-1.36.0" diff --git a/recipes/bioconductor-seqcat/meta.yaml b/recipes/bioconductor-seqcat/meta.yaml index a3fe883852757..4c3f9796fbf43 100644 --- a/recipes/bioconductor-seqcat/meta.yaml +++ b/recipes/bioconductor-seqcat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "seqCAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 28f42128bb177d143b80d274175364f0 + md5: a7694d3599501816a63d4b6e831af35d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqcat", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-dplyr >=0.5.0' - 'r-ggplot2 >=2.2.1' @@ -35,13 +36,13 @@ requirements: - 'r-scales >=0.4.1' - 'r-tidyr >=0.6.1' run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-dplyr >=0.5.0' - 'r-ggplot2 >=2.2.1' diff --git a/recipes/bioconductor-seqcna.annot/meta.yaml b/recipes/bioconductor-seqcna.annot/meta.yaml index b6742c5e3f45a..586086b68b240 100644 --- a/recipes/bioconductor-seqcna.annot/meta.yaml +++ b/recipes/bioconductor-seqcna.annot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "seqCNA.annot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: feee6a27f305149bdfec8a823e2134ec + md5: a61df6e0824d7c3c3f4c697b5bd73e30 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqcna.annot", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-seqcna.annot/post-link.sh b/recipes/bioconductor-seqcna.annot/post-link.sh index d92e89050b20f..55de60d88d9ad 100644 --- a/recipes/bioconductor-seqcna.annot/post-link.sh +++ b/recipes/bioconductor-seqcna.annot/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "seqcna.annot-1.36.0" +installBiocDataPackage.sh "seqcna.annot-1.38.0" diff --git a/recipes/bioconductor-seqcna/meta.yaml b/recipes/bioconductor-seqcna/meta.yaml index 564887adce0e2..fbd5dc10071c8 100644 --- a/recipes/bioconductor-seqcna/meta.yaml +++ b/recipes/bioconductor-seqcna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "seqCNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dfe25506e95aa7a625d69e2e5420f168 + md5: 06ae9363110630b77cd3e5b4ae70b188 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqcna", max_pin="x.x") }}' # SystemRequirements: samtools requirements: host: - - 'bioconductor-glad >=2.64.0,<2.65.0' - - 'bioconductor-seqcna.annot >=1.36.0,<1.37.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' + - 'bioconductor-seqcna.annot >=1.38.0,<1.39.0' - 'r-adehabitatlt >=0.3.4' - r-base - 'r-dosnow >=1.0.5' @@ -29,8 +30,8 @@ requirements: - liblapack - samtools run: - - 'bioconductor-glad >=2.64.0,<2.65.0' - - 'bioconductor-seqcna.annot >=1.36.0,<1.37.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' + - 'bioconductor-seqcna.annot >=1.38.0,<1.39.0' - 'r-adehabitatlt >=0.3.4' - r-base - 'r-dosnow >=1.0.5' diff --git a/recipes/bioconductor-seqcombo/meta.yaml b/recipes/bioconductor-seqcombo/meta.yaml index 9f21f96fe79ad..4afa58a79f493 100644 --- a/recipes/bioconductor-seqcombo/meta.yaml +++ b/recipes/bioconductor-seqcombo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "seqcombo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0ce813d4dc3284696f90d33e05f11f56 + md5: 76a401edd5e5583a94ab3a1b599b7a78 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqcombo", max_pin="x.x") }}' noarch: generic # Suggests: emojifont, knitr, rmarkdown, prettydoc, tibble requirements: diff --git a/recipes/bioconductor-seqgate/meta.yaml b/recipes/bioconductor-seqgate/meta.yaml index 0d2e5925bdbe2..5ca65b1d94bf3 100644 --- a/recipes/bioconductor-seqgate/meta.yaml +++ b/recipes/bioconductor-seqgate/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "SeqGate" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: caca9e158a9bfe2b69e3423a86a81654 + md5: 786d9cf0f14de2b0056b9207daedbf45 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqgate", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biocmanager run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biocmanager test: diff --git a/recipes/bioconductor-seqgsea/meta.yaml b/recipes/bioconductor-seqgsea/meta.yaml index bd2c3d5d81d64..0d91107a888ec 100644 --- a/recipes/bioconductor-seqgsea/meta.yaml +++ b/recipes/bioconductor-seqgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "SeqGSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c106db6ce0aeec4190b5f7fd7495a99a + md5: 13213924066a18535220d42938e923fa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqgsea", max_pin="x.x") }}' noarch: generic # Suggests: GenomicRanges requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - r-base - r-doparallel run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - r-base - r-doparallel test: diff --git a/recipes/bioconductor-seqlogo/meta.yaml b/recipes/bioconductor-seqlogo/meta.yaml index 6ecaf507c15ab..7f32797f34d61 100644 --- a/recipes/bioconductor-seqlogo/meta.yaml +++ b/recipes/bioconductor-seqlogo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "seqLogo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea278495fc179bf6ef9309b2479b0671 + md5: 0771c35a7929a3e71aa5eebaf4a624ef build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqlogo", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-seqpattern/meta.yaml b/recipes/bioconductor-seqpattern/meta.yaml index e00aa28fe26ec..78b4fabd8eb99 100644 --- a/recipes/bioconductor-seqpattern/meta.yaml +++ b/recipes/bioconductor-seqpattern/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "seqPattern" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ae45cac8349ba8a6cf5114662c3dd7f + md5: 90ef37347887673ee80f12fa953e02f3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqpattern", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-kernsmooth - r-plotrix run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-kernsmooth - r-plotrix diff --git a/recipes/bioconductor-seqsetvis/meta.yaml b/recipes/bioconductor-seqsetvis/meta.yaml index 3ae2dd43d0f62..fce6340743e95 100644 --- a/recipes/bioconductor-seqsetvis/meta.yaml +++ b/recipes/bioconductor-seqsetvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "seqsetvis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0593e5b221ee0dcaa6edeabb195bb9ff + md5: 0119c8a5e2475e3a0d35059b3c35dfd6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqsetvis", max_pin="x.x") }}' noarch: generic # Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-data.table @@ -39,16 +40,17 @@ requirements: - r-pbmcapply - r-png - r-rcolorbrewer + - r-scales - r-upsetr run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-data.table @@ -59,6 +61,7 @@ requirements: - r-pbmcapply - r-png - r-rcolorbrewer + - r-scales - r-upsetr test: commands: diff --git a/recipes/bioconductor-seqsqc/meta.yaml b/recipes/bioconductor-seqsqc/meta.yaml index a47cc4ce41ef6..dfcf859b73495 100644 --- a/recipes/bioconductor-seqsqc/meta.yaml +++ b/recipes/bioconductor-seqsqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "SeqSQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 195f7e2bff5ce9fbd8e350f1022a530e + md5: 10e877d23b5c1572319af0515baca2c1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqsqc", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' - r-base - r-e1071 - r-ggally @@ -36,12 +37,12 @@ requirements: - r-reshape2 - r-rmarkdown run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' - r-base - r-e1071 - r-ggally diff --git a/recipes/bioconductor-seqtools/meta.yaml b/recipes/bioconductor-seqtools/meta.yaml index 583d647382fcf..93a07f90dca3c 100644 --- a/recipes/bioconductor-seqtools/meta.yaml +++ b/recipes/bioconductor-seqtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "seqTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0fc462bf24881e9f121c7e8e734055ef + md5: be9be6eb0ee1ff4ab001720970d68da8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqtools", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-seqvartools/meta.yaml b/recipes/bioconductor-seqvartools/meta.yaml index b50ab43f0dadf..cd40a732cfeb5 100644 --- a/recipes/bioconductor-seqvartools/meta.yaml +++ b/recipes/bioconductor-seqvartools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "SeqVarTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f0de0a3c46d81cc184e94e9f9258a01d + md5: 160f56cd78339c2e4d4b5c0766a47846 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqvartools", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, RUnit, stringr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' - r-base - r-data.table - r-gwasexacthw - r-logistf - r-matrix run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' - r-base - r-data.table - r-gwasexacthw diff --git a/recipes/bioconductor-serumstimulation/meta.yaml b/recipes/bioconductor-serumstimulation/meta.yaml index 08afdb968f69b..7304fb6ceb832 100644 --- a/recipes/bioconductor-serumstimulation/meta.yaml +++ b/recipes/bioconductor-serumstimulation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "serumStimulation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 642cc4d3939f4a05e331ef5d1f965835 + md5: 4d3f1a4e58f500d7e424eef0b22c05ad build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-serumstimulation", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-serumstimulation/post-link.sh b/recipes/bioconductor-serumstimulation/post-link.sh index 36e810aea6f28..f74707b1a8b74 100644 --- a/recipes/bioconductor-serumstimulation/post-link.sh +++ b/recipes/bioconductor-serumstimulation/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "serumstimulation-1.36.0" +installBiocDataPackage.sh "serumstimulation-1.38.0" diff --git a/recipes/bioconductor-sesame/meta.yaml b/recipes/bioconductor-sesame/meta.yaml index 5234aea678109..bef67f6a17dd4 100644 --- a/recipes/bioconductor-sesame/meta.yaml +++ b/recipes/bioconductor-sesame/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.4" %} +{% set version = "1.20.0" %} {% set name = "sesame" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d1f0f5e0d15b5b3e01160d6028497a58 + md5: 9bb9cc07a6c773f324fdee69d75a8427 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sesame", max_pin="x.x") }}' noarch: generic -# Suggests: scales, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals +# Suggests: scales, BiocManager, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sesamedata >=1.18.0,<1.19.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sesamedata >=1.20.0,<1.21.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -41,16 +42,16 @@ requirements: - r-tibble - 'r-wheatmap >=0.2.0' run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sesamedata >=1.18.0,<1.19.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sesamedata >=1.20.0,<1.21.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-sesamedata/meta.yaml b/recipes/bioconductor-sesamedata/meta.yaml index 60840cc790ad0..48d75153c0584 100644 --- a/recipes/bioconductor-sesamedata/meta.yaml +++ b/recipes/bioconductor-sesamedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "sesameData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4af907a4ed795d2493573b88d55fd4de + md5: 4cd44c4f5307d2775d94f2051b9a7f46 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sesamedata", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, sesame, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-readr - r-stringr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-readr - r-stringr - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sesamedata/post-link.sh b/recipes/bioconductor-sesamedata/post-link.sh index 6efd3a74642d9..f5cc75f5ec748 100644 --- a/recipes/bioconductor-sesamedata/post-link.sh +++ b/recipes/bioconductor-sesamedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "sesamedata-1.18.0" +installBiocDataPackage.sh "sesamedata-1.20.0" diff --git a/recipes/bioconductor-setools/meta.yaml b/recipes/bioconductor-setools/meta.yaml index c7e0e948dd6b9..364be9dc5ca55 100644 --- a/recipes/bioconductor-setools/meta.yaml +++ b/recipes/bioconductor-setools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SEtools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e6a9df3ebf6eaacc2cce51d39040f13 + md5: 4b6f28a6fdf032d51f29793f25729114 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-setools", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, ggplot2 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sechm >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sechm >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-circlize - r-data.table @@ -35,13 +36,13 @@ requirements: - r-openxlsx - r-pheatmap run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sechm >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sechm >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-circlize - r-data.table diff --git a/recipes/bioconductor-sevenbridges/meta.yaml b/recipes/bioconductor-sevenbridges/meta.yaml index cd03d3e9b99cd..66cb3290bcdbe 100644 --- a/recipes/bioconductor-sevenbridges/meta.yaml +++ b/recipes/bioconductor-sevenbridges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "sevenbridges" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f09e6b0788100a89ac38eb13887d8993 + md5: 1c204add9c56d7518a5362b99111ec18 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sevenbridges", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, readr requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-curl - r-data.table @@ -33,7 +34,7 @@ requirements: - r-uuid - r-yaml run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-curl - r-data.table diff --git a/recipes/bioconductor-sevenc/meta.yaml b/recipes/bioconductor-sevenc/meta.yaml index 38be4b0ddbb31..e56d3a0da93e1 100644 --- a/recipes/bioconductor-sevenc/meta.yaml +++ b/recipes/bioconductor-sevenc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "sevenC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e943999c0ef7fc1049dd87b19bd4520e + md5: 575914dcdfdff58d10d7e926182801b9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sevenc", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-boot >=1.3-20' - 'r-data.table >=1.10.4' - 'r-purrr >=0.2.2' - 'r-readr >=1.1.0' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-boot >=1.3-20' - 'r-data.table >=1.10.4' diff --git a/recipes/bioconductor-seventygenedata/meta.yaml b/recipes/bioconductor-seventygenedata/meta.yaml index f77017c68ad61..076afa9211ab5 100644 --- a/recipes/bioconductor-seventygenedata/meta.yaml +++ b/recipes/bioconductor-seventygenedata/meta.yaml @@ -25,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20230706 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sfedata/meta.yaml b/recipes/bioconductor-sfedata/meta.yaml index e7fd005710ab3..7b97631753e5d 100644 --- a/recipes/bioconductor-sfedata/meta.yaml +++ b/recipes/bioconductor-sfedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "SFEData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 405e15fbe6e99736481e40164abf3b04 + md5: 7f3376870c972cba309b26d52d24fcbb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sfedata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, SpatialFeatureExperiment, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sfedata/post-link.sh b/recipes/bioconductor-sfedata/post-link.sh index 05d7347ba3e7f..f690a3a41ff4f 100644 --- a/recipes/bioconductor-sfedata/post-link.sh +++ b/recipes/bioconductor-sfedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "sfedata-1.2.0" +installBiocDataPackage.sh "sfedata-1.4.0" diff --git a/recipes/bioconductor-sgcp/meta.yaml b/recipes/bioconductor-sgcp/meta.yaml index 9af3e937efa45..eaaca7d8f94e0 100644 --- a/recipes/bioconductor-sgcp/meta.yaml +++ b/recipes/bioconductor-sgcp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "SGCP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 34dc1d2d2ed37410c921ae70f7b10965 + md5: 46986c7dd18ef80a29c389500ed5023b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sgcp", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocManager requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-caret - r-desctools @@ -43,14 +44,14 @@ requirements: - r-rspectra - r-xtable run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-caret - r-desctools diff --git a/recipes/bioconductor-sgseq/meta.yaml b/recipes/bioconductor-sgseq/meta.yaml index b4fc72a14d8b6..a88e1160be342 100644 --- a/recipes/bioconductor-sgseq/meta.yaml +++ b/recipes/bioconductor-sgseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "SGSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,44 +11,45 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ffeb95713ad100a5988daf418801096 + md5: 874492401a4a17bf0836f9fa011f459a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sgseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-runit run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-runit diff --git a/recipes/bioconductor-sharedobject/build.sh b/recipes/bioconductor-sharedobject/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sharedobject/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sharedobject/meta.yaml b/recipes/bioconductor-sharedobject/meta.yaml new file mode 100644 index 0000000000000..849fb0abf9871 --- /dev/null +++ b/recipes/bioconductor-sharedobject/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.16.0" %} +{% set name = "SharedObject" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7c47265b6a5f61385088d6146c7e4879 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sharedobject", max_pin="x.x") }}' +# Suggests: testthat, parallel, knitr, rmarkdown, BiocStyle +# SystemRequirements: GNU make, C++11 +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - r-base + - r-bh + - r-rcpp + - libblas + - liblapack + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - r-base + - r-bh + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Sharing R objects across multiple R processes without memory duplication' + description: 'This package is developed for facilitating parallel computing in R. It is capable to create an R object in the shared memory space and share the data across multiple R processes. It avoids the overhead of memory dulplication and data transfer, which make sharing big data object across many clusters possible.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-shdz.db/meta.yaml b/recipes/bioconductor-shdz.db/meta.yaml index db050bfdcd0ac..b7927519c0bdf 100644 --- a/recipes/bioconductor-shdz.db/meta.yaml +++ b/recipes/bioconductor-shdz.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "SHDZ.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 63c4439a272a5cd0c4746e9e53a7bdc7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-shdz.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-shinyepico/meta.yaml b/recipes/bioconductor-shinyepico/meta.yaml index d2a600fdca1a7..352d8232c1e6f 100644 --- a/recipes/bioconductor-shinyepico/meta.yaml +++ b/recipes/bioconductor-shinyepico/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "shinyepico" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4eb22bc9e04f69e4d52faf1dafc43809 + md5: 044010b7c6b7570adb28be7374473f82 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-shinyepico", max_pin="x.x") }}' noarch: generic # Suggests: knitr (>= 1.30.0), mCSEA (>= 1.10.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICmanifest, testthat, minfiData, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - 'r-data.table >=1.13.0' - 'r-doparallel >=1.0.0' @@ -47,10 +48,10 @@ requirements: - 'r-tidyr >=1.2.0' - 'r-zip >=2.1.0' run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - 'r-data.table >=1.13.0' - 'r-doparallel >=1.0.0' diff --git a/recipes/bioconductor-shinymethyl/meta.yaml b/recipes/bioconductor-shinymethyl/meta.yaml index 505a32b6f3332..09cdddcbcd8cc 100644 --- a/recipes/bioconductor-shinymethyl/meta.yaml +++ b/recipes/bioconductor-shinymethyl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "shinyMethyl" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f8531aa5c428db361db5abf32e59111 + md5: 21f2fe819a72a5c4db3694a22dcda934 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-shinymethyl", max_pin="x.x") }}' noarch: generic # Suggests: shinyMethylData, minfiData, BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - r-htmltools - r-rcolorbrewer - r-shiny run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - r-htmltools - r-rcolorbrewer diff --git a/recipes/bioconductor-shinymethyldata/meta.yaml b/recipes/bioconductor-shinymethyldata/meta.yaml index 11cedfd25f71c..e41c94e7ad9f3 100644 --- a/recipes/bioconductor-shinymethyldata/meta.yaml +++ b/recipes/bioconductor-shinymethyldata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "shinyMethylData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f633d8b104a4f61c393b15f59671039b + md5: 46f32db849aaa1467d09b0a371769374 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-shinymethyldata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-shinymethyldata/post-link.sh b/recipes/bioconductor-shinymethyldata/post-link.sh index 51a237e07d36e..3d514dc1f7ffc 100644 --- a/recipes/bioconductor-shinymethyldata/post-link.sh +++ b/recipes/bioconductor-shinymethyldata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "shinymethyldata-1.20.0" +installBiocDataPackage.sh "shinymethyldata-1.22.0" diff --git a/recipes/bioconductor-shortread/meta.yaml b/recipes/bioconductor-shortread/meta.yaml index 3aada6e844fcc..9b4eee6ba99c3 100644 --- a/recipes/bioconductor-shortread/meta.yaml +++ b/recipes/bioconductor-shortread/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "ShortRead" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8547be10c12f7765d3e25a4a735af39 + md5: 480786b1db8f8138a7a4e8c36f9bdfc4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-shortread", max_pin="x.x") }}' # Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-hwriter - r-lattice @@ -40,19 +41,19 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-hwriter - r-lattice diff --git a/recipes/bioconductor-siamcat/meta.yaml b/recipes/bioconductor-siamcat/meta.yaml index 956cab8ec228e..d94c3be14962d 100644 --- a/recipes/bioconductor-siamcat/meta.yaml +++ b/recipes/bioconductor-siamcat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "SIAMCAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 38b6d1bc1d77495fe3faf0efc44cabb5 + md5: 36938473e8b2bd9b269fae69ec312e8d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-siamcat", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, optparse, testthat, knitr, rmarkdown, tidyverse, ggpubr +# Suggests: BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr requirements: host: - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-beanplot - r-corrplot @@ -44,7 +45,7 @@ requirements: - r-scales - r-stringr run: - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-beanplot - r-corrplot diff --git a/recipes/bioconductor-sictools/build.sh b/recipes/bioconductor-sictools/build.sh index 8ed8c159a97a0..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sictools/build.sh +++ b/recipes/bioconductor-sictools/build.sh @@ -2,10 +2,10 @@ mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION mkdir -p ~/.R -echo -e "CC=$CC -I$PREFIX/include -L$PREFIX/lib +echo -e "CC=$CC FC=$FC -CXX=$CXX -I$PREFIX/include -L$PREFIX/lib +CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -MAKE="make LIBCURSES=-lncurses" $R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sictools/build_failure.linux-64.yaml b/recipes/bioconductor-sictools/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..c447c0a1d2387 --- /dev/null +++ b/recipes/bioconductor-sictools/build_failure.linux-64.yaml @@ -0,0 +1,37 @@ +recipe_sha: d0341aa6f0be4917a820c67382d360ac5f5e76815434d7cecb1769b617051f44 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bgzf.h:33:10: fatal error: zlib.h: No such file or directory +category: |- + compiler error +log: |- + 13:35:37 BIOCONDA INFO (OUT) In file included from bgzf.c:32: + 13:35:37 BIOCONDA INFO (OUT) bgzf.h:33:10: fatal error: zlib.h: No such file or directory + 13:35:37 BIOCONDA INFO (OUT) 33 | #include + 13:35:37 BIOCONDA INFO (OUT) | ^~~~~~~~ + 13:35:37 BIOCONDA INFO (OUT) compilation terminated. + 13:35:37 BIOCONDA INFO (OUT) make[2]: *** [Makefile:56: bgzf.o] Error 1 + 13:35:37 BIOCONDA INFO (OUT) make[2]: Leaving directory '$SRC_DIR/src' + 13:35:37 BIOCONDA INFO (OUT) make[1]: *** [Makefile:27: lib-recur] Error 1 + 13:35:37 BIOCONDA INFO (OUT) make[1]: Leaving directory '$SRC_DIR/src' + 13:35:37 BIOCONDA INFO (OUT) make: *** [Makefile:27: all-recur] Error 1 + 13:35:37 BIOCONDA INFO (OUT) ERROR: compilation failed for package ‘SICtools’ + 13:35:37 BIOCONDA INFO (OUT) * removing ‘/opt/conda/conda-bld/bioconductor-sictools_1702301527486/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/SICtools’ + 13:35:38 BIOCONDA INFO (OUT) Traceback (most recent call last): + 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/bin/conda-mambabuild", line 10, in + 13:35:38 BIOCONDA INFO (OUT) sys.exit(main()) + 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + 13:35:38 BIOCONDA INFO (OUT) call_conda_build(action, config) + 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + 13:35:38 BIOCONDA INFO (OUT) result = api.build( + 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + 13:35:38 BIOCONDA INFO (OUT) return build_tree( + 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + 13:35:38 BIOCONDA INFO (OUT) packages_from_this = build(metadata, stats, + 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build + 13:35:38 BIOCONDA INFO (OUT) utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, + 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + 13:35:38 BIOCONDA INFO (OUT) return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + 13:35:38 BIOCONDA INFO (OUT) raise subprocess.CalledProcessError(proc.returncode, _args) + 13:35:38 BIOCONDA INFO (OUT) subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-sictools_1702301527486/work/conda_build.sh']' returned non-zero exit status 1. diff --git a/recipes/bioconductor-sictools/meta.yaml b/recipes/bioconductor-sictools/meta.yaml index ffcbe6f486b4f..12a5dc2cb5ca8 100644 --- a/recipes/bioconductor-sictools/meta.yaml +++ b/recipes/bioconductor-sictools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "SICtools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b83944eeafc064c998ad1c3acfa3b0e + md5: 1df54634cb8bc00e60963b0ca10886d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sictools", max_pin="x.x") }}' # Suggests: knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - 'r-doparallel >=1.0.8' - 'r-matrixstats >=0.10.0' @@ -31,20 +32,16 @@ requirements: - 'r-stringr >=0.6.2' - libblas - liblapack - - zlib - - ncurses run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - 'r-doparallel >=1.0.8' - 'r-matrixstats >=0.10.0' - 'r-plyr >=1.8.3' - 'r-stringr >=0.6.2' - - zlib - - ncurses build: - {{ compiler('c') }} - make diff --git a/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml b/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml index c7d63153dc4b1..63f65568f82da 100644 --- a/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml +++ b/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.2" %} {% set name = "SIFT.Hsapiens.dbSNP132" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,24 +13,25 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c374f0bf4c99357cfe99e0b192c00d75 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sift.hsapiens.dbsnp132", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-rsqlite >=0.11.0' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-rsqlite >=0.11.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml b/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml index c422913f4d133..f0f7108912e36 100644 --- a/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml +++ b/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "SIFT.Hsapiens.dbSNP137" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,24 +13,25 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3c3e73f826399af5ff368d1aab12cfd1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sift.hsapiens.dbsnp137", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-rsqlite >=0.11.0' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-rsqlite >=0.11.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sigcheck/meta.yaml b/recipes/bioconductor-sigcheck/meta.yaml index c2a7a7a09e7c3..d0bf27e007237 100644 --- a/recipes/bioconductor-sigcheck/meta.yaml +++ b/recipes/bioconductor-sigcheck/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "SigCheck" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a66d9ee5f9009f29346bdfca24346288 + md5: 0c956bbf06058a0a494f887fbdf6549f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sigcheck", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, breastCancerNKI, qusage requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-mlinterfaces >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-mlinterfaces >=1.82.0,<1.83.0' - r-base - r-e1071 - r-survival run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-mlinterfaces >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-mlinterfaces >=1.82.0,<1.83.0' - r-base - r-e1071 - r-survival diff --git a/recipes/bioconductor-sigfeature/meta.yaml b/recipes/bioconductor-sigfeature/meta.yaml index 0f6d1c3a4c5b4..9c09d518d848e 100644 --- a/recipes/bioconductor-sigfeature/meta.yaml +++ b/recipes/bioconductor-sigfeature/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "sigFeature" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 63592ed4b877d9961ce62abd53541a7c + md5: 96249637034c39dc1924cd78c1a0ba58 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sigfeature", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-matrix @@ -33,9 +34,9 @@ requirements: - r-rcolorbrewer - r-sparsem run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-matrix diff --git a/recipes/bioconductor-sigfuge/meta.yaml b/recipes/bioconductor-sigfuge/meta.yaml index 2966d00f7cd0c..b5a313692d97c 100644 --- a/recipes/bioconductor-sigfuge/meta.yaml +++ b/recipes/bioconductor-sigfuge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "SigFuge" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 474286ce316b812744a7f7b2ed8a49d4 + md5: cb03ecb39c2df4b4f5e1b49f8ba5d594 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sigfuge", max_pin="x.x") }}' noarch: generic # Suggests: org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0), TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-ggplot2 - r-matlab - r-reshape - r-sigclust run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-ggplot2 - r-matlab diff --git a/recipes/bioconductor-siggenes/meta.yaml b/recipes/bioconductor-siggenes/meta.yaml index ab2e1e6eaead6..7b70075ae924b 100644 --- a/recipes/bioconductor-siggenes/meta.yaml +++ b/recipes/bioconductor-siggenes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "siggenes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a4eb4fbc80332b7d40a1c74e92243af6 + md5: ae9899f2a3587a423169a27502868709 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-siggenes", max_pin="x.x") }}' noarch: generic # Suggests: affy, annotate, genefilter, KernSmooth requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - 'r-scrime >=1.2.5' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - 'r-scrime >=1.2.5' test: diff --git a/recipes/bioconductor-sights/meta.yaml b/recipes/bioconductor-sights/meta.yaml index c98adcfb1b0ac..6e11b18225760 100644 --- a/recipes/bioconductor-sights/meta.yaml +++ b/recipes/bioconductor-sights/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "sights" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 290c43f8616319bdca706779a2e7ad05 + md5: 566e869c884c7b12f1a42a9dbaeec05a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sights", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx requirements: host: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - 'r-ggplot2 >=2.0' - 'r-lattice >=0.2' - 'r-mass >=7.3' - 'r-reshape2 >=1.4' run: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - 'r-ggplot2 >=2.0' - 'r-lattice >=0.2' diff --git a/recipes/bioconductor-signaturesearch/meta.yaml b/recipes/bioconductor-signaturesearch/meta.yaml index 561e436f8b679..f1ab00dc3f3f6 100644 --- a/recipes/bioconductor-signaturesearch/meta.yaml +++ b/recipes/bioconductor-signaturesearch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "signatureSearch" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a35d0c11a34a2880ca935789599bd02 + md5: 9585172c7764e755ee67aee1c5a1adba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-signaturesearch", max_pin="x.x") }}' # Suggests: knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT # SystemRequirements: C++11 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr @@ -53,21 +54,21 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-signaturesearchdata/meta.yaml b/recipes/bioconductor-signaturesearchdata/meta.yaml index 25ed2008fb3b8..c53b81dce19ae 100644 --- a/recipes/bioconductor-signaturesearchdata/meta.yaml +++ b/recipes/bioconductor-signaturesearchdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "signatureSearchData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b3174e0e3af77fea49a107ef423adb3 + md5: b30a7f1715a7525279c47db6df5ad995 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-signaturesearchdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-dplyr - r-magrittr - r-r.utils run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-dplyr - r-magrittr - r-r.utils - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-signaturesearchdata/post-link.sh b/recipes/bioconductor-signaturesearchdata/post-link.sh index 3151921fff67c..505a2c08ce197 100644 --- a/recipes/bioconductor-signaturesearchdata/post-link.sh +++ b/recipes/bioconductor-signaturesearchdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "signaturesearchdata-1.14.0" +installBiocDataPackage.sh "signaturesearchdata-1.16.0" diff --git a/recipes/bioconductor-signer/meta.yaml b/recipes/bioconductor-signer/meta.yaml index 0619c6c177669..8c8f0364b486a 100644 --- a/recipes/bioconductor-signer/meta.yaml +++ b/recipes/bioconductor-signer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.1" %} +{% set version = "2.4.0" %} {% set name = "signeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90a383b5dfb52f507eec10ac958b1c53 + md5: 36ca120021611cebddf20efa74c6bbf7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-signer", max_pin="x.x") }}' # Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, rmarkdown # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-ada - r-base - r-bsplus @@ -77,15 +78,15 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-ada - r-base - r-bsplus @@ -141,7 +142,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Empirical Bayesian approach to mutational signature discovery' - description: 'The signeR package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variaton (SNV) counts in cancer genomes, but can also be applied to other features as well. Functionalities to characterize signatures or genome samples according to exposure patterns are also provided.' + description: 'The signeR package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variation (SNV) counts in cancer genomes, but can also be applied to other features as well. Functionalities to characterize signatures or genome samples according to exposure patterns are also provided.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: identifiers: diff --git a/recipes/bioconductor-signifinder/meta.yaml b/recipes/bioconductor-signifinder/meta.yaml index 5699d1c83b780..13db755d08530 100644 --- a/recipes/bioconductor-signifinder/meta.yaml +++ b/recipes/bioconductor-signifinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "signifinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aa726b8d8e8127426f3eb6f883b36bed + md5: f24a46dbbbc9b688450e9f2a0e2e221e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-signifinder", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, kableExtra, testthat (>= 3.0.0), edgeR, limma requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-consensusov >=1.22.0,<1.23.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-consensusov >=1.24.0,<1.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-cowplot - r-dgeobj.utils @@ -48,17 +50,18 @@ requirements: - r-survminer - r-viridis run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-consensusov >=1.22.0,<1.23.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-consensusov >=1.24.0,<1.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-cowplot - r-dgeobj.utils diff --git a/recipes/bioconductor-sigspack/meta.yaml b/recipes/bioconductor-sigspack/meta.yaml index 46326eaad55d4..4b9d64c027d97 100644 --- a/recipes/bioconductor-sigspack/meta.yaml +++ b/recipes/bioconductor-sigspack/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SigsPack" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cb7c27412e07f6a833b6a46af887b508 + md5: 5fde29d53a470944ef9a4ba82bcca75d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sigspack", max_pin="x.x") }}' noarch: generic # Suggests: IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-quadprog >=1.5-5' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-quadprog >=1.5-5' test: diff --git a/recipes/bioconductor-sigsquared/meta.yaml b/recipes/bioconductor-sigsquared/meta.yaml index 135799c1f6676..2970f841bef59 100644 --- a/recipes/bioconductor-sigsquared/meta.yaml +++ b/recipes/bioconductor-sigsquared/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "sigsquared" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9d98cbf7704581f4c430ba2b5e8a00ec + md5: f7dfbb4c066df8fe146b2b73f8180195 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sigsquared", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-survival run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-survival test: diff --git a/recipes/bioconductor-sim/meta.yaml b/recipes/bioconductor-sim/meta.yaml index a3b8f14087b87..b5f1d18e0e31c 100644 --- a/recipes/bioconductor-sim/meta.yaml +++ b/recipes/bioconductor-sim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "SIM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d3c5c65ce115197dca40594a4b16b539 + md5: 72c2ca38244f4d53842bece2abdfadee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sim", max_pin="x.x") }}' # Suggests: biomaRt, RColorBrewer requirements: host: - - 'bioconductor-globaltest >=5.54.0,<5.55.0' - - 'bioconductor-quantsmooth >=1.66.0,<1.67.0' + - 'bioconductor-globaltest >=5.56.0,<5.57.0' + - 'bioconductor-quantsmooth >=1.68.0,<1.69.0' - r-base - r-quantreg - libblas - liblapack run: - - 'bioconductor-globaltest >=5.54.0,<5.55.0' - - 'bioconductor-quantsmooth >=1.66.0,<1.67.0' + - 'bioconductor-globaltest >=5.56.0,<5.57.0' + - 'bioconductor-quantsmooth >=1.68.0,<1.69.0' - r-base - r-quantreg build: diff --git a/recipes/bioconductor-simat/meta.yaml b/recipes/bioconductor-simat/meta.yaml index 0eea27535c90e..c8c53947eb7d9 100644 --- a/recipes/bioconductor-simat/meta.yaml +++ b/recipes/bioconductor-simat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "SIMAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a58d1eff9379ec914d5895269592ca8e + md5: 4482fbb67b81a5c0c2ed553f6b44faa2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simat", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-base - r-ggplot2 - 'r-rcpp >=0.11.3' @@ -28,7 +29,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-base - r-ggplot2 - 'r-rcpp >=0.11.3' diff --git a/recipes/bioconductor-simbenchdata/meta.yaml b/recipes/bioconductor-simbenchdata/meta.yaml index 777409b6375f3..a21401c5931bd 100644 --- a/recipes/bioconductor-simbenchdata/meta.yaml +++ b/recipes/bioconductor-simbenchdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "SimBenchData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b2d78e96922a7935cbe5ba91a129b0f + md5: c801056ea68c668cd98230e8956d551b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simbenchdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, Seurat requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-simbenchdata/post-link.sh b/recipes/bioconductor-simbenchdata/post-link.sh index f1b9f38693847..29b22974ec81f 100644 --- a/recipes/bioconductor-simbenchdata/post-link.sh +++ b/recipes/bioconductor-simbenchdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "simbenchdata-1.8.0" +installBiocDataPackage.sh "simbenchdata-1.10.0" diff --git a/recipes/bioconductor-simbindprofiles/meta.yaml b/recipes/bioconductor-simbindprofiles/meta.yaml index 52de2f9221cf6..5ad27d6918d6d 100644 --- a/recipes/bioconductor-simbindprofiles/meta.yaml +++ b/recipes/bioconductor-simbindprofiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "SimBindProfiles" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fa3f1e8271ff94bd2590512f9c80073d + md5: 9785a8acda5c3423edaefd09f14e6ca2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simbindprofiles", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-ringo >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-ringo >=1.66.0,<1.67.0' - r-base - r-mclust run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-ringo >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-ringo >=1.66.0,<1.67.0' - r-base - r-mclust test: diff --git a/recipes/bioconductor-simbu/meta.yaml b/recipes/bioconductor-simbu/meta.yaml index cc46b06a2ea82..122d2cdc3c9af 100644 --- a/recipes/bioconductor-simbu/meta.yaml +++ b/recipes/bioconductor-simbu/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "SimBu" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1fef87275d51f572073a477f69bfbb0f + md5: 50f7ac0bde39513f3ca816495b7ec9fc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simbu", max_pin="x.x") }}' noarch: generic # Suggests: curl, knitr, matrixStats, rmarkdown, Seurat, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr @@ -37,11 +38,11 @@ requirements: - r-reticulate - r-tidyr run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-simd/meta.yaml b/recipes/bioconductor-simd/meta.yaml index f268f9b562fe7..a50dbbec80a87 100644 --- a/recipes/bioconductor-simd/meta.yaml +++ b/recipes/bioconductor-simd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "SIMD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2931556d02416a254a308886a78297fe + md5: 3fa4a3f26b9c42aa5026f0a22956195b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simd", max_pin="x.x") }}' # Suggests: BiocStyle, knitr,rmarkdown requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-methylmnm >=1.38.0,<1.39.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-methylmnm >=1.40.0,<1.41.0' - r-base - r-statmod - libblas - liblapack run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-methylmnm >=1.38.0,<1.39.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-methylmnm >=1.40.0,<1.41.0' - r-base - r-statmod build: diff --git a/recipes/bioconductor-simffpe/meta.yaml b/recipes/bioconductor-simffpe/meta.yaml index df7db42d051fd..8e72d0c1e17b1 100644 --- a/recipes/bioconductor-simffpe/meta.yaml +++ b/recipes/bioconductor-simffpe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "SimFFPE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6741039d6c2006d51a571456d16cf063 + md5: 95d6710ea184127f659f0c6f7786234c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simffpe", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-doparallel - r-dplyr - r-foreach - r-truncnorm run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-doparallel - r-dplyr diff --git a/recipes/bioconductor-similarpeak/meta.yaml b/recipes/bioconductor-similarpeak/meta.yaml index 6860b904508b4..9f2da87d43c8c 100644 --- a/recipes/bioconductor-similarpeak/meta.yaml +++ b/recipes/bioconductor-similarpeak/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "similaRpeak" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 35dd8b1abb325af118f05e56c1ebdb8f + md5: 3d91ba41941b12c9f93e77872e444c4d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-similarpeak", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle requirements: diff --git a/recipes/bioconductor-simlr/meta.yaml b/recipes/bioconductor-simlr/meta.yaml index 4851267fb6058..ab2a37047dc77 100644 --- a/recipes/bioconductor-simlr/meta.yaml +++ b/recipes/bioconductor-simlr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.1" %} +{% set version = "1.28.0" %} {% set name = "SIMLR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7f02d88ffc083881d030ff8f24e2d790 + md5: 9692308a74c8781b41b55409edf594ce build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simlr", max_pin="x.x") }}' # Suggests: BiocGenerics, BiocStyle, testthat, knitr, igraph requirements: host: diff --git a/recipes/bioconductor-simona/build.sh b/recipes/bioconductor-simona/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-simona/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-simona/meta.yaml b/recipes/bioconductor-simona/meta.yaml new file mode 100644 index 0000000000000..7cbbb253de34d --- /dev/null +++ b/recipes/bioconductor-simona/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.0.2" %} +{% set name = "simona" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: be691f3b2b1908a5af3180d4c9e47232 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simona", max_pin="x.x") }}' +# Suggests: knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png +# SystemRequirements: Perl, Java +requirements: + host: + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-circlize + - r-getoptlong + - r-globaloptions + - r-igraph + - r-matrixstats + - r-polychrome + - r-rcpp + - 'r-xml2 >=1.3.3' + - libblas + - liblapack + - 'perl >=5.6.0' + run: + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-circlize + - r-getoptlong + - r-globaloptions + - r-igraph + - r-matrixstats + - r-polychrome + - r-rcpp + - 'r-xml2 >=1.3.3' + - 'perl >=5.6.0' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Semantic Similarity in Bio-Ontologies' + description: 'This package implements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. It provides a robust toolbox supporting over 70 methods for semantic similarity analysis.' + license_file: LICENSE + diff --git a/recipes/bioconductor-simpintlists/meta.yaml b/recipes/bioconductor-simpintlists/meta.yaml index 12cae66ad17f9..a51d0edccc031 100644 --- a/recipes/bioconductor-simpintlists/meta.yaml +++ b/recipes/bioconductor-simpintlists/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "simpIntLists" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eb06f66a10c4e02738fdfaff769c2dfd + md5: 9dbe0a1f390843a49bb11d05ac5f2e28 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simpintlists", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-simpintlists/post-link.sh b/recipes/bioconductor-simpintlists/post-link.sh index 9a5168f1dc3f2..20fa4fcd46724 100644 --- a/recipes/bioconductor-simpintlists/post-link.sh +++ b/recipes/bioconductor-simpintlists/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "simpintlists-1.36.0" +installBiocDataPackage.sh "simpintlists-1.38.0" diff --git a/recipes/bioconductor-simpleseg/meta.yaml b/recipes/bioconductor-simpleseg/meta.yaml index 75e64bc6223f9..37f94dc135935 100644 --- a/recipes/bioconductor-simpleseg/meta.yaml +++ b/recipes/bioconductor-simpleseg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "simpleSeg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 341edd78b0499ac89cb89fe2ed0882f4 + md5: d0e40e9be3d3e9c8a16d0390040f3da8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simpleseg", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat (>= 3.0.0), knitr, ggplot2 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-cytomapper >=1.12.0,<1.13.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-cytomapper >=1.14.0,<1.15.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-spatstat.geom - r-terra run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-cytomapper >=1.12.0,<1.13.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-cytomapper >=1.14.0,<1.15.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-spatstat.geom - r-terra diff --git a/recipes/bioconductor-simplifyenrichment/meta.yaml b/recipes/bioconductor-simplifyenrichment/meta.yaml index 4bd40b28cab06..83eeed1cbd3c8 100644 --- a/recipes/bioconductor-simplifyenrichment/meta.yaml +++ b/recipes/bioconductor-simplifyenrichment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "simplifyEnrichment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 00527c9634ea2aa7918e582ad61af42c + md5: d54c7188ca88dd43802296650e5b80e1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simplifyenrichment", max_pin="x.x") }}' noarch: generic # Suggests: knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, clusterProfiler, msigdbr, DOSE, DO.db, reactome.db, flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11), shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter, gridtext, fpc requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-circlize - r-clue @@ -40,12 +41,12 @@ requirements: - r-slam - r-tm run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-circlize - r-clue diff --git a/recipes/bioconductor-sincell/meta.yaml b/recipes/bioconductor-sincell/meta.yaml index 15a94a94e5060..f42dbd1131da1 100644 --- a/recipes/bioconductor-sincell/meta.yaml +++ b/recipes/bioconductor-sincell/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "sincell" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ba6ef4928190ede2dd94b4775f66387b + md5: 308aa15c851a99b7f345dbd0af122f07 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sincell", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, biomaRt, stringr, monocle requirements: host: diff --git a/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml b/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml index bcaef7e34a460..d9ce115024fa4 100644 --- a/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml +++ b/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "Single.mTEC.Transcriptomes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11ebbf5ecaf89f0433719a71a8df67b2 + md5: 574ee45ff1177688d68e6ae8295e67a2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-single.mtec.transcriptomes", max_pin="x.x") }}' noarch: generic # Suggests: DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod, gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid, gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap, BiocStyle, knitr, BiocParallel requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh b/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh index ccdcaffe7f29a..c09b613681aa7 100644 --- a/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh +++ b/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "single.mtec.transcriptomes-1.28.0" +installBiocDataPackage.sh "single.mtec.transcriptomes-1.30.0" diff --git a/recipes/bioconductor-single/meta.yaml b/recipes/bioconductor-single/meta.yaml index 0443a953bc07d..4bde20f315321 100644 --- a/recipes/bioconductor-single/meta.yaml +++ b/recipes/bioconductor-single/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "single" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 60fe993d492e1e3354f4a4d066cbd78e + md5: 61242086622646ed92a4304d33bc1457 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-single", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-dplyr - r-reshape2 @@ -33,11 +34,11 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-dplyr - r-reshape2 diff --git a/recipes/bioconductor-singlecellexperiment/meta.yaml b/recipes/bioconductor-singlecellexperiment/meta.yaml index e62fc8618dab0..3f8eefc75d7b5 100644 --- a/recipes/bioconductor-singlecellexperiment/meta.yaml +++ b/recipes/bioconductor-singlecellexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "SingleCellExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0d2806a0547fdcea6688a4d96bdfa5a8 + md5: ef057b77f40efba992f311486e83448b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-singlecellexperiment", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>= 2.9.1), Rtsne requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-singlecellmultimodal/meta.yaml b/recipes/bioconductor-singlecellmultimodal/meta.yaml index 52e2bf35b2f0f..7a3421ef82fa5 100644 --- a/recipes/bioconductor-singlecellmultimodal/meta.yaml +++ b/recipes/bioconductor-singlecellmultimodal/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.2" %} +{% set version = "1.14.0" %} {% set name = "SingleCellMultiModal" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,43 +11,44 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 599f48321756805173d2069623a0319d + md5: e397bc4fbd9ea63f6660758f01d01d38 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-singlecellmultimodal", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown, scater, scran, UpSetR, uwot requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-singlecellmultimodal/post-link.sh b/recipes/bioconductor-singlecellmultimodal/post-link.sh index a8c1076f77b7e..a9af6b4051d35 100644 --- a/recipes/bioconductor-singlecellmultimodal/post-link.sh +++ b/recipes/bioconductor-singlecellmultimodal/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "singlecellmultimodal-1.12.2" +installBiocDataPackage.sh "singlecellmultimodal-1.14.0" diff --git a/recipes/bioconductor-singlecellsignalr/meta.yaml b/recipes/bioconductor-singlecellsignalr/meta.yaml index 547b3ca6726fc..65343241fe4ed 100644 --- a/recipes/bioconductor-singlecellsignalr/meta.yaml +++ b/recipes/bioconductor-singlecellsignalr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "SingleCellSignalR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bbced887bff155cb16721818e1614e98 + md5: d00060a859db9cd8c87ce9673cc9d886 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-singlecellsignalr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' - r-base - r-biocmanager - r-circlize @@ -36,10 +37,10 @@ requirements: - r-rtsne - r-stringr run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' - r-base - r-biocmanager - r-circlize diff --git a/recipes/bioconductor-singlecelltk/meta.yaml b/recipes/bioconductor-singlecelltk/meta.yaml index 1e6c259583316..9455db96d8260 100644 --- a/recipes/bioconductor-singlecelltk/meta.yaml +++ b/recipes/bioconductor-singlecelltk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "singleCellTK" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,55 +11,57 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd24cbf92dd3998cb79b244fd070910a + md5: 5efaf76211a6a623f6657383677474bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-singlecelltk", max_pin="x.x") }}' noarch: generic # Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, spelling, org.Mm.eg.db, stringr, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics, RColorBrewer, fastmap (>= 1.1.0), harmony requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-batchelor >=1.16.0,<1.17.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-celda >=1.16.0,<1.17.0' - - 'bioconductor-celldex >=1.10.0,<1.11.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-eds >=1.2.0,<1.3.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-gsvadata >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mast >=1.26.0,<1.27.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scdblfinder >=1.14.0,<1.15.0' - - 'bioconductor-scds >=1.16.0,<1.17.0' - - 'bioconductor-scmerge >=1.16.0,<1.17.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scrnaseq >=2.14.0,<2.15.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-singler >=2.2.0,<2.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' - - 'bioconductor-tenxpbmcdata >=1.18.0,<1.19.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' - - 'bioconductor-tscan >=1.38.0,<1.39.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' - - 'bioconductor-zellkonverter >=1.10.0,<1.11.0' - - 'bioconductor-zinbwave >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-batchelor >=1.18.0,<1.19.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-celda >=1.18.0,<1.19.0' + - 'bioconductor-celldex >=1.12.0,<1.13.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-eds >=1.4.0,<1.5.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-gsvadata >=1.38.0,<1.39.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mast >=1.28.0,<1.29.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scdblfinder >=1.16.0,<1.17.0' + - 'bioconductor-scds >=1.18.0,<1.19.0' + - 'bioconductor-scmerge >=1.18.0,<1.19.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scrnaseq >=2.16.0,<2.17.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-singler >=2.4.0,<2.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' + - 'bioconductor-tenxpbmcdata >=1.20.0,<1.21.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' + - 'bioconductor-tscan >=1.40.0,<1.41.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' + - 'bioconductor-zellkonverter >=1.12.0,<1.13.0' + - 'bioconductor-zinbwave >=1.24.0,<1.25.0' + - r-anndata - r-ape - r-base - r-circlize @@ -70,7 +72,7 @@ requirements: - r-data.table - r-dplyr - r-dt - - r-enrichr + - 'r-enrichr >=3.2' - r-fields - r-ggplot2 - r-ggplotify @@ -103,45 +105,46 @@ requirements: - r-withr - r-yaml run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-batchelor >=1.16.0,<1.17.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-celda >=1.16.0,<1.17.0' - - 'bioconductor-celldex >=1.10.0,<1.11.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-eds >=1.2.0,<1.3.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-gsvadata >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mast >=1.26.0,<1.27.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scdblfinder >=1.14.0,<1.15.0' - - 'bioconductor-scds >=1.16.0,<1.17.0' - - 'bioconductor-scmerge >=1.16.0,<1.17.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scrnaseq >=2.14.0,<2.15.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-singler >=2.2.0,<2.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' - - 'bioconductor-tenxpbmcdata >=1.18.0,<1.19.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' - - 'bioconductor-tscan >=1.38.0,<1.39.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' - - 'bioconductor-zellkonverter >=1.10.0,<1.11.0' - - 'bioconductor-zinbwave >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-batchelor >=1.18.0,<1.19.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-celda >=1.18.0,<1.19.0' + - 'bioconductor-celldex >=1.12.0,<1.13.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-eds >=1.4.0,<1.5.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-gsvadata >=1.38.0,<1.39.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mast >=1.28.0,<1.29.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scdblfinder >=1.16.0,<1.17.0' + - 'bioconductor-scds >=1.18.0,<1.19.0' + - 'bioconductor-scmerge >=1.18.0,<1.19.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scrnaseq >=2.16.0,<2.17.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-singler >=2.4.0,<2.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' + - 'bioconductor-tenxpbmcdata >=1.20.0,<1.21.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' + - 'bioconductor-tscan >=1.40.0,<1.41.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' + - 'bioconductor-zellkonverter >=1.12.0,<1.13.0' + - 'bioconductor-zinbwave >=1.24.0,<1.25.0' + - r-anndata - r-ape - r-base - r-circlize @@ -152,7 +155,7 @@ requirements: - r-data.table - r-dplyr - r-dt - - r-enrichr + - 'r-enrichr >=3.2' - r-fields - r-ggplot2 - r-ggplotify diff --git a/recipes/bioconductor-singlemoleculefootprinting/meta.yaml b/recipes/bioconductor-singlemoleculefootprinting/meta.yaml index 7e1a72be15812..0a49754cd4e22 100644 --- a/recipes/bioconductor-singlemoleculefootprinting/meta.yaml +++ b/recipes/bioconductor-singlemoleculefootprinting/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "SingleMoleculeFootprinting" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c6f36357ed42062a6d48b14986fb50aa + md5: dcdbbace0f6394ce22397640da1dd03f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-singlemoleculefootprinting", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, parallel, rmarkdown, readr, SingleMoleculeFootprintingData, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-quasr >=1.40.0,<1.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-quasr >=1.42.0,<1.43.0' - r-base - r-data.table - r-plyr - r-rcolorbrewer run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-quasr >=1.40.0,<1.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-quasr >=1.42.0,<1.43.0' - r-base - r-data.table - r-plyr diff --git a/recipes/bioconductor-singlemoleculefootprintingdata/meta.yaml b/recipes/bioconductor-singlemoleculefootprintingdata/meta.yaml index 9f59a0011a77f..6a54bd67dd050 100644 --- a/recipes/bioconductor-singlemoleculefootprintingdata/meta.yaml +++ b/recipes/bioconductor-singlemoleculefootprintingdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "SingleMoleculeFootprintingData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc061d235ffc26615634a650aedd4ac0 + md5: 451ecbdbb964607afbbe3b778b290246 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-singlemoleculefootprintingdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-singlemoleculefootprintingdata/post-link.sh b/recipes/bioconductor-singlemoleculefootprintingdata/post-link.sh index 178987ba30e16..a016eff25036b 100644 --- a/recipes/bioconductor-singlemoleculefootprintingdata/post-link.sh +++ b/recipes/bioconductor-singlemoleculefootprintingdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "singlemoleculefootprintingdata-1.8.0" +installBiocDataPackage.sh "singlemoleculefootprintingdata-1.10.0" diff --git a/recipes/bioconductor-singler/meta.yaml b/recipes/bioconductor-singler/meta.yaml index b0b34a8280eff..8bf68ce82b2b1 100644 --- a/recipes/bioconductor-singler/meta.yaml +++ b/recipes/bioconductor-singler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "SingleR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 58b4a0cd038cc175cd966a32f0195f30 + md5: 83651106a9f823febc5859dff16b48a7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-singler", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scater, scran, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex # SystemRequirements: C++17 requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-singscore/meta.yaml b/recipes/bioconductor-singscore/meta.yaml index 1266b324ae624..9fb6b973e6177 100644 --- a/recipes/bioconductor-singscore/meta.yaml +++ b/recipes/bioconductor-singscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "singscore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 79764544605a5b1de41856c897375ad2 + md5: c3ab598fd61c5bb54a842f9738133d24 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-singscore", max_pin="x.x") }}' noarch: generic # Suggests: pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggrepel @@ -39,12 +40,12 @@ requirements: - r-reshape2 - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-sipsic/meta.yaml b/recipes/bioconductor-sipsic/meta.yaml index b89be2584da1b..b7be8ce59689b 100644 --- a/recipes/bioconductor-sipsic/meta.yaml +++ b/recipes/bioconductor-sipsic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "SiPSiC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a749994a28fcd113adbf13ff1fdb9e6 + md5: e85e0e9b34b9a1e0a93dd653868061ef build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sipsic", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-matrix run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-sitadela/meta.yaml b/recipes/bioconductor-sitadela/meta.yaml index d18d8e6cb05de..81f00ad65a55e 100644 --- a/recipes/bioconductor-sitadela/meta.yaml +++ b/recipes/bioconductor-sitadela/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "sitadela" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0a9e771d4e00d39c87e1731fcdaa3999 + md5: 109b3096c37f30906c8c009097e45c59 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sitadela", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BSgenome, knitr, rmarkdown, RMySQL, RUnit requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rsqlite run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rsqlite test: diff --git a/recipes/bioconductor-sitepath/meta.yaml b/recipes/bioconductor-sitepath/meta.yaml index 5485b4e65b010..9470f4a08a362 100644 --- a/recipes/bioconductor-sitepath/meta.yaml +++ b/recipes/bioconductor-sitepath/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "sitePath" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f713347fa5b74763d60d1f91db80838 + md5: f5742fbe513f4d3cec29d3d3ee714d13 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sitepath", max_pin="x.x") }}' # Suggests: BiocStyle, devtools, knitr, magick, rmarkdown, testthat requirements: host: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-ape - r-aplot - r-base @@ -34,7 +35,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-ape - r-aplot - r-base diff --git a/recipes/bioconductor-sizepower/meta.yaml b/recipes/bioconductor-sizepower/meta.yaml index 49ff669f27e7b..bdcda1851859b 100644 --- a/recipes/bioconductor-sizepower/meta.yaml +++ b/recipes/bioconductor-sizepower/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "sizepower" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f168cdc6e987a88dda51d11e9fabfa1a + md5: 4edf7f08a26ccaa8ae0d08e17b6ef0cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sizepower", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-skewr/meta.yaml b/recipes/bioconductor-skewr/meta.yaml index 8d4c837add74c..4c0aea4605a0e 100644 --- a/recipes/bioconductor-skewr/meta.yaml +++ b/recipes/bioconductor-skewr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "skewr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c00d797ae9ac8e4b1f40a352409df4cb + md5: 083671e386afa1b9ec5766e6a8c50bba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-skewr", max_pin="x.x") }}' noarch: generic # Suggests: GEOquery, knitr, minfiData requirements: host: - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-watermelon >=2.6.0,<2.7.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-watermelon >=2.8.0,<2.9.0' - r-base - r-mixsmsn - r-rcolorbrewer run: - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-watermelon >=2.6.0,<2.7.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-watermelon >=2.8.0,<2.9.0' - r-base - r-mixsmsn - r-rcolorbrewer diff --git a/recipes/bioconductor-slalom/meta.yaml b/recipes/bioconductor-slalom/meta.yaml index cb544f8714472..9a66e56b5ce25 100644 --- a/recipes/bioconductor-slalom/meta.yaml +++ b/recipes/bioconductor-slalom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "slalom" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 398713b48231b0d9d9197f0a8af1e6f7 + md5: cf8b2aec440cd0fd79260a1f0199db2f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-slalom", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rhdf5, rmarkdown, scater, testthat requirements: host: - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-ggplot2 @@ -32,9 +33,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-ggplot2 diff --git a/recipes/bioconductor-slingshot/meta.yaml b/recipes/bioconductor-slingshot/meta.yaml index c9b05a6884e98..6031c6d4802c9 100644 --- a/recipes/bioconductor-slingshot/meta.yaml +++ b/recipes/bioconductor-slingshot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "slingshot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2f610f3a1f4538cff7e7f17240e2c3fb + md5: 556fe5835a602547c3475065eb5c11d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-slingshot", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' - r-base - r-igraph - r-matrixstats - 'r-princurve >=2.0.4' run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' - r-base - r-igraph - r-matrixstats diff --git a/recipes/bioconductor-slqpcr/meta.yaml b/recipes/bioconductor-slqpcr/meta.yaml index d802eb5b5b6be..51064b62afbb9 100644 --- a/recipes/bioconductor-slqpcr/meta.yaml +++ b/recipes/bioconductor-slqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "SLqPCR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7929611dce4a5093abfd58b6df35039 + md5: 72759fb6b62f3852f458e695318c0f6f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-slqpcr", max_pin="x.x") }}' noarch: generic # Suggests: RColorBrewer requirements: diff --git a/recipes/bioconductor-smad/meta.yaml b/recipes/bioconductor-smad/meta.yaml index 138e48d614390..1fe978fb29b01 100644 --- a/recipes/bioconductor-smad/meta.yaml +++ b/recipes/bioconductor-smad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "SMAD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c224400a2f1d4715e3a4274544b34915 + md5: 65f0eba6ed0bf086797b95b2c9da6dd6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-smad", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: diff --git a/recipes/bioconductor-smap/meta.yaml b/recipes/bioconductor-smap/meta.yaml index fa97b77650cb6..85c8a5cbef687 100644 --- a/recipes/bioconductor-smap/meta.yaml +++ b/recipes/bioconductor-smap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "SMAP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e90b812af45d9a171b490e282d28f91 + md5: f29ffdead8f34c2f531dd7ea764febe0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-smap", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-smite/meta.yaml b/recipes/bioconductor-smite/meta.yaml index 8084f012aca37..84c7ff35a230a 100644 --- a/recipes/bioconductor-smite/meta.yaml +++ b/recipes/bioconductor-smite/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "SMITE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 611558066283955f055323c81446ec75 + md5: 47c578785a426c3c7850880ed58033e8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-smite", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-bionet >=1.60.0,<1.61.0' - - 'bioconductor-genelendatabase >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-goseq >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-bionet >=1.62.0,<1.63.0' + - 'bioconductor-genelendatabase >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-goseq >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-hmisc @@ -39,17 +40,17 @@ requirements: - r-plyr - r-scales run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-bionet >=1.60.0,<1.61.0' - - 'bioconductor-genelendatabase >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-goseq >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-bionet >=1.62.0,<1.63.0' + - 'bioconductor-genelendatabase >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-goseq >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-hmisc diff --git a/recipes/bioconductor-smokingmouse/meta.yaml b/recipes/bioconductor-smokingmouse/meta.yaml new file mode 100644 index 0000000000000..95d226795b7e7 --- /dev/null +++ b/recipes/bioconductor-smokingmouse/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.0.0" %} +{% set name = "smokingMouse" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0c2fad6bf0e911ae8c140c02bc29150e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-smokingmouse", max_pin="x.x") }}' + noarch: generic +# Suggests: ExperimentHub, AnnotationHubData, BiocStyle, covr, ExperimentHubData, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) +requirements: + host: + - r-base + run: + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Provides access to smokingMouse project data' + description: 'This is an ExperimentHub package that provides access to the data at the gene, exon, transcript and junction level used in the analyses of the smokingMouse project. See https://github.com/LieberInstitute/smokingMouse_Indirects. This datasets contain the expression counts of genes, transcripts, exons and exon-exon junctions across 208 mice samples from pup and adult brains and adult blood. They also contain relevant information of these samples and features, such as conditions, QC metrics and if they were used after filtering steps and also if the features were differently expressed in the different experiments.' + diff --git a/recipes/bioconductor-smokingmouse/post-link.sh b/recipes/bioconductor-smokingmouse/post-link.sh new file mode 100644 index 0000000000000..d023daf8a973e --- /dev/null +++ b/recipes/bioconductor-smokingmouse/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "smokingmouse-1.0.0" diff --git a/recipes/bioconductor-smokingmouse/pre-unlink.sh b/recipes/bioconductor-smokingmouse/pre-unlink.sh new file mode 100644 index 0000000000000..aa46890e613d8 --- /dev/null +++ b/recipes/bioconductor-smokingmouse/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ smokingMouse diff --git a/recipes/bioconductor-snadata/meta.yaml b/recipes/bioconductor-snadata/meta.yaml index e787901ae7435..326d0f4f2d6e1 100644 --- a/recipes/bioconductor-snadata/meta.yaml +++ b/recipes/bioconductor-snadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "SNAData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d83f5e312b308aacb8c9c83d3226115 + md5: bfbd447afa550db44aa1db55e227cc10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snadata", max_pin="x.x") }}' noarch: generic # Suggests: Rgraphviz requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snadata/post-link.sh b/recipes/bioconductor-snadata/post-link.sh index 2b6df30c5257c..15572eae53e04 100644 --- a/recipes/bioconductor-snadata/post-link.sh +++ b/recipes/bioconductor-snadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "snadata-1.46.0" +installBiocDataPackage.sh "snadata-1.48.0" diff --git a/recipes/bioconductor-snagee/meta.yaml b/recipes/bioconductor-snagee/meta.yaml index 1834a5bc44880..88fa7034220c6 100644 --- a/recipes/bioconductor-snagee/meta.yaml +++ b/recipes/bioconductor-snagee/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "SNAGEE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 352732bbf9406a70370117c7ac521fa5 + md5: faadcab23b170f71a29ac7fd67b2a5d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snagee", max_pin="x.x") }}' noarch: generic # Suggests: ALL, hgu95av2.db requirements: host: - - 'bioconductor-snageedata >=1.36.0,<1.37.0' + - 'bioconductor-snageedata >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-snageedata >=1.36.0,<1.37.0' + - 'bioconductor-snageedata >=1.38.0,<1.39.0' - r-base test: commands: diff --git a/recipes/bioconductor-snageedata/meta.yaml b/recipes/bioconductor-snageedata/meta.yaml index 45c4aa8bef0f0..06c4621e7b240 100644 --- a/recipes/bioconductor-snageedata/meta.yaml +++ b/recipes/bioconductor-snageedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "SNAGEEdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e7786160ad882aea9132d3fb2ba77789 + md5: bfd0a2689cb9ac612cb2f8995c3a03d5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snageedata", max_pin="x.x") }}' noarch: generic # Suggests: ALL, hgu95av2.db, SNAGEE requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snageedata/post-link.sh b/recipes/bioconductor-snageedata/post-link.sh index a2bcecbea365f..5e8bb8a522c3c 100644 --- a/recipes/bioconductor-snageedata/post-link.sh +++ b/recipes/bioconductor-snageedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "snageedata-1.36.0" +installBiocDataPackage.sh "snageedata-1.38.0" diff --git a/recipes/bioconductor-snapcgh/meta.yaml b/recipes/bioconductor-snapcgh/meta.yaml index d34947ac5d13e..e534b5ccc7b74 100644 --- a/recipes/bioconductor-snapcgh/meta.yaml +++ b/recipes/bioconductor-snapcgh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "snapCGH" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7484b0baccb980c615fb9ecd6fb86ab9 + md5: d21dbae207756cb76e04cadbcfa8b086 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snapcgh", max_pin="x.x") }}' requirements: host: - - 'bioconductor-acgh >=1.78.0,<1.79.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-glad >=2.64.0,<2.65.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-tilingarray >=1.78.0,<1.79.0' + - 'bioconductor-acgh >=1.80.0,<1.81.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-tilingarray >=1.80.0,<1.81.0' - r-base - r-cluster - libblas - liblapack run: - - 'bioconductor-acgh >=1.78.0,<1.79.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-glad >=2.64.0,<2.65.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-tilingarray >=1.78.0,<1.79.0' + - 'bioconductor-acgh >=1.80.0,<1.81.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-tilingarray >=1.80.0,<1.81.0' - r-base - r-cluster build: diff --git a/recipes/bioconductor-snapcount/meta.yaml b/recipes/bioconductor-snapcount/meta.yaml index 8ec421e639259..e40c86fed787a 100644 --- a/recipes/bioconductor-snapcount/meta.yaml +++ b/recipes/bioconductor-snapcount/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "snapcount" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1a80d0c735e1b5059c4f0376f75fa61a + md5: 8efa036bfe73acf9c31a279b3c365ae7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snapcount", max_pin="x.x") }}' noarch: generic # Suggests: BiocManager, bit64, covr, knitcitations, knitr (>= 1.6), devtools, BiocStyle (>= 2.5.19), rmarkdown (>= 0.9.5), testthat (>= 2.1.0) requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-data.table @@ -36,9 +37,9 @@ requirements: - r-rlang - r-stringr run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-data.table diff --git a/recipes/bioconductor-snifter/meta.yaml b/recipes/bioconductor-snifter/meta.yaml index 8de266ad1bedc..2da36a360a549 100644 --- a/recipes/bioconductor-snifter/meta.yaml +++ b/recipes/bioconductor-snifter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "snifter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 105db4c0e2b10570d93fe359524beccc + md5: a6cfc8a05013cd2d050a1adba2b3fe4d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snifter", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' - r-assertthat - r-base - r-irlba - r-reticulate run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' - r-assertthat - r-base - r-irlba diff --git a/recipes/bioconductor-snm/meta.yaml b/recipes/bioconductor-snm/meta.yaml index 5ec09c740d1f3..16a1786338618 100644 --- a/recipes/bioconductor-snm/meta.yaml +++ b/recipes/bioconductor-snm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "snm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1585a1bef1fe800b8ce9fd1dab014e9b + md5: 103ab8eb4cca35d12c53c48615ebd5da build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snm", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-snpediar/meta.yaml b/recipes/bioconductor-snpediar/meta.yaml index 682d2d3ff2b7e..163a5977bdb6d 100644 --- a/recipes/bioconductor-snpediar/meta.yaml +++ b/recipes/bioconductor-snpediar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "SNPediaR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4335833edff43f6406eeed4294fa83ff + md5: 25d5eec5081ccfac687eba26102eb826 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snpediar", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-snphood/meta.yaml b/recipes/bioconductor-snphood/meta.yaml index c3cddcd6c75bf..9b8303698581a 100644 --- a/recipes/bioconductor-snphood/meta.yaml +++ b/recipes/bioconductor-snphood/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "SNPhood" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95aecf97b2fc6fda26705f4c0b7f83b9 + md5: f5a30ae405bebdb97e51cb2782debcbf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snphood", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-checkmate - r-cluster @@ -43,17 +44,17 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-checkmate - r-cluster diff --git a/recipes/bioconductor-snphooddata/meta.yaml b/recipes/bioconductor-snphooddata/meta.yaml index 13452dc4c61f6..b7e1b79ba3652 100644 --- a/recipes/bioconductor-snphooddata/meta.yaml +++ b/recipes/bioconductor-snphooddata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "SNPhoodData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fbc9419fda8d78b06f76e62df5639ae9 + md5: 72ac86008c225c71df946cc8a7de1fa1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snphooddata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle,knitr,rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snphooddata/post-link.sh b/recipes/bioconductor-snphooddata/post-link.sh index fdf543333018e..7fd81f93fc969 100644 --- a/recipes/bioconductor-snphooddata/post-link.sh +++ b/recipes/bioconductor-snphooddata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "snphooddata-1.30.0" +installBiocDataPackage.sh "snphooddata-1.32.0" diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml index 327d00aae5fcf..9e6b83fb2ab62 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP144.GRCh37" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: bd338bb583cacc18f210e871dac79ebf build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snplocs.hsapiens.dbsnp144.grch37", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml index d54fe98d34148..62e24e4082892 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP144.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 128c95e327adf72ae137fb5ae58270fc build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snplocs.hsapiens.dbsnp144.grch38", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml index d70675ec90785..f6a6fc11e513c 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP149.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8cf749a8649a53449066b54160a3745c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snplocs.hsapiens.dbsnp149.grch38", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml index 6d37b8ed2a26f..f066bc2eeae6b 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP150.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 575a7aaa9125d52ca0634b3ac586c9a7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snplocs.hsapiens.dbsnp150.grch38", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch37/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch37/meta.yaml index b62ab1e5462cc..64217e319f370 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch37/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch37/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.24" %} {% set name = "SNPlocs.Hsapiens.dbSNP155.GRCh37" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -17,27 +17,28 @@ build: rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snplocs.hsapiens.dbsnp155.grch37", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch38/meta.yaml index 7c427bc75106a..cfda415a59962 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.24" %} {% set name = "SNPlocs.Hsapiens.dbSNP155.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -17,27 +17,28 @@ build: rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snplocs.hsapiens.dbsnp155.grch38", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snprelate/meta.yaml b/recipes/bioconductor-snprelate/meta.yaml index fb0f78bb75ad3..a0e37b7d6801a 100644 --- a/recipes/bioconductor-snprelate/meta.yaml +++ b/recipes/bioconductor-snprelate/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.1" %} +{% set version = "1.36.0" %} {% set name = "SNPRelate" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8392e87cb9c26212c12cebd76de12cf + md5: f4e5095c6b99014e02d770e7f4bd5617 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snprelate", max_pin="x.x") }}' # Suggests: parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS, BiocGenerics requirements: host: - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - r-base - libblas - liblapack run: - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-snpstats/meta.yaml b/recipes/bioconductor-snpstats/meta.yaml index c5ed6fbea506f..0203a1cda4481 100644 --- a/recipes/bioconductor-snpstats/meta.yaml +++ b/recipes/bioconductor-snpstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "snpStats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fba193a357b1be45597d537425b2c62f + md5: 0625c920470937a31fd278cf8bd8982a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snpstats", max_pin="x.x") }}' # Suggests: hexbin requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-matrix - r-survival - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-matrix - r-survival diff --git a/recipes/bioconductor-soggi/meta.yaml b/recipes/bioconductor-soggi/meta.yaml index fddf936914ea7..b4b76b787681f 100644 --- a/recipes/bioconductor-soggi/meta.yaml +++ b/recipes/bioconductor-soggi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "soGGi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,46 +11,47 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3e73483964e8c438966ac51a33187c0 + md5: 6b8a823ad7812fdda198d38b28c00f6f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-soggi", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-chipseq >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-chipseq >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-chipseq >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-chipseq >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-reshape2 diff --git a/recipes/bioconductor-somascan.db/meta.yaml b/recipes/bioconductor-somascan.db/meta.yaml new file mode 100644 index 0000000000000..06a3f52706efd --- /dev/null +++ b/recipes/bioconductor-somascan.db/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "0.99.7" %} +{% set name = "SomaScan.db" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: aa52f4f12dfb2f0aa4c7fe3633de4646 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-somascan.db", max_pin="x.x") }}' + noarch: generic +# Suggests: annotate, BiocStyle, dplyr, GO.db, hgu95av2.db, KEGGREST, knitr, rmarkdown, SomaDataIO, testthat (>= 3.0.0), withr +requirements: + host: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - r-base + - r-dbi + run: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - r-base + - r-dbi + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Somalogic SomaScan Annotation Data' + description: 'An R package providing extended biological annotations for the SomaScan Assay, a proteomics platform developed by SomaLogic Operating Co., Inc. The annotations in this package were assembled using data from public repositories. For more information about the SomaScan assay and its data, please reference the ''SomaLogic/SomaLogic-Data'' GitHub repository.' + license_file: LICENSE + diff --git a/recipes/bioconductor-somascan.db/post-link.sh b/recipes/bioconductor-somascan.db/post-link.sh new file mode 100644 index 0000000000000..5a86e22124d74 --- /dev/null +++ b/recipes/bioconductor-somascan.db/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "somascan.db-0.99.7" diff --git a/recipes/bioconductor-somascan.db/pre-unlink.sh b/recipes/bioconductor-somascan.db/pre-unlink.sh new file mode 100644 index 0000000000000..2bd6437f78149 --- /dev/null +++ b/recipes/bioconductor-somascan.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SomaScan.db diff --git a/recipes/bioconductor-somaticadata/meta.yaml b/recipes/bioconductor-somaticadata/meta.yaml index 6f7e9ab2135e6..00bdf05078a09 100644 --- a/recipes/bioconductor-somaticadata/meta.yaml +++ b/recipes/bioconductor-somaticadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "SomatiCAData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1ec746e24a46ea58a782f2d7e18b9c29 + md5: 31d9100d6b5fa5f95c59eda9995f2684 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-somaticadata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-somaticadata/post-link.sh b/recipes/bioconductor-somaticadata/post-link.sh index e0381f4000f6d..ae240efdbcd9e 100644 --- a/recipes/bioconductor-somaticadata/post-link.sh +++ b/recipes/bioconductor-somaticadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "somaticadata-1.38.0" +installBiocDataPackage.sh "somaticadata-1.40.0" diff --git a/recipes/bioconductor-somaticcanceralterations/meta.yaml b/recipes/bioconductor-somaticcanceralterations/meta.yaml index 6dfdcd891ec29..45d47329efb01 100644 --- a/recipes/bioconductor-somaticcanceralterations/meta.yaml +++ b/recipes/bioconductor-somaticcanceralterations/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "SomaticCancerAlterations" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09b8e014009801826dde224175c1f774 + md5: 77b2b0312705c2a9581cdf7aab591db8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-somaticcanceralterations", max_pin="x.x") }}' noarch: generic # Suggests: testthat, ggbio, ggplot2, knitr requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-somaticcanceralterations/post-link.sh b/recipes/bioconductor-somaticcanceralterations/post-link.sh index 6fe8d5d9a642b..d63db0e4c80a7 100644 --- a/recipes/bioconductor-somaticcanceralterations/post-link.sh +++ b/recipes/bioconductor-somaticcanceralterations/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "somaticcanceralterations-1.36.0" +installBiocDataPackage.sh "somaticcanceralterations-1.38.0" diff --git a/recipes/bioconductor-somaticsignatures/meta.yaml b/recipes/bioconductor-somaticsignatures/meta.yaml index c455794f053be..9db50d019bf36 100644 --- a/recipes/bioconductor-somaticsignatures/meta.yaml +++ b/recipes/bioconductor-somaticsignatures/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.36.0" %} +{% set version = "2.38.0" %} {% set name = "SomaticSignatures" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c70a8ab04a25f675f456adae05f672a3 + md5: 46d14334be0098323bc956bade5d5e9e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-somaticsignatures", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, parallel, BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations, ggdendro, fastICA, sva requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggplot2 - r-nmf - r-proxy - r-reshape2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggplot2 - r-nmf diff --git a/recipes/bioconductor-somnibus/meta.yaml b/recipes/bioconductor-somnibus/meta.yaml index 391796666a2c9..3d26442edc700 100644 --- a/recipes/bioconductor-somnibus/meta.yaml +++ b/recipes/bioconductor-somnibus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.7.0" %} +{% set version = "1.10.0" %} {% set name = "SOMNiBUS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,52 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3686657266b274a93233dd24d23f1294 + md5: 0865c015122f915127302bf751a10812 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-somnibus", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown, testthat +# Suggests: BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, requirements: host: + - 'bioconductor-annotatr >=1.28.0,<1.29.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base + - r-biocmanager + - r-data.table + - r-ggplot2 - r-matrix - r-mgcv + - r-reshape2 + - r-tidyr - r-vgam + - r-yaml run: + - 'bioconductor-annotatr >=1.28.0,<1.29.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base + - r-biocmanager + - r-data.table + - r-ggplot2 - r-matrix - r-mgcv + - r-reshape2 + - r-tidyr - r-vgam + - r-yaml test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-soybeancdf/meta.yaml b/recipes/bioconductor-soybeancdf/meta.yaml index ebd6fea315882..fa809e0be223a 100644 --- a/recipes/bioconductor-soybeancdf/meta.yaml +++ b/recipes/bioconductor-soybeancdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "soybeancdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a18e0ba5dbcf2291bdec91091dc528e6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-soybeancdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-soybeanprobe/meta.yaml b/recipes/bioconductor-soybeanprobe/meta.yaml index 21b5bdee97dbd..37c26efb68ab5 100644 --- a/recipes/bioconductor-soybeanprobe/meta.yaml +++ b/recipes/bioconductor-soybeanprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "soybeanprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3057a5c387ff35b6c647c4db27041a13 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-soybeanprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-spacepac/meta.yaml b/recipes/bioconductor-spacepac/meta.yaml index da89c68eb3064..af052e29be413 100644 --- a/recipes/bioconductor-spacepac/meta.yaml +++ b/recipes/bioconductor-spacepac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "SpacePAC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ff52a3613f9c0d46581f626a41a29f9 + md5: aa35450e9ef0b3cd7ca3d90262d36ddf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spacepac", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, rgl requirements: host: - - 'bioconductor-ipac >=1.44.0,<1.45.0' + - 'bioconductor-ipac >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-ipac >=1.44.0,<1.45.0' + - 'bioconductor-ipac >=1.46.0,<1.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-spaniel/meta.yaml b/recipes/bioconductor-spaniel/meta.yaml index cb7b2d8a46f9d..5dbb8445371d2 100644 --- a/recipes/bioconductor-spaniel/meta.yaml +++ b/recipes/bioconductor-spaniel/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "Spaniel" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a456611860cdb19712e117ca3bb5811 + md5: fb29666756a1db567f16b5c72420de4c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spaniel", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, devtools requirements: host: - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -38,12 +39,12 @@ requirements: - r-seurat - r-shiny run: - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-sparrow/meta.yaml b/recipes/bioconductor-sparrow/meta.yaml index cb8a9b9527ac9..5d45dc6ab1c96 100644 --- a/recipes/bioconductor-sparrow/meta.yaml +++ b/recipes/bioconductor-sparrow/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "sparrow" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d48cb1cab6f2032d3e8101f5ff9b527a + md5: 072ccf02fa2cc42410000f238dce492b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sparrow", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle, DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin, magrittr, matrixStats, msigdbr (>= 7.4.1), KernSmooth, knitr, PANTHER.db (>= 1.0.3), R.utils, reactome.db, rmarkdown, SummarizedExperiment, statmod, stringr, testthat, webshot requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocset >=1.14.0,<1.15.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocset >=1.16.0,<1.17.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - 'r-babelgene >=21.4' - r-base - r-checkmate @@ -40,14 +41,14 @@ requirements: - 'r-plotly >=4.9.0' - r-viridis run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocset >=1.14.0,<1.15.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocset >=1.16.0,<1.17.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - 'r-babelgene >=21.4' - r-base - r-checkmate diff --git a/recipes/bioconductor-sparsearray/meta.yaml b/recipes/bioconductor-sparsearray/meta.yaml index f5acf6cd63e10..b055e619a974e 100644 --- a/recipes/bioconductor-sparsearray/meta.yaml +++ b/recipes/bioconductor-sparsearray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.10" %} +{% set version = "1.2.2" %} {% set name = "SparseArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e5ecc9eaa58af506cbf7340f9c890f1 + md5: a73b2e316ce8135de81af01a9a9610ec build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sparsearray", max_pin="x.x") }}' # Suggests: DelayedArray, testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4arrays >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4arrays >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-matrix - r-matrixstats - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4arrays >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4arrays >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-matrix - r-matrixstats diff --git a/recipes/bioconductor-sparsematrixstats/meta.yaml b/recipes/bioconductor-sparsematrixstats/meta.yaml index 2f11958509062..5b0186e8e00f3 100644 --- a/recipes/bioconductor-sparsematrixstats/meta.yaml +++ b/recipes/bioconductor-sparsematrixstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.2" %} +{% set version = "1.14.0" %} {% set name = "sparseMatrixStats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7669451759bb18ece433548b067ac73e + md5: 4319e6fb04b91467bd08cc4ce2ad609c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sparsematrixstats", max_pin="x.x") }}' # Suggests: testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle # SystemRequirements: C++11 requirements: host: - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - r-base - r-matrix - 'r-matrixstats >=0.60.0' @@ -29,7 +30,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - r-base - r-matrix - 'r-matrixstats >=0.60.0' diff --git a/recipes/bioconductor-sparsenetgls/meta.yaml b/recipes/bioconductor-sparsenetgls/meta.yaml index 3492a6b81e9fd..9568b17a7c9b5 100644 --- a/recipes/bioconductor-sparsenetgls/meta.yaml +++ b/recipes/bioconductor-sparsenetgls/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "sparsenetgls" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e3b4604f61dbbc07c2acdad62b980e2f + md5: 32b8f3b9fe86b40386aee23ac4ea55fd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sparsenetgls", max_pin="x.x") }}' noarch: generic # Suggests: testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) # SystemRequirements: GNU make diff --git a/recipes/bioconductor-sparsesignatures/meta.yaml b/recipes/bioconductor-sparsesignatures/meta.yaml index 313e0c984a18a..5f81cb9307a38 100644 --- a/recipes/bioconductor-sparsesignatures/meta.yaml +++ b/recipes/bioconductor-sparsesignatures/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "SparseSignatures" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eaa4a346f4ce804bdd6e4f684a8889f5 + md5: 832b206679a06252fa3b76f2700a70e9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sparsesignatures", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5, BiocStyle, testthat, knitr, requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-data.table - r-ggplot2 @@ -35,11 +36,11 @@ requirements: - r-nnls - r-reshape2 run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-spasim/meta.yaml b/recipes/bioconductor-spasim/meta.yaml index c899699a568f0..4189527c513c5 100644 --- a/recipes/bioconductor-spasim/meta.yaml +++ b/recipes/bioconductor-spasim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "spaSim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a6294d1b8bfe4bacae22708e5043fa8f + md5: d69e70975aaaa9bffc5e52f95885e59c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spasim", max_pin="x.x") }}' noarch: generic # Suggests: RefManageR, BiocStyle, knitr, testthat (>= 3.0.0), sessioninfo, rmarkdown, markdown requirements: host: - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -30,8 +31,8 @@ requirements: - r-spatstat.geom - r-spatstat.random run: - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-spatialcpie/meta.yaml b/recipes/bioconductor-spatialcpie/meta.yaml index ccddfc1fa8f6c..2a26cea000a99 100644 --- a/recipes/bioconductor-spatialcpie/meta.yaml +++ b/recipes/bioconductor-spatialcpie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "SpatialCPie" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5b9f134b000016e4ac3171cb99f9bfc + md5: f7f622f0a9e08b387870bddc9a52cfc2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialcpie", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 2.8.2), jpeg (>= 0.1-8), knitr (>= 1.20), rmarkdown (>= 1.10), testthat (>= 2.0.0) requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-colorspace >=1.3-2' - 'r-data.table >=1.12.2' @@ -45,7 +46,7 @@ requirements: - 'r-tidyselect >=0.2.4' - 'r-zeallot >=0.1.0' run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-colorspace >=1.3-2' - 'r-data.table >=1.12.2' diff --git a/recipes/bioconductor-spatialdatasets/meta.yaml b/recipes/bioconductor-spatialdatasets/meta.yaml new file mode 100644 index 0000000000000..59eeabf7949e9 --- /dev/null +++ b/recipes/bioconductor-spatialdatasets/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.0.0" %} +{% set name = "SpatialDatasets" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 36fd913ef0d7109d0be40afbc1255548 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialdatasets", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Collection of spatial omics datasets' + description: 'This is a collection of publically available spatial omics datasets. Where possible we have curated these datasets as either SpatialExperiments, MoleculeExperiments or CytoImageLists and included annotations of the sample characteristics.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-spatialdatasets/post-link.sh b/recipes/bioconductor-spatialdatasets/post-link.sh new file mode 100644 index 0000000000000..072e49b3171c7 --- /dev/null +++ b/recipes/bioconductor-spatialdatasets/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "spatialdatasets-1.0.0" diff --git a/recipes/bioconductor-spatialdatasets/pre-unlink.sh b/recipes/bioconductor-spatialdatasets/pre-unlink.sh new file mode 100644 index 0000000000000..b5bdda7982391 --- /dev/null +++ b/recipes/bioconductor-spatialdatasets/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SpatialDatasets diff --git a/recipes/bioconductor-spatialde/meta.yaml b/recipes/bioconductor-spatialde/meta.yaml index 9229b7cb57066..113377b6f586e 100644 --- a/recipes/bioconductor-spatialde/meta.yaml +++ b/recipes/bioconductor-spatialde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "spatialDE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 62f672c7a70d4a0d0b4895b103e73379 + md5: 4227d5d446ef2399e1b325cfa7ef65b7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialde", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-ggplot2 @@ -33,9 +34,9 @@ requirements: - r-reticulate - r-scales run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-ggplot2 diff --git a/recipes/bioconductor-spatialdecon/meta.yaml b/recipes/bioconductor-spatialdecon/meta.yaml index c6f443962be21..dd83c38cceac5 100644 --- a/recipes/bioconductor-spatialdecon/meta.yaml +++ b/recipes/bioconductor-spatialdecon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "SpatialDecon" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c6fb182168a8f4c35626e71f3f9ad301 + md5: a3dd72587ea55dc018231523782d225f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialdecon", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, qpdf requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geomxtools >=3.4.0,<3.5.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geomxtools >=3.5.0,<3.6.0' - r-base - 'r-lognormreg >=0.4' - r-matrix - r-repmis - r-seuratobject run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geomxtools >=3.4.0,<3.5.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geomxtools >=3.5.0,<3.6.0' - r-base - 'r-lognormreg >=0.4' - r-matrix diff --git a/recipes/bioconductor-spatialdmelxsim/meta.yaml b/recipes/bioconductor-spatialdmelxsim/meta.yaml index 9141957e86303..2e4dbaa680488 100644 --- a/recipes/bioconductor-spatialdmelxsim/meta.yaml +++ b/recipes/bioconductor-spatialdmelxsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "spatialDmelxsim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f999976552a56f39d49fd9ee186b017 + md5: 2fec38c7672022e76f2b7a7ba7b9a677 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialdmelxsim", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230713 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-spatialdmelxsim/post-link.sh b/recipes/bioconductor-spatialdmelxsim/post-link.sh index 73a1e9d948c9a..b6c6cfed4f1e5 100644 --- a/recipes/bioconductor-spatialdmelxsim/post-link.sh +++ b/recipes/bioconductor-spatialdmelxsim/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "spatialdmelxsim-1.6.1" +installBiocDataPackage.sh "spatialdmelxsim-1.8.0" diff --git a/recipes/bioconductor-spatialexperiment/meta.yaml b/recipes/bioconductor-spatialexperiment/meta.yaml index 470bebc56e1f2..61e7e4da5902d 100644 --- a/recipes/bioconductor-spatialexperiment/meta.yaml +++ b/recipes/bioconductor-spatialexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "SpatialExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9541a84eef622297d0a26bc0de26da03 + md5: 7dbd7938c005104df763ecf3d016154f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialexperiment", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix +# Suggests: knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-magick - r-rjson run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-magick - r-rjson diff --git a/recipes/bioconductor-spatialfeatureexperiment/meta.yaml b/recipes/bioconductor-spatialfeatureexperiment/meta.yaml index 7ae7a555748f0..72a314a96d05f 100644 --- a/recipes/bioconductor-spatialfeatureexperiment/meta.yaml +++ b/recipes/bioconductor-spatialfeatureexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "SpatialFeatureExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e6b58208d533b7d157f3f736da0c77bd + md5: 56d4ad5144861bea16c2f677e096ac75 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialfeatureexperiment", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, dplyr, DropletUtils, knitr, rhdf5, rmarkdown, sfarrow, SFEData, vroom, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rjson @@ -36,13 +37,13 @@ requirements: - 'r-spdep >=1.1-7' - r-terra run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rjson diff --git a/recipes/bioconductor-spatialheatmap/meta.yaml b/recipes/bioconductor-spatialheatmap/meta.yaml index cb8a49efac777..d4edc6ad928bf 100644 --- a/recipes/bioconductor-spatialheatmap/meta.yaml +++ b/recipes/bioconductor-spatialheatmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "spatialHeatmap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,83 +11,68 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 99f9415e7f96f98c824aac703586776b + md5: 2fe3c68f9bbfb419d0afd3d329e65747 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialheatmap", max_pin="x.x") }}' noarch: generic -# Suggests: AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, distinct, dendextend, DT, HDF5Array, htmltools, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db, org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, rmarkdown, rols, rappdirs, RUnit, Rtsne, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, uwot +# Suggests: AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, distinct, dendextend, DT, dynamicTreeCut, flashClust, ggdendro, HDF5Array, htmltools, htmlwidgets, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db, org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, plotly, rmarkdown, rols, rappdirs, RUnit, Rtsne, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, yaml requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr - - r-dynamictreecut - - r-flashclust - - r-ggdendro - r-ggplot2 - r-ggplotify - r-gplots - r-gridextra - r-grimport - - r-htmlwidgets - r-igraph - r-matrix - - r-plotly - r-reshape2 - r-rsvg - r-shiny - r-shinydashboard + - 'r-spscomps >=0.3.3.0' - r-tibble - - r-upsetr - - r-visnetwork - - r-wgcna - r-xml2 - - r-yaml run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr - - r-dynamictreecut - - r-flashclust - - r-ggdendro - r-ggplot2 - r-ggplotify - r-gplots - r-gridextra - r-grimport - - r-htmlwidgets - r-igraph - r-matrix - - r-plotly - r-reshape2 - r-rsvg - r-shiny - r-shinydashboard + - 'r-spscomps >=0.3.3.0' - r-tibble - - r-upsetr - - r-visnetwork - - r-wgcna - r-xml2 - - r-yaml test: commands: - '$R -e "library(''{{ name }}'')"' @@ -95,5 +80,5 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: spatialHeatmap - description: 'The spatialHeatmap package provides functionalities for visualizing cell-, tissue- and organ-specific data of biological assays by coloring the corresponding spatial features defined in anatomical images according to a numeric color key.' + description: 'The spatialHeatmap package offers the primary functionality for visualizing cell-, tissue- and organ-specific assay data in spatial anatomical images. Additionally, it provides extended functionalities for large-scale data mining routines and co-visualizing bulk and single-cell data.' diff --git a/recipes/bioconductor-spatiallibd/meta.yaml b/recipes/bioconductor-spatiallibd/meta.yaml index 30f9d535b5b41..9c66105422f97 100644 --- a/recipes/bioconductor-spatiallibd/meta.yaml +++ b/recipes/bioconductor-spatiallibd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.1" %} {% set name = "spatialLIBD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c14166eb3d988b152448d770f491507 + md5: cd8c85a03e555f2dfdeb1627f7087002 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatiallibd", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, lobstr +# Suggests: knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, lobstr, DropletUtils requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-benchmarkme - r-cowplot @@ -57,21 +58,21 @@ requirements: - r-tibble - r-viridislite run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-benchmarkme - r-cowplot @@ -93,7 +94,7 @@ requirements: - r-tibble - r-viridislite - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-spatiallibd/post-link.sh b/recipes/bioconductor-spatiallibd/post-link.sh index ef2ee65ad274e..9ef1f36f1b430 100644 --- a/recipes/bioconductor-spatiallibd/post-link.sh +++ b/recipes/bioconductor-spatiallibd/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "spatiallibd-1.12.0" +installBiocDataPackage.sh "spatiallibd-1.14.1" diff --git a/recipes/bioconductor-spatialomicsoverlay/meta.yaml b/recipes/bioconductor-spatialomicsoverlay/meta.yaml index a65ec0d5984ba..8d46d91ef4271 100644 --- a/recipes/bioconductor-spatialomicsoverlay/meta.yaml +++ b/recipes/bioconductor-spatialomicsoverlay/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.1" %} {% set name = "SpatialOmicsOverlay" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 596d07d8c2f6f59deafd7d6d3f24162e + md5: 149a968f19aa22b57caca243b3480378 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialomicsoverlay", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr +# Suggests: knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr, sf requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-geomxtools >=3.4.0,<3.5.0' - - 'bioconductor-rbioformats >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-geomxtools >=3.5.0,<3.6.0' + - 'bioconductor-rbioformats >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-base64enc - r-data.table @@ -41,12 +42,12 @@ requirements: - r-stringr - r-xml run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-geomxtools >=3.4.0,<3.5.0' - - 'bioconductor-rbioformats >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-geomxtools >=3.5.0,<3.6.0' + - 'bioconductor-rbioformats >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-base64enc - r-data.table diff --git a/recipes/bioconductor-spatzie/meta.yaml b/recipes/bioconductor-spatzie/meta.yaml index 30b812f536f85..98199da5b24e6 100644 --- a/recipes/bioconductor-spatzie/meta.yaml +++ b/recipes/bioconductor-spatzie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "spatzie" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,44 +11,45 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 001f0345a1039c53f6f585f2950ef7f7 + md5: fa887a71329c75cde9ab0b1aaeb0d481 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatzie", max_pin="x.x") }}' noarch: generic # Suggests: BiocManager, Biostrings, knitr, pheatmap, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicinteractions >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-ggplot2 - r-matrixstats run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicinteractions >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-ggplot2 - r-matrixstats diff --git a/recipes/bioconductor-speckle/meta.yaml b/recipes/bioconductor-speckle/meta.yaml index 5f7896bf030f5..76d5d70a76e25 100644 --- a/recipes/bioconductor-speckle/meta.yaml +++ b/recipes/bioconductor-speckle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "speckle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f95c51e61cd908d7bdc1c09c0f818eea + md5: 4603cad300c83d6e6374e5989b5fe32a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-speckle", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, statmod, CellBench, scater, patchwork, jsonlite, vdiffr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-ggplot2 - r-seurat run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-ggplot2 - r-seurat diff --git a/recipes/bioconductor-specl/meta.yaml b/recipes/bioconductor-specl/meta.yaml index 64f32842e8a77..df05401abb956 100644 --- a/recipes/bioconductor-specl/meta.yaml +++ b/recipes/bioconductor-specl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "specL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94afc529140346a23f2b1b46026b482b + md5: a3a436585f26f8353106b030a26cbf98 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-specl", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4) requirements: diff --git a/recipes/bioconductor-specond/meta.yaml b/recipes/bioconductor-specond/meta.yaml index 59647e5a09f72..dce56f3e7bbba 100644 --- a/recipes/bioconductor-specond/meta.yaml +++ b/recipes/bioconductor-specond/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "SpeCond" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7b33052af7d4b397953ca36153d07a8d + md5: f189b2d0a72f0fb1b7a99bd0b2bb73ab build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-specond", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-fields - 'r-hwriter >=1.1' - 'r-mclust >=3.3.1' - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-fields - 'r-hwriter >=1.1' diff --git a/recipes/bioconductor-spectra/meta.yaml b/recipes/bioconductor-spectra/meta.yaml index 436634bf9685e..dd269b5bb66be 100644 --- a/recipes/bioconductor-spectra/meta.yaml +++ b/recipes/bioconductor-spectra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "Spectra" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 617b4d14b39808599e781280c128fe1e + md5: 32589596593389b703c87d7a05479fe3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spectra", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, knitr (>= 1.1.0), msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0), rmarkdown, vdiffr (>= 1.0.0) +# Suggests: testthat, knitr (>= 1.1.0), msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0), rmarkdown, vdiffr (>= 1.0.0), msentropy, patrick requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fs run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fs test: diff --git a/recipes/bioconductor-spectraltad/meta.yaml b/recipes/bioconductor-spectraltad/meta.yaml index 763c5722c6bf4..dc69aaf8e4fd8 100644 --- a/recipes/bioconductor-spectraltad/meta.yaml +++ b/recipes/bioconductor-spectraltad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "SpectralTAD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 39074ac3986665a8f47831b0931adcca + md5: 359760e22303de30ab396fcc7d5938af build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spectraltad", max_pin="x.x") }}' noarch: generic # Suggests: BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hiccompare >=1.22.0,<1.23.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hiccompare >=1.24.0,<1.25.0' - r-base - r-cluster - r-dplyr @@ -31,9 +32,9 @@ requirements: - r-matrix - r-primme run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hiccompare >=1.22.0,<1.23.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hiccompare >=1.24.0,<1.25.0' - r-base - r-cluster - r-dplyr diff --git a/recipes/bioconductor-spem/meta.yaml b/recipes/bioconductor-spem/meta.yaml index 0e0876ae2f0af..a841243035900 100644 --- a/recipes/bioconductor-spem/meta.yaml +++ b/recipes/bioconductor-spem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "SPEM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 785ed40eb3c06926a7e4dc2d327d6d74 + md5: 2b0ef40bd2428559cf559dfeb2a384f3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spem", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-rsolnp run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-rsolnp test: diff --git a/recipes/bioconductor-spia/meta.yaml b/recipes/bioconductor-spia/meta.yaml index 3fd1d648db072..dc1d20edf94e0 100644 --- a/recipes/bioconductor-spia/meta.yaml +++ b/recipes/bioconductor-spia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.52.0" %} +{% set version = "2.54.0" %} {% set name = "SPIA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 108b8d0a425842f59317eb392085a48c + md5: 1a03ed18c41344eb23d6836cb337b9dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spia", max_pin="x.x") }}' noarch: generic # Suggests: graph, Rgraphviz, hgu133plus2.db requirements: host: - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-spiat/meta.yaml b/recipes/bioconductor-spiat/meta.yaml index a6bb194d78112..584c9b01bc639 100644 --- a/recipes/bioconductor-spiat/meta.yaml +++ b/recipes/bioconductor-spiat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.2" %} +{% set version = "1.4.1" %} {% set name = "SPIAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9cfee83cf9df8a5f738501c50a9deb30 + md5: 45342ea9b5cbfbc01e38d6c7b7866852 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spiat", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, plotly (>= 4.9.0), knitr, rmarkdown, pkgdown, testthat, graphics, alphahull, Rtsne, umap, rlang, ComplexHeatmap, elsa +# Suggests: BiocStyle, plotly (>= 4.9.0), knitr, rmarkdown, pkgdown, testthat, graphics, alphahull, Rtsne, umap, ComplexHeatmap, elsa requirements: host: - - 'bioconductor-dittoseq >=1.12.0,<1.13.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-dittoseq >=1.14.0,<1.15.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'r-apcluster >=1.4.7' - r-base - 'r-dbscan >=1.1-5' @@ -36,15 +37,16 @@ requirements: - 'r-rann >=2.6.1' - r-raster - 'r-reshape2 >=1.4.3' + - r-rlang - r-sp - r-spatstat.explore - r-spatstat.geom - 'r-tibble >=2.1.3' - r-vroom run: - - 'bioconductor-dittoseq >=1.12.0,<1.13.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-dittoseq >=1.14.0,<1.15.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'r-apcluster >=1.4.7' - r-base - 'r-dbscan >=1.1-5' @@ -57,6 +59,7 @@ requirements: - 'r-rann >=2.6.1' - r-raster - 'r-reshape2 >=1.4.3' + - r-rlang - r-sp - r-spatstat.explore - r-spatstat.geom @@ -67,7 +70,8 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 + license: 'Artistic-2.0 + file LICENSE' summary: 'Spatial Image Analysis of Tissues' description: 'SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.' + license_file: LICENSE diff --git a/recipes/bioconductor-spicyr/meta.yaml b/recipes/bioconductor-spicyr/meta.yaml index 758db5f04d27a..cac91262c0ec4 100644 --- a/recipes/bioconductor-spicyr/meta.yaml +++ b/recipes/bioconductor-spicyr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.2" %} {% set name = "spicyR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ce45c72613383f9d7f5502ac6856060b + md5: 36cba4820e1206ad3a7220e0430b245f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spicyr", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, pkgdown +# Suggests: BiocStyle, knitr, rmarkdown, pkgdown, imcRtools requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-classifyr >=3.6.0,<3.7.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-concaveman - r-data.table - r-dplyr - r-ggforce - r-ggplot2 - - r-lme4 - r-lmertest - r-mgcv - r-pheatmap @@ -42,22 +43,23 @@ requirements: - r-scam - r-spatstat.explore - r-spatstat.geom + - r-tibble - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-classifyr >=3.6.0,<3.7.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-concaveman - r-data.table - r-dplyr - r-ggforce - r-ggplot2 - - r-lme4 - r-lmertest - r-mgcv - r-pheatmap @@ -65,6 +67,7 @@ requirements: - r-scam - r-spatstat.explore - r-spatstat.geom + - r-tibble - r-tidyr test: commands: @@ -73,6 +76,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Spatial analysis of in situ cytometry data' - description: 'spicyR provides a series of functions to aid in the analysis of both immunofluorescence and mass cytometry imaging data as well as other assays that can deeply phenotype individual cells and their spatial location.' + description: 'The spicyR package provides a framework for performing inference on changes in spatial relationships between pairs of cell types for cell-resolution spatial omics technologies. spicyR consists of three primary steps: (i) summarizing the degree of spatial localization between pairs of cell types for each image; (ii) modelling the variability in localization summary statistics as a function of cell counts and (iii) testing for changes in spatial localizations associated with a response variable.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-spidermir/meta.yaml b/recipes/bioconductor-spidermir/meta.yaml index bdf9c8b33201c..efa9330b4c45e 100644 --- a/recipes/bioconductor-spidermir/meta.yaml +++ b/recipes/bioconductor-spidermir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "SpidermiR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 611d3128b08997448bf2f5b68f7c646e + md5: 86d54ea72377eb5f3fc8f92ba3b55374 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spidermir", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-mirnatap >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-mirnatap >=1.36.0,<1.37.0' - 'bioconductor-mirnatap.db >=0.99.0,<0.100.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-gdata - r-httr - r-igraph run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-mirnatap >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-mirnatap >=1.36.0,<1.37.0' - 'bioconductor-mirnatap.db >=0.99.0,<0.100.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-gdata - r-httr diff --git a/recipes/bioconductor-spikein/meta.yaml b/recipes/bioconductor-spikein/meta.yaml index b44831908e204..f995b553eabe6 100644 --- a/recipes/bioconductor-spikein/meta.yaml +++ b/recipes/bioconductor-spikein/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "SpikeIn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e738872c55386dae6334ee399c4674a3 + md5: 439f9d2eda54024edb7c1c81862d74c8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spikein", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-spikein/post-link.sh b/recipes/bioconductor-spikein/post-link.sh index 57a7e13c948a6..2b5335dd03814 100644 --- a/recipes/bioconductor-spikein/post-link.sh +++ b/recipes/bioconductor-spikein/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "spikein-1.42.0" +installBiocDataPackage.sh "spikein-1.44.0" diff --git a/recipes/bioconductor-spikeinsubset/meta.yaml b/recipes/bioconductor-spikeinsubset/meta.yaml index 7737f7b5325e7..1cbb90bd6c7ae 100644 --- a/recipes/bioconductor-spikeinsubset/meta.yaml +++ b/recipes/bioconductor-spikeinsubset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "SpikeInSubset" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 25b553c357880acdabf962253d55d69b + md5: 0c9b5af679c89a1468c9a6f581202e2b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spikeinsubset", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-spikeinsubset/post-link.sh b/recipes/bioconductor-spikeinsubset/post-link.sh index 7151258b59659..0c176d193c9ac 100644 --- a/recipes/bioconductor-spikeinsubset/post-link.sh +++ b/recipes/bioconductor-spikeinsubset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "spikeinsubset-1.40.0" +installBiocDataPackage.sh "spikeinsubset-1.42.0" diff --git a/recipes/bioconductor-spikeli/meta.yaml b/recipes/bioconductor-spikeli/meta.yaml index fe565d7c8c501..eaaa49bf1b204 100644 --- a/recipes/bioconductor-spikeli/meta.yaml +++ b/recipes/bioconductor-spikeli/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.60.0" %} +{% set version = "2.62.0" %} {% set name = "spikeLI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7922faf962c15610b2a0f116187e1b1a + md5: 15e5851707938b83c34b9d5667d62f79 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spikeli", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-spiky/meta.yaml b/recipes/bioconductor-spiky/meta.yaml index bb24ac3af4889..e7f1720f0e287 100644 --- a/recipes/bioconductor-spiky/meta.yaml +++ b/recipes/bioconductor-spiky/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "spiky" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 55cbf8a3742386f0db93aadf07b4306f + md5: 8f710d2ecca4f24247ab38805d665b41 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spiky", max_pin="x.x") }}' noarch: generic # Suggests: covr, testthat, rmarkdown, markdown, knitr, devtools, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-bamlss - r-base - r-blandaltmanleh - r-ggplot2 - r-scales run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-bamlss - r-base - r-blandaltmanleh diff --git a/recipes/bioconductor-spktools/meta.yaml b/recipes/bioconductor-spktools/meta.yaml index d604e37b7aa86..e82233da53f09 100644 --- a/recipes/bioconductor-spktools/meta.yaml +++ b/recipes/bioconductor-spktools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "spkTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a32ef23d5786b41a3428e9b84edda198 + md5: 9cc7d56d0cf0eec1e65d47d262525ba1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spktools", max_pin="x.x") }}' noarch: generic # Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-gtools - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-gtools - r-rcolorbrewer diff --git a/recipes/bioconductor-splatter/meta.yaml b/recipes/bioconductor-splatter/meta.yaml index c196f33726a43..15276553de261 100644 --- a/recipes/bioconductor-splatter/meta.yaml +++ b/recipes/bioconductor-splatter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "splatter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a5dfb529cb37945588d026098a760bea + md5: 1afec799cae913802068b5b20b32a598 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-splatter", max_pin="x.x") }}' noarch: generic # Suggests: BASiCS (>= 1.7.10), BiocManager, BiocSingular, BiocStyle, Biostrings, covr, cowplot, GenomeInfoDb, GenomicRanges, ggplot2 (>= 3.4.0), IRanges, igraph, knitr, limSolve, lme4, magick, mfa, phenopath, progress, preprocessCore, pscl, rmarkdown, scales, scater (>= 1.15.16), scDD, scran, SparseDC, spelling, testthat, VariantAnnotation, zinbwave, requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-checkmate >=2.0.0' - r-crayon @@ -37,13 +38,13 @@ requirements: - r-rlang - r-withr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-checkmate >=2.0.0' - r-crayon diff --git a/recipes/bioconductor-splicewiz/meta.yaml b/recipes/bioconductor-splicewiz/meta.yaml index c949a95ada69b..9a264cf06a4ec 100644 --- a/recipes/bioconductor-splicewiz/meta.yaml +++ b/recipes/bioconductor-splicewiz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.2" %} +{% set version = "1.4.0" %} {% set name = "SpliceWiz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14454891d1a6d00f4b3935681f0619de + md5: 95ad1603bebc847d12b7dc715aef923a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-splicewiz", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, openssl, crayon, splines, testthat (>= 3.0.0), DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, fgsea, Rsubread # SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-nxtirfdata >=1.6.0,<1.7.0' - - 'bioconductor-ompbam >=1.4.0,<1.5.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-nxtirfdata >=1.8.0,<1.9.0' + - 'bioconductor-ompbam >=1.6.0,<1.7.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-data.table - r-dt @@ -69,26 +70,26 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-nxtirfdata >=1.6.0,<1.7.0' - - 'bioconductor-ompbam >=1.4.0,<1.5.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-nxtirfdata >=1.8.0,<1.9.0' + - 'bioconductor-ompbam >=1.6.0,<1.7.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-data.table - r-dt diff --git a/recipes/bioconductor-splicingfactory/meta.yaml b/recipes/bioconductor-splicingfactory/meta.yaml index 2a3a973d23961..79a03bd119400 100644 --- a/recipes/bioconductor-splicingfactory/meta.yaml +++ b/recipes/bioconductor-splicingfactory/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "SplicingFactory" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 597502530bf80359bb918678702bb2b7 + md5: 354167193190b04ec94fac9c097b4503 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-splicingfactory", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, ggplot2, tidyr requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-splicinggraphs/meta.yaml b/recipes/bioconductor-splicinggraphs/meta.yaml index 70cfb611423c8..dd2329883597e 100644 --- a/recipes/bioconductor-splicinggraphs/meta.yaml +++ b/recipes/bioconductor-splicinggraphs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "SplicingGraphs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9d15a3c6a52e0cf2e5821f90fd992053 + md5: 04e2a057bc1c6935ee13333acdf5ba52 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-splicinggraphs", max_pin="x.x") }}' noarch: generic # Suggests: igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-igraph run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-igraph test: diff --git a/recipes/bioconductor-splinetimer/meta.yaml b/recipes/bioconductor-splinetimer/meta.yaml index add5dbe8d4d52..19a7f65b4f424 100644 --- a/recipes/bioconductor-splinetimer/meta.yaml +++ b/recipes/bioconductor-splinetimer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "splineTimeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cad5d2654b4b510de7aba9fefd73e46b + md5: 09454e29df75ff3f9d9e3f2780fb5db6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-splinetimer", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-fis >=1.28.0,<1.29.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-fis >=1.30.0,<1.31.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - 'r-genenet >=1.2.13' - r-gtools - r-igraph - 'r-longitudinal >=1.1.12' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-fis >=1.28.0,<1.29.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-fis >=1.30.0,<1.31.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - 'r-genenet >=1.2.13' - r-gtools diff --git a/recipes/bioconductor-splinter/meta.yaml b/recipes/bioconductor-splinter/meta.yaml index 76c565ec2b60b..e96e229c81b4a 100644 --- a/recipes/bioconductor-splinter/meta.yaml +++ b/recipes/bioconductor-splinter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "SPLINTER" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,44 +11,45 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfa5400f767658eb668ccf62c50f4914 + md5: f328ebcc0e4d27dee8a98c2e230bd8dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-splinter", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' - r-base - r-ggplot2 - r-googlevis - r-plyr - r-stringr run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' - r-base - r-ggplot2 - r-googlevis diff --git a/recipes/bioconductor-splots/meta.yaml b/recipes/bioconductor-splots/meta.yaml index bb84e57882648..adc7ad8e35825 100644 --- a/recipes/bioconductor-splots/meta.yaml +++ b/recipes/bioconductor-splots/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "splots" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,14 +11,15 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6b86fd185efeaeb6bb38515bf577b0e2 + md5: 5f497af3c7a5fcdbba178a1ff3b411b9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-splots", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, assertthat, HD2013SGI +# Suggests: BiocStyle, knitr, rmarkdown, assertthat, HD2013SGI, dplyr, ggplot2 requirements: host: - r-base @@ -33,7 +34,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Visualization of high-throughput assays in microtitre plate or slide format' - description: 'This package is provided to support legacy code and reverse dependencies, but it should not be used as a dependency for new code development. It provides a single function, plotScreen, for visualising data in microtitre plate or slide format. As a better alternative for such functionality, please consider the platetools package on CRAN (https://cran.r-project.org/package=platetools and https://github.com/Swarchal/platetools), or generic ggplot2 graphics functionality.' + description: 'This package is here to support legacy usages of it, but it should not be used for new code development. It provides a single function, plotScreen, for visualising data in microtitre plate or slide format. As a better alternative for such functionality, please consider the platetools package on CRAN (https://cran.r-project.org/package=platetools and https://github.com/Swarchal/platetools), or ggplot2 (geom_raster, facet_wrap) as exemplified in the vignette of this package.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' extra: identifiers: diff --git a/recipes/bioconductor-spotclean/meta.yaml b/recipes/bioconductor-spotclean/meta.yaml index e8d0b89ae307f..8832e69eae5ea 100644 --- a/recipes/bioconductor-spotclean/meta.yaml +++ b/recipes/bioconductor-spotclean/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.1" %} {% set name = "SpotClean" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 649c0a781c17b134925269f6696e8bf0 + md5: b6e7be89394d959837993f3fd385ad55 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spotclean", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils, spelling requirements: host: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -37,10 +38,10 @@ requirements: - r-tibble - r-viridis run: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-spotlight/meta.yaml b/recipes/bioconductor-spotlight/meta.yaml index 898bf91b3f4fe..a29d88c4d27da 100644 --- a/recipes/bioconductor-spotlight/meta.yaml +++ b/recipes/bioconductor-spotlight/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.3" %} {% set name = "SPOTlight" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e3cf368e27ab8dba4f20ca904271c4ea + md5: 00759051612f8f17697afd03507d6d8c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spotlight", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, colorBlindness, ExperimentHub, DelayedArray, ggcorrplot, grDevices, grid, igraph, jpeg, knitr, methods, png, rmarkdown, scater, scatterpie, scran, Seurat, SeuratObject, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat +# Suggests: BiocStyle, colorBlindness, DelayedArray, DropletUtils, ExperimentHub, ggcorrplot, grDevices, grid, igraph, jpeg, knitr, methods, png, rmarkdown, scater, scatterpie, scran, Seurat, SeuratObject, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-ggplot2 - r-matrix @@ -29,7 +30,7 @@ requirements: - r-nmf - r-nnls run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-ggplot2 - r-matrix diff --git a/recipes/bioconductor-spqn/meta.yaml b/recipes/bioconductor-spqn/meta.yaml index 6dd80e885fe8d..c6aa1696bc6a1 100644 --- a/recipes/bioconductor-spqn/meta.yaml +++ b/recipes/bioconductor-spqn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "spqn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d36cc99c0915e86aba64cafad9a690af + md5: 63599cd8ebe97287b176d98cb3d9de43 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spqn", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, tools, spqnData (>= 0.99.3), RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggridges - r-matrixstats run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggridges diff --git a/recipes/bioconductor-spqndata/meta.yaml b/recipes/bioconductor-spqndata/meta.yaml index e8d06d0ab7422..efac37f68f5cb 100644 --- a/recipes/bioconductor-spqndata/meta.yaml +++ b/recipes/bioconductor-spqndata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "spqnData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1588ea6c755eb468f60af1a67712cac0 + md5: 453bf944ea40956afef2bd868f92d747 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spqndata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-spqndata/post-link.sh b/recipes/bioconductor-spqndata/post-link.sh index eb0052e45a644..4468f52ef6133 100644 --- a/recipes/bioconductor-spqndata/post-link.sh +++ b/recipes/bioconductor-spqndata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "spqndata-1.12.0" +installBiocDataPackage.sh "spqndata-1.14.0" diff --git a/recipes/bioconductor-spsimseq/meta.yaml b/recipes/bioconductor-spsimseq/meta.yaml index c327a1072ec78..e85f49127980d 100644 --- a/recipes/bioconductor-spsimseq/meta.yaml +++ b/recipes/bioconductor-spsimseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "SPsimSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 433fef1a4f51ce4bbe425b88d9b7eec7 + md5: 1ccc188618b92dcf94489a00d7faa5b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spsimseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, LSD, testthat, BiocStyle requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-fitdistrplus - r-hmisc - r-mvtnorm - r-wgcna run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-fitdistrplus - r-hmisc diff --git a/recipes/bioconductor-sqldataframe/meta.yaml b/recipes/bioconductor-sqldataframe/meta.yaml index 911d736933457..4ab1d6af33f2c 100644 --- a/recipes/bioconductor-sqldataframe/meta.yaml +++ b/recipes/bioconductor-sqldataframe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SQLDataFrame" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e85f08b5a38073be4f7ae655d57c139f + md5: 4153fe66ee281c087e77c6706a2b2faf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sqldataframe", max_pin="x.x") }}' noarch: generic -# Suggests: RMySQL, bigrquery, testthat, knitr, rmarkdown, DelayedArray +# Suggests: RMySQL, bigrquery, testthat, knitr, rmarkdown, DelayedArray, GenomicRanges requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - 'r-dbplyr >=1.4.0' @@ -31,8 +32,8 @@ requirements: - r-rsqlite - r-tibble run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - 'r-dbplyr >=1.4.0' diff --git a/recipes/bioconductor-squadd/meta.yaml b/recipes/bioconductor-squadd/meta.yaml index ad4a8ea5b03e9..0a8548a01dd6e 100644 --- a/recipes/bioconductor-squadd/meta.yaml +++ b/recipes/bioconductor-squadd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "SQUADD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 07c942ac0b69c5a285a49341451afb5f + md5: 8837e27ab065ddae145da3cc5ca2ad32 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-squadd", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-sracipe/meta.yaml b/recipes/bioconductor-sracipe/meta.yaml index 858cccbb7efec..3b7c215452e39 100644 --- a/recipes/bioconductor-sracipe/meta.yaml +++ b/recipes/bioconductor-sracipe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "sRACIPE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b032be2639312a58690b6190dca69d2f + md5: 84a1b79b944741fc6ecab26168020841 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sracipe", max_pin="x.x") }}' # Suggests: knitr, BiocStyle, rmarkdown, tinytest, doFuture requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-gplots @@ -37,9 +38,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-gplots diff --git a/recipes/bioconductor-sradb/meta.yaml b/recipes/bioconductor-sradb/meta.yaml index d88957529f1e9..25db5e723e5ca 100644 --- a/recipes/bioconductor-sradb/meta.yaml +++ b/recipes/bioconductor-sradb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "SRAdb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a74df8413362db72d8e415e5bb2dcdf + md5: 6bc0aa8bd176c1b388f4da270b4f668b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sradb", max_pin="x.x") }}' noarch: generic # Suggests: Rgraphviz requirements: host: - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-rcurl - r-rsqlite run: - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-rcurl - r-rsqlite diff --git a/recipes/bioconductor-srnadiff/build.sh b/recipes/bioconductor-srnadiff/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-srnadiff/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-srnadiff/meta.yaml b/recipes/bioconductor-srnadiff/meta.yaml new file mode 100644 index 0000000000000..916fb53ca5359 --- /dev/null +++ b/recipes/bioconductor-srnadiff/meta.yaml @@ -0,0 +1,79 @@ +{% set version = "1.22.0" %} +{% set name = "srnadiff" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0125777227eab34f7839615139aacb91 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-srnadiff", max_pin="x.x") }}' +# Suggests: knitr, rmarkdown, testthat, BiocManager, BiocStyle +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-biocmanager + - r-devtools + - 'r-rcpp >=0.12.8' + - libblas + - liblapack + run: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-biocmanager + - r-devtools + - 'r-rcpp >=0.12.8' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Finding differentially expressed unannotated genomic regions from RNA-seq data' + description: 'srnadiff is a package that finds differently expressed regions from RNA-seq data at base-resolution level without relying on existing annotation. To do so, the package implements the identify-then-annotate methodology that builds on the idea of combining two pipelines approachs differential expressed regions detection and differential expression quantification. It reads BAM files as input, and outputs a list differentially regions, together with the adjusted p-values.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-sscu/meta.yaml b/recipes/bioconductor-sscu/meta.yaml index 674ac072e84b2..2d4fb8c20013f 100644 --- a/recipes/bioconductor-sscu/meta.yaml +++ b/recipes/bioconductor-sscu/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "sscu" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 361e476bdd720a428c36c352bccb9802 + md5: 3856e06321ac866e2664573b452c6a85 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sscu", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - 'r-seqinr >=3.1-3' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - 'r-seqinr >=3.1-3' test: diff --git a/recipes/bioconductor-sseq/meta.yaml b/recipes/bioconductor-sseq/meta.yaml index 0e4be979404ea..2ecb6cdba2b18 100644 --- a/recipes/bioconductor-sseq/meta.yaml +++ b/recipes/bioconductor-sseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "sSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43ed8739950672325635df07770212a3 + md5: 9276919acd944871a6e05a8dbeed6b9f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sseq", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-ssize/meta.yaml b/recipes/bioconductor-ssize/meta.yaml index cb93b69f91109..e7e2942a52185 100644 --- a/recipes/bioconductor-ssize/meta.yaml +++ b/recipes/bioconductor-ssize/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "ssize" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4b0c875620b8d1a31e166b27a3538a6d + md5: b61fbe78b68fecd3090e1c658a284b83 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ssize", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-ssnappy/meta.yaml b/recipes/bioconductor-ssnappy/meta.yaml index 7160a4a6be7a5..5b49df2a9511a 100644 --- a/recipes/bioconductor-ssnappy/meta.yaml +++ b/recipes/bioconductor-ssnappy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.1" %} {% set name = "sSNAPPY" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,61 +11,55 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 263387c3d870cf83e91c5da6a2cbac8c + md5: 15f7a550e110c069710c3f6572a06e83 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocManager, BiocStyle, cowplot, DT, htmltools, knitr, pander, rmarkdown, spelling, testthat (>= 3.0.0), tidyverse + run_exports: '{{ pin_subpackage("bioconductor-ssnappy", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools, knitr, pander, patchwork, rmarkdown, spelling, testthat (>= 3.0.0), tidyverse # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-dplyr >=1.1' - r-ggforce - r-ggplot2 - r-ggraph + - r-gtools - r-igraph - r-magrittr - r-pheatmap - - r-rcpp - - r-rcpparmadillo - r-reshape2 - r-rlang - r-stringr - r-tibble - - libblas - - liblapack + - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-dplyr >=1.1' - r-ggforce - r-ggplot2 - r-ggraph + - r-gtools - r-igraph - r-magrittr - r-pheatmap - - r-rcpp - - r-rcpparmadillo - r-reshape2 - r-rlang - r-stringr - r-tibble - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-tidyr test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sspaths/meta.yaml b/recipes/bioconductor-sspaths/meta.yaml index c9f863931d308..e7f074e25161c 100644 --- a/recipes/bioconductor-sspaths/meta.yaml +++ b/recipes/bioconductor-sspaths/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "ssPATHS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 31fd9abb3ebbad68e476099511cd0161 + md5: 121909c57596e3cd0d817cac2deb22c9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sspaths", max_pin="x.x") }}' noarch: generic # Suggests: ggplot2, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dml - r-mess - r-rocr run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dml - r-mess diff --git a/recipes/bioconductor-ssrch/meta.yaml b/recipes/bioconductor-ssrch/meta.yaml index 04d1b9d146627..b3495f2f86488 100644 --- a/recipes/bioconductor-ssrch/meta.yaml +++ b/recipes/bioconductor-ssrch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "ssrch" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4cb99d0771a2949808a20c55c687044e + md5: 095c153ce56b89d040c929a8c1af6840 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ssrch", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown, BiocStyle requirements: diff --git a/recipes/bioconductor-ssviz/meta.yaml b/recipes/bioconductor-ssviz/meta.yaml index 717d098cdee5d..87ac9b79c48bf 100644 --- a/recipes/bioconductor-ssviz/meta.yaml +++ b/recipes/bioconductor-ssviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "ssviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3d62d00ec992873217d787aa0aee02e6 + md5: 00bd4a7d6a57af51b74187993bdf84c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ssviz", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-ggplot2 - r-rcolorbrewer - r-reshape run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-ggplot2 - r-rcolorbrewer diff --git a/recipes/bioconductor-stager/meta.yaml b/recipes/bioconductor-stager/meta.yaml index 170a3ed5a0ef3..afdbee6634400 100644 --- a/recipes/bioconductor-stager/meta.yaml +++ b/recipes/bioconductor-stager/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "stageR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 53be8e8637660075a5dd3a5788bb887e + md5: cdbf6ab3c35c3e019b0ce786ad85eb38 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stager", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma, DEXSeq, testthat requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-standr/meta.yaml b/recipes/bioconductor-standr/meta.yaml index 976227bf60283..c54e0c516383c 100644 --- a/recipes/bioconductor-standr/meta.yaml +++ b/recipes/bioconductor-standr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.2" %} +{% set version = "1.6.0" %} {% set name = "standR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a59d4f2ed1a9301c835e2c4bf83d74ea + md5: 94e29a2001fbb9d0bfa1488ae7039aa7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-standr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr, ggrepel, cluster, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggalluvial @@ -42,15 +43,15 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggalluvial diff --git a/recipes/bioconductor-starank/meta.yaml b/recipes/bioconductor-starank/meta.yaml index e820622caca23..684cceb9f69d6 100644 --- a/recipes/bioconductor-starank/meta.yaml +++ b/recipes/bioconductor-starank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "staRank" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0125b4deecba9bf4db3f9bcac2326be7 + md5: 6284ebc665a24e39437e707b4fc1ad80 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-starank", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-cellhts2 >=2.64.0,<2.65.0' + - 'bioconductor-cellhts2 >=2.66.0,<2.67.0' - r-base run: - - 'bioconductor-cellhts2 >=2.64.0,<2.65.0' + - 'bioconductor-cellhts2 >=2.66.0,<2.67.0' - r-base test: commands: diff --git a/recipes/bioconductor-starbiotrek/meta.yaml b/recipes/bioconductor-starbiotrek/meta.yaml index 6e426df618368..1ca02bc22bc51 100644 --- a/recipes/bioconductor-starbiotrek/meta.yaml +++ b/recipes/bioconductor-starbiotrek/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "StarBioTrek" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cba511d5a1ac1494e491455c893ed3d9 + md5: a1a892a63f09a57e18eb825ab8a0ec7e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-starbiotrek", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, qgraph, png, grid requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-spidermir >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-spidermir >=1.32.0,<1.33.0' - r-base - r-e1071 - r-ggplot2 @@ -32,9 +33,9 @@ requirements: - r-reshape2 - r-rocr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-spidermir >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-spidermir >=1.32.0,<1.33.0' - r-base - r-e1071 - r-ggplot2 diff --git a/recipes/bioconductor-stategra/meta.yaml b/recipes/bioconductor-stategra/meta.yaml index 8693cc153ae6b..21e069eaf1b45 100644 --- a/recipes/bioconductor-stategra/meta.yaml +++ b/recipes/bioconductor-stategra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "STATegRa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c23bae33718cd7c94ef30beb97344cb0 + md5: be42ca7786d4b038ad3f706492c74022 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stategra", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>= 1.3), roxygen2, doSNOW requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-calibrate - r-foreach @@ -33,10 +34,10 @@ requirements: - r-gridextra - r-mass run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-calibrate - r-foreach diff --git a/recipes/bioconductor-statial/meta.yaml b/recipes/bioconductor-statial/meta.yaml index aeef3a2b9c3cd..d414780320fc2 100644 --- a/recipes/bioconductor-statial/meta.yaml +++ b/recipes/bioconductor-statial/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.5" %} {% set name = "Statial" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,60 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef5801f844d0bc314ecf0e208e2a29f0 + md5: e7151f23bb952401803e4d239390c210 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-statial", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, knitr, testthat (>= 3.0.0) +# Suggests: BiocStyle, knitr, testthat (>= 3.0.0), ClassifyR, spicyR, ggsurvfit, lisaClust, survival requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-concaveman - r-data.table - r-dplyr - r-ggplot2 + - r-magrittr + - r-plotly + - r-purrr + - r-ranger - r-spatstat.explore - r-spatstat.geom - r-stringr - r-tibble - r-tidyr - r-tidyselect - - r-tidyverse run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-concaveman - r-data.table - r-dplyr - r-ggplot2 + - r-magrittr + - r-plotly + - r-purrr + - r-ranger - r-spatstat.explore - r-spatstat.geom - r-stringr - r-tibble - r-tidyr - r-tidyselect - - r-tidyverse test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-stattarget/meta.yaml b/recipes/bioconductor-stattarget/meta.yaml index ae19bb6675d09..c3b72f32f6d1c 100644 --- a/recipes/bioconductor-stattarget/meta.yaml +++ b/recipes/bioconductor-stattarget/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "statTarget" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bebae7ea2293cdbc8e26baddba59605c + md5: 8a504e674b8756201ca93b590dd0b078 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stattarget", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-roc >=1.76.0,<1.77.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' - r-base - r-pdist - r-pls @@ -30,8 +31,8 @@ requirements: - r-randomforest - r-rrcov run: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-roc >=1.76.0,<1.77.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' - r-base - r-pdist - r-pls diff --git a/recipes/bioconductor-stdeconvolve/build_failure.linux-64.yaml b/recipes/bioconductor-stdeconvolve/build_failure.linux-64.yaml index d06518ec443cf..46b164e797e06 100644 --- a/recipes/bioconductor-stdeconvolve/build_failure.linux-64.yaml +++ b/recipes/bioconductor-stdeconvolve/build_failure.linux-64.yaml @@ -1,4 +1,4 @@ -recipe_sha: 8b208f8587b5f20c9475a1a086aa90016f4f780fe772c97b3e6a7391f4848065 # The commit at which this recipe failed to build. +recipe_sha: b11c54aa8b5803ac796aadaf1ab911295658038c435eea768cf62514aa5c4e79 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- r-vctrs: 0.6.3-r43ha503ecb_0 conda-forge @@ -102,3 +102,7 @@ log: |2- raise subprocess.CalledProcessError(proc.returncode, _args) subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-stdeconvolve_1689833080445/work/conda_build.sh']' returned non-zero exit status 1. # Last 100 lines of the build log. +reason: |- + 07:50:52 BIOCONDA INFO (OUT) ERROR: dependency ‘liger’ is not available for package ‘STdeconvolve’ +category: |- + dependency issue diff --git a/recipes/bioconductor-stdeconvolve/meta.yaml b/recipes/bioconductor-stdeconvolve/meta.yaml index 1834a810f856e..0e9d14b87e1da 100644 --- a/recipes/bioconductor-stdeconvolve/meta.yaml +++ b/recipes/bioconductor-stdeconvolve/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "STdeconvolve" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a5cf6d8c89d292cd28df0c245c25d51 + md5: 2908e0d59713b2c3ef6c7bc549d0d123 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stdeconvolve", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown, testthat, rcmdcheck, gplots, gridExtra, hash, dplyr, parallel requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-clue - r-ggplot2 @@ -34,7 +35,7 @@ requirements: - r-topicmodels - r-viridis run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-clue - r-ggplot2 diff --git a/recipes/bioconductor-stemhypoxia/meta.yaml b/recipes/bioconductor-stemhypoxia/meta.yaml index c3a6d2e8b2cfc..1bf4c404eb5a3 100644 --- a/recipes/bioconductor-stemhypoxia/meta.yaml +++ b/recipes/bioconductor-stemhypoxia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "stemHypoxia" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 53b049bafffb969dea77f35479720221 + md5: 22ec9d76cac05ac7118873f7815225ba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stemhypoxia", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-stemhypoxia/post-link.sh b/recipes/bioconductor-stemhypoxia/post-link.sh index c47b0e4558bb3..519f3ce64e7b7 100644 --- a/recipes/bioconductor-stemhypoxia/post-link.sh +++ b/recipes/bioconductor-stemhypoxia/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "stemhypoxia-1.36.0" +installBiocDataPackage.sh "stemhypoxia-1.38.0" diff --git a/recipes/bioconductor-stepnorm/meta.yaml b/recipes/bioconductor-stepnorm/meta.yaml index 3b3f5a1ca9c77..a109683e28058 100644 --- a/recipes/bioconductor-stepnorm/meta.yaml +++ b/recipes/bioconductor-stepnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "stepNorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9a7edda3646c8d02d776e7e8b62ef64d + md5: a8f357efcff85a6d723734d6e0a91ba0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stepnorm", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-mass run: - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-stexampledata/meta.yaml b/recipes/bioconductor-stexampledata/meta.yaml index 60acf470da223..422e84e76f070 100644 --- a/recipes/bioconductor-stexampledata/meta.yaml +++ b/recipes/bioconductor-stexampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "STexampleData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 21ccea26e0677e8ff1ec5ddfe7da0a32 + md5: 5fa4bfb2e58e7f6bbcd957aa1aa7e938 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stexampledata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, BumpyMatrix requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-stexampledata/post-link.sh b/recipes/bioconductor-stexampledata/post-link.sh index 20643afbd8feb..6dea914d714c1 100644 --- a/recipes/bioconductor-stexampledata/post-link.sh +++ b/recipes/bioconductor-stexampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "stexampledata-1.8.0" +installBiocDataPackage.sh "stexampledata-1.10.0" diff --git a/recipes/bioconductor-stjoincount/meta.yaml b/recipes/bioconductor-stjoincount/meta.yaml index 9de2419b16348..38b3392c1fcd2 100644 --- a/recipes/bioconductor-stjoincount/meta.yaml +++ b/recipes/bioconductor-stjoincount/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "stJoincount" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6bf5da007b58f88706124d298422dde7 + md5: 85dd3f81a773ede72a70185cb4132d2b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stjoincount", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -33,8 +34,8 @@ requirements: - r-sp - r-spdep run: - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-stjudem/meta.yaml b/recipes/bioconductor-stjudem/meta.yaml index e49fa8565cb43..f224b6a78e11d 100644 --- a/recipes/bioconductor-stjudem/meta.yaml +++ b/recipes/bioconductor-stjudem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "stjudem" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d793d5b3f5abf684f188723111097faf + md5: 4c6868a60726df51408834a227e551bf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stjudem", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-stjudem/post-link.sh b/recipes/bioconductor-stjudem/post-link.sh index 98f05a794211c..bbadc4df501c3 100644 --- a/recipes/bioconductor-stjudem/post-link.sh +++ b/recipes/bioconductor-stjudem/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "stjudem-1.40.0" +installBiocDataPackage.sh "stjudem-1.42.0" diff --git a/recipes/bioconductor-strandcheckr/meta.yaml b/recipes/bioconductor-strandcheckr/meta.yaml index efba83d3688df..21ce40d74e7fd 100644 --- a/recipes/bioconductor-strandcheckr/meta.yaml +++ b/recipes/bioconductor-strandcheckr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "strandCheckR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3212c9f0350eb46edfa4d2aed1741f3f + md5: d9544940bb53aa96ca4e14fda712581d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-strandcheckr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-dplyr - r-ggplot2 @@ -38,14 +39,14 @@ requirements: - r-rmarkdown - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-streamer/meta.yaml b/recipes/bioconductor-streamer/meta.yaml index 683510919b546..b98467148e69a 100644 --- a/recipes/bioconductor-streamer/meta.yaml +++ b/recipes/bioconductor-streamer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "Streamer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d23715dbf4aec29873e6c2bfd6257817 + md5: d41ea52d04a44b0705846078ffe3b1e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-streamer", max_pin="x.x") }}' # Suggests: RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-stringdb/meta.yaml b/recipes/bioconductor-stringdb/meta.yaml index b7c61cecb2c7e..64027a236667d 100644 --- a/recipes/bioconductor-stringdb/meta.yaml +++ b/recipes/bioconductor-stringdb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "STRINGdb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 099f3db99ae7033c75db37df090e8d3e + md5: 6dc5819519574f0656e4b811e4618db7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stringdb", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: diff --git a/recipes/bioconductor-struct/meta.yaml b/recipes/bioconductor-struct/meta.yaml index 92e18d7183956..6436c5e2462f7 100644 --- a/recipes/bioconductor-struct/meta.yaml +++ b/recipes/bioconductor-struct/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "struct" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 63b865919a93b7112c758393c9b9795b + md5: ef5fb8febc9f7bfed87fba9bc24cbebc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-struct", max_pin="x.x") }}' noarch: generic # Suggests: testthat, rstudioapi, rmarkdown, covr, BiocStyle, openxlsx, ggplot2, magick requirements: host: - - 'bioconductor-rols >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-rols >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-knitr - r-ontologyindex run: - - 'bioconductor-rols >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-rols >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-knitr - r-ontologyindex diff --git a/recipes/bioconductor-structstrings/meta.yaml b/recipes/bioconductor-structstrings/meta.yaml index 64c50442ec9f0..adcd3be37235e 100644 --- a/recipes/bioconductor-structstrings/meta.yaml +++ b/recipes/bioconductor-structstrings/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Structstrings" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 30a130dd232ccb09f2680746ae3c65f2 + md5: 8d4afbd61a5546b52947869b7912eecb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-structstrings", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-crayon - r-stringi @@ -32,11 +33,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-crayon - r-stringi diff --git a/recipes/bioconductor-structtoolbox/meta.yaml b/recipes/bioconductor-structtoolbox/meta.yaml index 085906542fe3f..4a6d887b6e887 100644 --- a/recipes/bioconductor-structtoolbox/meta.yaml +++ b/recipes/bioconductor-structtoolbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.2" %} +{% set version = "1.14.0" %} {% set name = "structToolbox" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2c6bb1a435086c8f3fb3462c38e50fcd + md5: d6e4aa6631f797571a7ec07348cfbd30 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-structtoolbox", max_pin="x.x") }}' noarch: generic +# Suggests: agricolae, BiocFileCache, BiocStyle, car, covr, cowplot, e1071, emmeans, ggdendro, knitr, magick, nlme, openxlsx, pls, pmp, reshape2, ropls, rmarkdown, Rtsne, testthat, rappdirs requirements: host: - - 'bioconductor-struct >=1.12.0,<1.13.0' + - 'bioconductor-struct >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-ggthemes @@ -28,34 +30,13 @@ requirements: - r-scales - r-sp run: - - 'bioconductor-struct >=1.12.0,<1.13.0' + - 'bioconductor-struct >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-ggthemes - r-gridextra - r-scales - r-sp - - bioconductor-BiocFileCache - - bioconductor-BiocStyle - - bioconductor-pmp - - bioconductor-ropls - - r-agricolae - - r-car - - r-covr - - r-cowplot - - r-e1071 - - r-emmeans - - r-ggdendro - - r-knitr - - r-magick - - r-nlme - - r-openxlsx - - r-pls - - r-reshape2 - - r-rmarkdown - - r-rtsne - - r-testthat - - r-rappdirs test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-structuralvariantannotation/meta.yaml b/recipes/bioconductor-structuralvariantannotation/meta.yaml index 56b5c9d69db2d..33f925708abe9 100644 --- a/recipes/bioconductor-structuralvariantannotation/meta.yaml +++ b/recipes/bioconductor-structuralvariantannotation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "StructuralVariantAnnotation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,42 +11,43 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b202869069b95a7fc763f81e45a20f5d + md5: d72d8c88083ed0fc9319afa075360841 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-structuralvariantannotation", max_pin="x.x") }}' noarch: generic # Suggests: ggplot2, devtools, testthat (>= 2.1.0), roxygen2, rmarkdown, tidyverse, knitr, ggbio, biovizBase, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-assertthat - r-base - r-dplyr - r-rlang - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-assertthat - r-base - r-dplyr diff --git a/recipes/bioconductor-subcellbarcode/meta.yaml b/recipes/bioconductor-subcellbarcode/meta.yaml index 2bc92431495c5..e6f6ea30837ae 100644 --- a/recipes/bioconductor-subcellbarcode/meta.yaml +++ b/recipes/bioconductor-subcellbarcode/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "SubCellBarCode" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d51692e771904243e46346f6db1229b + md5: 9b3f34495b8132c4cbdc426e27ffc740 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-subcellbarcode", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-caret - r-e1071 @@ -33,8 +34,8 @@ requirements: - r-rtsne - r-scatterplot3d run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-caret - r-e1071 diff --git a/recipes/bioconductor-subseq/meta.yaml b/recipes/bioconductor-subseq/meta.yaml index 5296f6e59b98d..f482cf4d343f7 100644 --- a/recipes/bioconductor-subseq/meta.yaml +++ b/recipes/bioconductor-subseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "subSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 01708051b6affd954eb9c2b625d6c0db + md5: 81acfd896fc4e8c52e50475dca2c1519 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-subseq", max_pin="x.x") }}' noarch: generic # Suggests: limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-data.table - r-digest @@ -31,8 +32,8 @@ requirements: - r-magrittr - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-data.table - r-digest diff --git a/recipes/bioconductor-sugarcanecdf/meta.yaml b/recipes/bioconductor-sugarcanecdf/meta.yaml index 98084152b6f97..f35923e94468a 100644 --- a/recipes/bioconductor-sugarcanecdf/meta.yaml +++ b/recipes/bioconductor-sugarcanecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "sugarcanecdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f66d51868068f83d3693d3cb05be418a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sugarcanecdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sugarcaneprobe/meta.yaml b/recipes/bioconductor-sugarcaneprobe/meta.yaml index 3c7b6e3a9c55b..206f4292a4db3 100644 --- a/recipes/bioconductor-sugarcaneprobe/meta.yaml +++ b/recipes/bioconductor-sugarcaneprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "sugarcaneprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 66c101ac73e9235d258b9f996c42778e build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sugarcaneprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-suitor/meta.yaml b/recipes/bioconductor-suitor/meta.yaml index 707ed676d00f7..2c3b4b7017d9d 100644 --- a/recipes/bioconductor-suitor/meta.yaml +++ b/recipes/bioconductor-suitor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "SUITOR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e3df0f3c1651702438aecf49a67fb7f + md5: 5f4a5ea607ef7551025cf8b425d20bc7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-suitor", max_pin="x.x") }}' # Suggests: devtools, MutationalPatterns, RUnit, BiocManager, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-ggplot2 - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-ggplot2 build: diff --git a/recipes/bioconductor-summarizedbenchmark/meta.yaml b/recipes/bioconductor-summarizedbenchmark/meta.yaml index ff5f061ec8208..fc6634da01088 100644 --- a/recipes/bioconductor-summarizedbenchmark/meta.yaml +++ b/recipes/bioconductor-summarizedbenchmark/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "SummarizedBenchmark" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e72a284cb81ab58625cbc15c12b891fb + md5: f967c7e3db84713c2db5a2b0f1999ce4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-summarizedbenchmark", max_pin="x.x") }}' noarch: generic # Suggests: iCOBRA, BiocStyle, rmarkdown, knitr, magrittr, IHW, qvalue, testthat, DESeq2, edgeR, limma, tximport, readr, scRNAseq, splatter, scater, rnaseqcomp, biomaRt requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-crayon - r-digest @@ -38,10 +39,10 @@ requirements: - r-tidyr - r-upsetr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-crayon - r-digest diff --git a/recipes/bioconductor-summarizedexperiment/meta.yaml b/recipes/bioconductor-summarizedexperiment/meta.yaml index e2e9d98423b38..26284256593de 100644 --- a/recipes/bioconductor-summarizedexperiment/meta.yaml +++ b/recipes/bioconductor-summarizedexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.2" %} +{% set version = "1.32.0" %} {% set name = "SummarizedExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3785779b5e61a51d2be4f71c46e3b67a + md5: cf4b430247b40acb2be8e6c9ecf3aac7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-summarizedexperiment", max_pin="x.x") }}' noarch: generic # Suggests: HDF5Array (>= 1.7.5), annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, jsonlite, rhdf5, airway (>= 1.15.1), BiocStyle, knitr, rmarkdown, RUnit, testthat, digest requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4arrays >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4arrays >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4arrays >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4arrays >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-summix/meta.yaml b/recipes/bioconductor-summix/meta.yaml index 494356af38ef0..9426ca82a1bea 100644 --- a/recipes/bioconductor-summix/meta.yaml +++ b/recipes/bioconductor-summix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "Summix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d845748231aaea3953d1bb4814764356 + md5: 74d3140f7f5db9a648955b81abdfb769 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-summix", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, markdown, knitr requirements: diff --git a/recipes/bioconductor-supersigs/meta.yaml b/recipes/bioconductor-supersigs/meta.yaml index d75f2dbbc2cc4..7eb7f89d459f7 100644 --- a/recipes/bioconductor-supersigs/meta.yaml +++ b/recipes/bioconductor-supersigs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "supersigs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 42a9e56f253261e8adece79a7db5eb2a + md5: 35df3e9fd0272854b23baf15d93d300f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-supersigs", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, testthat, VariantAnnotation requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-caret @@ -31,8 +32,8 @@ requirements: - r-rsample - r-tidyr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-caret diff --git a/recipes/bioconductor-suprahex/meta.yaml b/recipes/bioconductor-suprahex/meta.yaml index 04eb6c4e30369..e36b5c278da3e 100644 --- a/recipes/bioconductor-suprahex/meta.yaml +++ b/recipes/bioconductor-suprahex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "supraHex" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e336ff1cb8560472beba7d8ccf5a09f + md5: 19685808f18718a58889c70e476888d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-suprahex", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-surfaltr/meta.yaml b/recipes/bioconductor-surfaltr/meta.yaml index 2ed649c1aa0a6..fec35c9c96474 100644 --- a/recipes/bioconductor-surfaltr/meta.yaml +++ b/recipes/bioconductor-surfaltr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "surfaltr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3a4fb02609853c9949dd59b780178915 + md5: 69ea67dd32fffa5376607fa6fa5c7e9f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-surfaltr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, devtools, kableExtra requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msa >=1.32.0,<1.33.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msa >=1.34.0,<1.35.0' - r-base - 'r-dplyr >=1.0.6' - 'r-ggplot2 >=3.3.2' @@ -35,9 +36,9 @@ requirements: - 'r-testthat >=3.0.0' - 'r-xml2 >=1.3.2' run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msa >=1.32.0,<1.33.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msa >=1.34.0,<1.35.0' - r-base - 'r-dplyr >=1.0.6' - 'r-ggplot2 >=3.3.2' diff --git a/recipes/bioconductor-survcomp/meta.yaml b/recipes/bioconductor-survcomp/meta.yaml index 2f2780ca4ccff..52adadac760d3 100644 --- a/recipes/bioconductor-survcomp/meta.yaml +++ b/recipes/bioconductor-survcomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "survcomp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bf071254fe286a0ece30502f89c7a76a + md5: 5026589c50042751474d3474dc24847d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-survcomp", max_pin="x.x") }}' # Suggests: Hmisc, clinfun, xtable, Biobase, BiocManager requirements: host: diff --git a/recipes/bioconductor-survtype/meta.yaml b/recipes/bioconductor-survtype/meta.yaml index 12039d62d24df..1d4612397856c 100644 --- a/recipes/bioconductor-survtype/meta.yaml +++ b/recipes/bioconductor-survtype/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "survtype" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 639c5a6fcc3ff8139f8c46a3cefd2e84 + md5: e939bd3726a715cb0a817d0541ff86ab build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-survtype", max_pin="x.x") }}' noarch: generic # Suggests: maftools, scales, knitr, rmarkdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-clustvarsel - r-pheatmap - r-survival - r-survminer run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-clustvarsel - r-pheatmap diff --git a/recipes/bioconductor-sva/meta.yaml b/recipes/bioconductor-sva/meta.yaml index 2e4dcb6704fdf..22e62492bff10 100644 --- a/recipes/bioconductor-sva/meta.yaml +++ b/recipes/bioconductor-sva/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.48.0" %} +{% set version = "3.50.0" %} {% set name = "sva" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6a2553ec4e50d85e75a764a83b8dc74b + md5: 8c42cd3e23be4d24f072d98394931552 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sva", max_pin="x.x") }}' # Suggests: pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-matrixstats - r-mgcv - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-matrixstats - r-mgcv diff --git a/recipes/bioconductor-svanumt/meta.yaml b/recipes/bioconductor-svanumt/meta.yaml index 3dba97073f8ec..03b3aa0e409af 100644 --- a/recipes/bioconductor-svanumt/meta.yaml +++ b/recipes/bioconductor-svanumt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "svaNUMT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b4ce1b0c7f1224d6703e8681aa643fa4 + md5: 1f25f8632f0e52d0826ee0b1b8a1fe28 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-svanumt", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, readr, plyranges, circlize, IRanges, SummarizedExperiment, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structuralvariantannotation >=1.16.0,<1.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structuralvariantannotation >=1.18.0,<1.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-assertthat - r-base - r-dplyr - r-rlang - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structuralvariantannotation >=1.16.0,<1.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structuralvariantannotation >=1.18.0,<1.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-assertthat - r-base - r-dplyr diff --git a/recipes/bioconductor-svaretro/meta.yaml b/recipes/bioconductor-svaretro/meta.yaml index b4fa14e5bae17..176e5ea539cc2 100644 --- a/recipes/bioconductor-svaretro/meta.yaml +++ b/recipes/bioconductor-svaretro/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "svaRetro" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b746169da6f49e96d3f4f50a2826f577 + md5: 56da2ed056a7078a5d9f2883885d5be5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-svaretro", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, BiocStyle, plyranges, circlize, tictoc, IRanges, stats, SummarizedExperiment, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structuralvariantannotation >=1.16.0,<1.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structuralvariantannotation >=1.18.0,<1.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-assertthat - r-base - r-dplyr - r-rlang - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structuralvariantannotation >=1.16.0,<1.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structuralvariantannotation >=1.18.0,<1.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-assertthat - r-base - r-dplyr diff --git a/recipes/bioconductor-svm2crmdata/meta.yaml b/recipes/bioconductor-svm2crmdata/meta.yaml index ea67ef2e8f814..7e8ea729d45d5 100644 --- a/recipes/bioconductor-svm2crmdata/meta.yaml +++ b/recipes/bioconductor-svm2crmdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "SVM2CRMdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e1d44ea0446ba41c2f9264ab088461e2 + md5: ce0c6615bfbb9a5a7cf4eeab0bd6199d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-svm2crmdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-svm2crmdata/post-link.sh b/recipes/bioconductor-svm2crmdata/post-link.sh index eb5d1751d701d..b48dec842f852 100644 --- a/recipes/bioconductor-svm2crmdata/post-link.sh +++ b/recipes/bioconductor-svm2crmdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "svm2crmdata-1.32.0" +installBiocDataPackage.sh "svm2crmdata-1.34.0" diff --git a/recipes/bioconductor-svmdo/meta.yaml b/recipes/bioconductor-svmdo/meta.yaml index 37e37aa503896..81368ffa43b1b 100644 --- a/recipes/bioconductor-svmdo/meta.yaml +++ b/recipes/bioconductor-svmdo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "SVMDO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1eb944647d9a94e7d36c9c9b94f03ab4 + md5: 3edf50ad6544537845fe263bb490b9e5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-svmdo", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 3.1.6), BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-bsda >=1.2.1' - 'r-caret >=6.0-93' @@ -41,10 +42,10 @@ requirements: - 'r-sjmisc >=2.8.9' - 'r-survival >=3.4-0' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-bsda >=1.2.1' - 'r-caret >=6.0-93' diff --git a/recipes/bioconductor-swath2stats/meta.yaml b/recipes/bioconductor-swath2stats/meta.yaml index 4af9facf1e894..8a7eef17ac912 100644 --- a/recipes/bioconductor-swath2stats/meta.yaml +++ b/recipes/bioconductor-swath2stats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.1" %} +{% set version = "1.32.0" %} {% set name = "SWATH2stats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 78daf29b8044f381022c2ffe6090c9d1 + md5: 3853f9f81af8bc0732ff0e2ceaf43441 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-swath2stats", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base - r-data.table - r-ggplot2 - r-reshape2 run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-swathxtend/meta.yaml b/recipes/bioconductor-swathxtend/meta.yaml index 60b0a2a5ede76..23a30c62141a5 100644 --- a/recipes/bioconductor-swathxtend/meta.yaml +++ b/recipes/bioconductor-swathxtend/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "SwathXtend" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ff355cc022731be52c04ba7c3642fbff + md5: 64b04f78ca92078b9ad63cee65bf012f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-swathxtend", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-swfdr/meta.yaml b/recipes/bioconductor-swfdr/meta.yaml index 18c52df32692d..5b1503ab08784 100644 --- a/recipes/bioconductor-swfdr/meta.yaml +++ b/recipes/bioconductor-swfdr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "swfdr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 81f7760a0a60bf0b4316d3c4331254c9 + md5: f873820993a9785dbca1c825b291abfb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-swfdr", max_pin="x.x") }}' noarch: generic # Suggests: dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-switchbox/meta.yaml b/recipes/bioconductor-switchbox/meta.yaml index d4d07d56b234b..a1db6b69845ce 100644 --- a/recipes/bioconductor-switchbox/meta.yaml +++ b/recipes/bioconductor-switchbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "switchBox" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d7459e39ae728ff2ea86be9d8b7dabe7 + md5: 29de2be8446a4f686acf75635f1539b9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-switchbox", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-switchde/meta.yaml b/recipes/bioconductor-switchde/meta.yaml index 34886fcb98e1f..7bd82e5a01c55 100644 --- a/recipes/bioconductor-switchde/meta.yaml +++ b/recipes/bioconductor-switchde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "switchde" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d51bc2a4680829c8c892a5338e9f3357 + md5: 9017dd3162508b4412c30ae21eef9328 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-switchde", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-synapsis/meta.yaml b/recipes/bioconductor-synapsis/meta.yaml index f0d3daec91acd..448748a38bafa 100644 --- a/recipes/bioconductor-synapsis/meta.yaml +++ b/recipes/bioconductor-synapsis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "synapsis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e13bb0dbe8bcba4ac4dffa389ec31ed8 + md5: 592572937da010f5fbd70fb7fc8e80d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-synapsis", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, tidyverse, BiocStyle requirements: host: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-base run: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-synapter/meta.yaml b/recipes/bioconductor-synapter/meta.yaml index 6f7e59fa0a2d8..74524f15fc539 100644 --- a/recipes/bioconductor-synapter/meta.yaml +++ b/recipes/bioconductor-synapter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "synapter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0a1b7bdc0e115bb14644630fdbb324ef + md5: a6c9ade32fbe35d5cb85adc0e9a5322c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-synapter", max_pin="x.x") }}' noarch: generic # Suggests: synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN, BiocStyle, knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-cleaver >=1.38.0,<1.39.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-cleaver >=1.40.0,<1.41.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-lattice - r-rcolorbrewer - 'r-readr >=0.2' - 'r-rmarkdown >=1.0' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-cleaver >=1.38.0,<1.39.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-cleaver >=1.40.0,<1.41.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-lattice - r-rcolorbrewer diff --git a/recipes/bioconductor-synapterdata/meta.yaml b/recipes/bioconductor-synapterdata/meta.yaml index 032f55aa8709c..a49f7875e36cd 100644 --- a/recipes/bioconductor-synapterdata/meta.yaml +++ b/recipes/bioconductor-synapterdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "synapterdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cfc22e448bd4d28d06535acfc93cea7b + md5: 255aa756f0b6c0c1d95cdfbc889a67a2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-synapterdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-synapter >=2.24.0,<2.25.0' + - 'bioconductor-synapter >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-synapter >=2.24.0,<2.25.0' + - 'bioconductor-synapter >=2.26.0,<2.27.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-synapterdata/post-link.sh b/recipes/bioconductor-synapterdata/post-link.sh index 2f003cfbef0d2..a426a8749af10 100644 --- a/recipes/bioconductor-synapterdata/post-link.sh +++ b/recipes/bioconductor-synapterdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "synapterdata-1.38.0" +installBiocDataPackage.sh "synapterdata-1.40.0" diff --git a/recipes/bioconductor-synaptome.data/meta.yaml b/recipes/bioconductor-synaptome.data/meta.yaml index 43d4767182ffc..d7106934d6d10 100644 --- a/recipes/bioconductor-synaptome.data/meta.yaml +++ b/recipes/bioconductor-synaptome.data/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.6" %} {% set name = "synaptome.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4388c63219782a9aa3e384fcdb51ed47 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-synaptome.data", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-synaptome.db/meta.yaml b/recipes/bioconductor-synaptome.db/meta.yaml index 95ca7d6cb55e6..1ee54ad6b3834 100644 --- a/recipes/bioconductor-synaptome.db/meta.yaml +++ b/recipes/bioconductor-synaptome.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.99.12" %} +{% set version = "0.99.15" %} {% set name = "synaptome.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 383e2a16688e13d40d1f8e2efd3168ef + md5: 7ed11d61ac8dca86372eeec59b5ab03b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-synaptome.db", max_pin="x.x") }}' noarch: generic -# Suggests: rmarkdown, knitr, pander, testthat, devtools, markdown +# Suggests: rmarkdown, knitr, pander, testthat, devtools, markdown, ggplot2 requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - 'bioconductor-synaptome.data >=0.99.0,<0.100.0' - r-base - r-dbi @@ -31,7 +32,7 @@ requirements: - r-rdpack - r-rsqlite run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - 'bioconductor-synaptome.data >=0.99.0,<0.100.0' - r-base - r-dbi @@ -41,7 +42,7 @@ requirements: - r-rdpack - r-rsqlite - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-synaptome.db/post-link.sh b/recipes/bioconductor-synaptome.db/post-link.sh index b5043fedb70cd..f2b7062f649b3 100644 --- a/recipes/bioconductor-synaptome.db/post-link.sh +++ b/recipes/bioconductor-synaptome.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "synaptome.db-0.99.12" +installBiocDataPackage.sh "synaptome.db-0.99.15" diff --git a/recipes/bioconductor-synergyfinder/meta.yaml b/recipes/bioconductor-synergyfinder/meta.yaml index 14e3d5a448a85..9eb18914024ce 100644 --- a/recipes/bioconductor-synergyfinder/meta.yaml +++ b/recipes/bioconductor-synergyfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.8.2" %} +{% set version = "3.10.0" %} {% set name = "synergyfinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6323a009044409b49239020be9cb7431 + md5: 8b511fc821bd8e8b344a439f5c641a72 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-synergyfinder", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-synextend/meta.yaml b/recipes/bioconductor-synextend/meta.yaml index c2ef67d7cee4d..f46ea364894f7 100644 --- a/recipes/bioconductor-synextend/meta.yaml +++ b/recipes/bioconductor-synextend/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "SynExtend" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3e01e05a7fad5a006ee4fa765002a728 + md5: f7ee0b985a06dbd6040329dd264648f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-synextend", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, igraph, markdown, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-synlet/meta.yaml b/recipes/bioconductor-synlet/meta.yaml index 06b0e3a65a979..42f0e6cfbeb87 100644 --- a/recipes/bioconductor-synlet/meta.yaml +++ b/recipes/bioconductor-synlet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.0" %} +{% set version = "2.2.0" %} {% set name = "synlet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ca162c2dc8ffc6452cd92f618e06c010 + md5: f56c634faaae3a0de5e46d18e6617d11 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-synlet", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-rankprod >=3.26.0,<3.27.0' + - 'bioconductor-rankprod >=3.28.0,<3.29.0' - r-base - r-data.table - r-ggplot2 @@ -29,7 +30,7 @@ requirements: - r-patchwork - r-rcolorbrewer run: - - 'bioconductor-rankprod >=3.26.0,<3.27.0' + - 'bioconductor-rankprod >=3.28.0,<3.29.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-synmut/meta.yaml b/recipes/bioconductor-synmut/meta.yaml index 2f76cc1ccdc30..e2cd14510aeba 100644 --- a/recipes/bioconductor-synmut/meta.yaml +++ b/recipes/bioconductor-synmut/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "SynMut" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a3be12d75414cd7bcaf19df34e812cc + md5: 485dd0770e2c64ad7ace9a3edf957fe8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-synmut", max_pin="x.x") }}' noarch: generic # Suggests: BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc, glue requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-seqinr - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-seqinr - r-stringr diff --git a/recipes/bioconductor-syntenet/meta.yaml b/recipes/bioconductor-syntenet/meta.yaml index d11bda0b6b26f..58a7b99d243ea 100644 --- a/recipes/bioconductor-syntenet/meta.yaml +++ b/recipes/bioconductor-syntenet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.4" %} +{% set version = "1.4.0" %} {% set name = "syntenet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 81bd02bbba83fcb7f62098b5fd2a1fc6 + md5: ab56b637f74d79cfba3dd6aab80b7ac9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-syntenet", max_pin="x.x") }}' # Suggests: BiocStyle, ggtree, labdsv, covr, knitr, rmarkdown, testthat (>= 3.0.0), xml2 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-ggnetwork - r-ggplot2 @@ -38,10 +39,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-ggnetwork - r-ggplot2 diff --git a/recipes/bioconductor-systempiper/meta.yaml b/recipes/bioconductor-systempiper/meta.yaml index dc1a2c0c6014b..2690b4fb73a2c 100644 --- a/recipes/bioconductor-systempiper/meta.yaml +++ b/recipes/bioconductor-systempiper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.3" %} +{% set version = "2.8.0" %} {% set name = "systemPipeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5abc2d7529b19cae2029a906ab790dde + md5: 67456347870d6c358e1209658cb930d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-systempiper", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, systemPipeRdata, GenomicAlignments, grid, dplyr, testthat, rjson, annotate, AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT, rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools, GenomicFeatures (>= 1.31.3), VariantAnnotation (>= 1.25.11) # SystemRequirements: systemPipeR can be used to run external command-line software (e.g. short read aligners), but the corresponding tool needs to be installed on a system. requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-crayon - r-ggplot2 @@ -37,13 +38,13 @@ requirements: - r-stringr - r-yaml run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-crayon - r-ggplot2 @@ -58,7 +59,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'systemPipeR: workflow management and report generation environment' - description: 'systemPipeR is a generic data analysis workflow environment that unifies R with command-line tools. It enables scientists to analyze many types of large- or small-scale data on local or distributed computer systems with a high level of reproducibility, scalability and portability. At its core is a command-line interface (CLI) that adopts the Common Workflow Language (CWL). This design allows users to choose for each analysis step the optimal R or command-line software. It supports both end-to-end and partial execution of workflows with built-in restart functionalities. Efficient management of complex analysis tasks is accomplished by a flexible workflow control container class. Handling of large numbers of input samples and experimental designs is facilitated by a consistently implemented sample annotation infrastructure. As a multi-purpose workflow toolkit, systemPipeR enables users to run existing workflows, customize them or design entirely new ones while taking advantage of widely adopted data structures within the Bioconductor ecosystem. Another important core functionality is the generation of reproducible scientific analysis and technical reports. For result interpretation, systemPipeR offers a wide range of plotting functionality, while an associated Shiny App offers many useful functionalities for interactive result exploration. The vignettes linked from this page include (1) a general introduction, (2) a description of technical details, and (3) a collection of workflow templates.' + description: 'systemPipeR is a multipurpose data analysis workflow environment that unifies R with command-line tools. It enables scientists to analyze many types of large- or small-scale data on local or distributed computer systems with a high level of reproducibility, scalability and portability. At its core is a command-line interface (CLI) that adopts the Common Workflow Language (CWL). This design allows users to choose for each analysis step the optimal R or command-line software. It supports both end-to-end and partial execution of workflows with built-in restart functionalities. Efficient management of complex analysis tasks is accomplished by a flexible workflow control container class. Handling of large numbers of input samples and experimental designs is facilitated by consistent sample annotation mechanisms. As a multi-purpose workflow toolkit, systemPipeR enables users to run existing workflows, customize them or design entirely new ones while taking advantage of widely adopted data structures within the Bioconductor ecosystem. Another important core functionality is the generation of reproducible scientific analysis and technical reports. For result interpretation, systemPipeR offers a wide range of plotting functionality, while an associated Shiny App offers many useful functionalities for interactive result exploration. The vignettes linked from this page include (1) a general introduction, (2) a description of technical details, and (3) a collection of workflow templates.' extra: identifiers: - biotools:systempiper diff --git a/recipes/bioconductor-systempiperdata/meta.yaml b/recipes/bioconductor-systempiperdata/meta.yaml index 54390564b9f98..40deed2560a71 100644 --- a/recipes/bioconductor-systempiperdata/meta.yaml +++ b/recipes/bioconductor-systempiperdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "systemPipeRdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: afa259f7cd53e2252902a48dd32df1b9 + md5: 1af59929fb95c3a017b88fce32a4c833 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-systempiperdata", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures, GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer, RUnit, BiocStyle, knitr, rmarkdown, systemPipeR requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-jsonlite - r-remotes run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-jsonlite - r-remotes - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-systempiperdata/post-link.sh b/recipes/bioconductor-systempiperdata/post-link.sh index f66ddefe81cd4..5e959d6d140be 100644 --- a/recipes/bioconductor-systempiperdata/post-link.sh +++ b/recipes/bioconductor-systempiperdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "systempiperdata-2.4.0" +installBiocDataPackage.sh "systempiperdata-2.6.0" diff --git a/recipes/bioconductor-systempipeshiny/meta.yaml b/recipes/bioconductor-systempipeshiny/meta.yaml index b2a420c776120..6a0d1fa4130e8 100644 --- a/recipes/bioconductor-systempipeshiny/meta.yaml +++ b/recipes/bioconductor-systempipeshiny/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "systemPipeShiny" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ac48a618b74b5c41efcec02c40c6690 + md5: 8880796c4c2bf213ffa98df7f3f8d164 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-systempipeshiny", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, systemPipeR (>= 2.2.0), systemPipeRdata (>= 2.0.0), rhandsontable, zip, callr, pushbar, fs, readr, R.utils, DESeq2, SummarizedExperiment, glmpca, pheatmap, grid, ape, Rtsne, UpSetR, tidyr, esquisse (>= 1.1.0), cicerone requirements: @@ -47,7 +48,7 @@ requirements: - r-shinyjs - r-shinytoastr - r-shinywidgets - - 'r-spscomps >=0.3.2' + - 'r-spscomps >=0.3.3' - 'r-spsutil >=0.2.2' - r-stringr - r-styler @@ -81,7 +82,7 @@ requirements: - r-shinyjs - r-shinytoastr - r-shinywidgets - - 'r-spscomps >=0.3.2' + - 'r-spscomps >=0.3.3' - 'r-spsutil >=0.2.2' - r-stringr - r-styler diff --git a/recipes/bioconductor-systempipetools/meta.yaml b/recipes/bioconductor-systempipetools/meta.yaml index a2aee49bccd5b..f406794a6855d 100644 --- a/recipes/bioconductor-systempipetools/meta.yaml +++ b/recipes/bioconductor-systempipetools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "systemPipeTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c9a22e57ab20cf5f5412adaee75b50c2 + md5: e0f74af8b351b49c68cbfed4e9e00adc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-systempipetools", max_pin="x.x") }}' noarch: generic # Suggests: systemPipeR, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocGenerics, Biostrings, methods requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-base - r-dplyr @@ -38,9 +39,9 @@ requirements: - r-rtsne - r-tibble run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-base - r-dplyr diff --git a/recipes/bioconductor-tabulamurisdata/meta.yaml b/recipes/bioconductor-tabulamurisdata/meta.yaml index e2cfdf8ef3cd9..c226941259d34 100644 --- a/recipes/bioconductor-tabulamurisdata/meta.yaml +++ b/recipes/bioconductor-tabulamurisdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "TabulaMurisData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c198946ebcce0c1e6c79c65f52a11642 + md5: 39c27cc6646ea3bcdb4637a226b219b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tabulamurisdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran, scater, iSEE, testthat requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tabulamurisdata/post-link.sh b/recipes/bioconductor-tabulamurisdata/post-link.sh index 4f3b46aad6d18..fb80612c77662 100644 --- a/recipes/bioconductor-tabulamurisdata/post-link.sh +++ b/recipes/bioconductor-tabulamurisdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tabulamurisdata-1.18.0" +installBiocDataPackage.sh "tabulamurisdata-1.20.0" diff --git a/recipes/bioconductor-tabulamurissenisdata/meta.yaml b/recipes/bioconductor-tabulamurissenisdata/meta.yaml index 092094204d602..0a4e957526051 100644 --- a/recipes/bioconductor-tabulamurissenisdata/meta.yaml +++ b/recipes/bioconductor-tabulamurissenisdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "TabulaMurisSenisData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c6a42dc2dc0bbabe7cfd25c91e11f050 + md5: 6d6120b18adce70e943a3da8e0e577b2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tabulamurissenisdata", max_pin="x.x") }}' noarch: generic # Suggests: ggplot2, testthat, knitr, rmarkdown, iSEE, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-gdata run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-gdata - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tabulamurissenisdata/post-link.sh b/recipes/bioconductor-tabulamurissenisdata/post-link.sh index 8c408f1ad763f..946a2b411a203 100644 --- a/recipes/bioconductor-tabulamurissenisdata/post-link.sh +++ b/recipes/bioconductor-tabulamurissenisdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tabulamurissenisdata-1.6.0" +installBiocDataPackage.sh "tabulamurissenisdata-1.8.0" diff --git a/recipes/bioconductor-tadar/build.sh b/recipes/bioconductor-tadar/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tadar/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tadar/meta.yaml b/recipes/bioconductor-tadar/meta.yaml new file mode 100644 index 0000000000000..a4d1aea0a2232 --- /dev/null +++ b/recipes/bioconductor-tadar/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.0.0" %} +{% set name = "tadar" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 88c91583a351bef3f3d8ca38b51c0c04 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tadar", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, covr, knitr, limma, rmarkdown, testthat (>= 3.0.0), tidyverse +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - r-base + - r-ggplot2 + - r-rlang + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - r-base + - r-ggplot2 + - r-rlang +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Transcriptome Analysis of Differential Allelic Representation' + description: 'This package provides functions to standardise the analysis of Differential Allelic Representation (DAR). DAR compromises the integrity of Differential Expression analysis results as it can bias expression, influencing the classification of genes (or transcripts) as being differentially expressed. DAR analysis results in an easy-to-interpret value between 0 and 1 for each genetic feature of interest, where 0 represents identical allelic representation and 1 represents complete diversity. This metric can be used to identify features prone to false-positive calls in Differential Expression analysis, and can be leveraged with statistical methods to alleviate the impact of such artefacts on RNA-seq data.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-tadcompare/meta.yaml b/recipes/bioconductor-tadcompare/meta.yaml index 7bde3530ca42a..db49b519eb40d 100644 --- a/recipes/bioconductor-tadcompare/meta.yaml +++ b/recipes/bioconductor-tadcompare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "TADCompare" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4e72268cea3f87bc16d914b4907ebcf4 + md5: 92966a38a0c202cfe7dbd09bb83b23b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tadcompare", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr, pheatmap, rGREAT, SpectralTAD requirements: host: - - 'bioconductor-hiccompare >=1.22.0,<1.23.0' + - 'bioconductor-hiccompare >=1.24.0,<1.25.0' - r-base - r-cluster - r-cowplot @@ -35,7 +36,7 @@ requirements: - r-reshape2 - r-tidyr run: - - 'bioconductor-hiccompare >=1.22.0,<1.23.0' + - 'bioconductor-hiccompare >=1.24.0,<1.25.0' - r-base - r-cluster - r-cowplot diff --git a/recipes/bioconductor-tanggle/meta.yaml b/recipes/bioconductor-tanggle/meta.yaml index 695da10676f27..f1e803a007b94 100644 --- a/recipes/bioconductor-tanggle/meta.yaml +++ b/recipes/bioconductor-tanggle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "tanggle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5582a23deea9db3af347e42b327e895f + md5: d23bc70f7c920e00bb14a3d05e8cfdea build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tanggle", max_pin="x.x") }}' noarch: generic # Suggests: tinytest, BiocStyle, ggimage, knitr, rmarkdown requirements: host: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - 'r-ape >=5.0' - r-base - 'r-ggplot2 >=2.2.0' - 'r-phangorn >=2.5' run: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - 'r-ape >=5.0' - r-base - 'r-ggplot2 >=2.2.0' diff --git a/recipes/bioconductor-tapseq/meta.yaml b/recipes/bioconductor-tapseq/meta.yaml index 112e6d082f8aa..39c94bc15447d 100644 --- a/recipes/bioconductor-tapseq/meta.yaml +++ b/recipes/bioconductor-tapseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.1" %} {% set name = "TAPseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0acc6577f95cf45253359a38029de75a + md5: 423853e9c2015594d616f9315d5c217d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tapseq", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer, BiocStyle # SystemRequirements: Primer3 (>= 2.5.0), BLAST+ (>=2.6.0) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-tidyr diff --git a/recipes/bioconductor-target/meta.yaml b/recipes/bioconductor-target/meta.yaml index 48f960fb213e3..9a6b3f33d033d 100644 --- a/recipes/bioconductor-target/meta.yaml +++ b/recipes/bioconductor-target/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "target" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5d1cce236aa72d723a2b0db48f97fb88 + md5: 96ca9fa7bed738941cd930b5e7491bc2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-target", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), knitr, rmarkdown, shinytest, shinyBS, covr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-matrixstats - r-shiny run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-matrixstats - r-shiny diff --git a/recipes/bioconductor-targetdecoy/meta.yaml b/recipes/bioconductor-targetdecoy/meta.yaml index 6a31ddf07787a..a48d89bad2795 100644 --- a/recipes/bioconductor-targetdecoy/meta.yaml +++ b/recipes/bioconductor-targetdecoy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "TargetDecoy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b5b99cde4bb8d267e2f094778feac42c + md5: ff49065b40e049f06bbe1ad9c74200fc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-targetdecoy", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, msdata, sessioninfo, rmarkdown, gridExtra, testthat (>= 3.0.0), covr requirements: host: - - 'bioconductor-mzid >=1.38.0,<1.39.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-mzid >=1.40.0,<1.41.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-base - r-ggplot2 - r-ggpubr - r-miniui - r-shiny run: - - 'bioconductor-mzid >=1.38.0,<1.39.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-mzid >=1.40.0,<1.41.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-base - r-ggplot2 - r-ggpubr diff --git a/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml b/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml index 3ad409739d7ea..1a5256aad3781 100644 --- a/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml +++ b/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.1" %} {% set name = "targetscan.Hs.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: d10569315400f6c1b95ad2688632b6de build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-targetscan.hs.eg.db", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml b/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml index 3a214e634c698..0a4db556725a7 100644 --- a/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml +++ b/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.1" %} {% set name = "targetscan.Mm.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1830815c9d1383739f1ff152da0508c5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-targetscan.mm.eg.db", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-targetscore/meta.yaml b/recipes/bioconductor-targetscore/meta.yaml index c50e4e01c9a53..b57d457d83c63 100644 --- a/recipes/bioconductor-targetscore/meta.yaml +++ b/recipes/bioconductor-targetscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "TargetScore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11b4e6f2896e28dac5a4b08485769f2a + md5: 92d3b6ca138c6c3081262a758ec63766 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-targetscore", max_pin="x.x") }}' noarch: generic # Suggests: TargetScoreData, gplots, Biobase, GEOquery requirements: diff --git a/recipes/bioconductor-targetscoredata/meta.yaml b/recipes/bioconductor-targetscoredata/meta.yaml index d519bd5b385f1..2da4addce3f26 100644 --- a/recipes/bioconductor-targetscoredata/meta.yaml +++ b/recipes/bioconductor-targetscoredata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "TargetScoreData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 63ccf68833f45d1a853a719046cf9def + md5: 61084f230f2c3dedb27988867f07f50f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-targetscoredata", max_pin="x.x") }}' noarch: generic # Suggests: TargetScore, gplots requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-targetscoredata/post-link.sh b/recipes/bioconductor-targetscoredata/post-link.sh index ffe6ca3e5bfb0..80e2477b8de59 100644 --- a/recipes/bioconductor-targetscoredata/post-link.sh +++ b/recipes/bioconductor-targetscoredata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "targetscoredata-1.36.0" +installBiocDataPackage.sh "targetscoredata-1.38.0" diff --git a/recipes/bioconductor-targetsearch/meta.yaml b/recipes/bioconductor-targetsearch/meta.yaml index a118d4918a513..c554006c9e67c 100644 --- a/recipes/bioconductor-targetsearch/meta.yaml +++ b/recipes/bioconductor-targetsearch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.1" %} {% set name = "TargetSearch" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f2ecd6d2c39b8705b55009a4e383dcf5 + md5: 652009cfa3df492780c9ea45715df0b9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-targetsearch", max_pin="x.x") }}' # Suggests: TargetSearchData, BiocStyle, knitr, tinytest requirements: host: diff --git a/recipes/bioconductor-targetsearchdata/meta.yaml b/recipes/bioconductor-targetsearchdata/meta.yaml index 91fb3650656ea..df32deec7a9b3 100644 --- a/recipes/bioconductor-targetsearchdata/meta.yaml +++ b/recipes/bioconductor-targetsearchdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "TargetSearchData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6dd9996121d44e6f753ce68434de7aad + md5: 96bbec70706d8adcf4ee321261620d79 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-targetsearchdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-targetsearchdata/post-link.sh b/recipes/bioconductor-targetsearchdata/post-link.sh index d1539a16f580a..1f74c111549e7 100644 --- a/recipes/bioconductor-targetsearchdata/post-link.sh +++ b/recipes/bioconductor-targetsearchdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "targetsearchdata-1.38.0" +installBiocDataPackage.sh "targetsearchdata-1.40.0" diff --git a/recipes/bioconductor-tartare/meta.yaml b/recipes/bioconductor-tartare/meta.yaml index 0e552a41f409a..880886341b0d0 100644 --- a/recipes/bioconductor-tartare/meta.yaml +++ b/recipes/bioconductor-tartare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "tartare" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 10b4601e60890e48d47840d2a4f03a22 + md5: 869743e16f05bc962de518ca925750d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tartare", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, tools requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tartare/post-link.sh b/recipes/bioconductor-tartare/post-link.sh index 41396cdf35cae..0017d5f89c426 100644 --- a/recipes/bioconductor-tartare/post-link.sh +++ b/recipes/bioconductor-tartare/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tartare-1.14.0" +installBiocDataPackage.sh "tartare-1.16.0" diff --git a/recipes/bioconductor-tbsignatureprofiler/meta.yaml b/recipes/bioconductor-tbsignatureprofiler/meta.yaml index 14eb668a3cdfd..4ef88100aca8b 100644 --- a/recipes/bioconductor-tbsignatureprofiler/meta.yaml +++ b/recipes/bioconductor-tbsignatureprofiler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "TBSignatureProfiler" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a00e9d71be544060c7eda4f08ba8322e + md5: 1cd38948c20b0f43904a8ff204f2940d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tbsignatureprofiler", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, caret, circlize, class, covr, dplyr, e1071, glmnet, HGNChelper, impute, knitr, lintr, MASS, plyr, pROC, randomForest, rmarkdown, shiny, spelling, sva, testthat requirements: host: - - 'bioconductor-assign >=1.36.0,<1.37.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singscore >=1.20.0,<1.21.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-assign >=1.38.0,<1.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singscore >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dt - r-gdata @@ -40,15 +41,15 @@ requirements: - r-rlang - r-rocit run: - - 'bioconductor-assign >=1.36.0,<1.37.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singscore >=1.20.0,<1.21.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-assign >=1.38.0,<1.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singscore >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dt - r-gdata diff --git a/recipes/bioconductor-tbx20bamsubset/meta.yaml b/recipes/bioconductor-tbx20bamsubset/meta.yaml index cb3222da9f6b5..18a9421aaee7e 100644 --- a/recipes/bioconductor-tbx20bamsubset/meta.yaml +++ b/recipes/bioconductor-tbx20bamsubset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "TBX20BamSubset" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b8761f75b20b32450d6cae46dc063a9 + md5: c158901ec6203e85569c600efb335ccf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tbx20bamsubset", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-xtable run: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-xtable - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tbx20bamsubset/post-link.sh b/recipes/bioconductor-tbx20bamsubset/post-link.sh index fbddcded07bfd..7c52406af39b8 100644 --- a/recipes/bioconductor-tbx20bamsubset/post-link.sh +++ b/recipes/bioconductor-tbx20bamsubset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tbx20bamsubset-1.36.0" +installBiocDataPackage.sh "tbx20bamsubset-1.38.0" diff --git a/recipes/bioconductor-tcc/build.sh b/recipes/bioconductor-tcc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tcc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tcc/meta.yaml b/recipes/bioconductor-tcc/meta.yaml new file mode 100644 index 0000000000000..a070ac06036b2 --- /dev/null +++ b/recipes/bioconductor-tcc/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.42.0" %} +{% set name = "TCC" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e36a17d628a68654296227603e0678da +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tcc", max_pin="x.x") }}' + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' + - r-base + run: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'TCC: Differential expression analysis for tag count data with robust normalization strategies' + description: 'This package provides a series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in depended packages.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + diff --git a/recipes/bioconductor-tcgabiolinks/meta.yaml b/recipes/bioconductor-tcgabiolinks/meta.yaml index 97ec14cf72ff7..a5d528634ec4a 100644 --- a/recipes/bioconductor-tcgabiolinks/meta.yaml +++ b/recipes/bioconductor-tcgabiolinks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.3" %} +{% set version = "2.30.0" %} {% set name = "TCGAbiolinks" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef3da29fc90f15d770fef2ae20629127 + md5: 91536d6234ebd992dac8102393c363d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tcgabiolinks", max_pin="x.x") }}' noarch: generic # Suggests: jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, dnet, Biobase, affy, testthat, sesame, AnnotationHub, ExperimentHub, pathview, clusterProfiler, Seurat, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph, supraHex, limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3), scales, grid requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgabiolinksgui.data >=1.20.0,<1.21.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgabiolinksgui.data >=1.22.0,<1.23.0' - r-base - r-data.table - 'r-downloader >=0.4' @@ -46,12 +47,12 @@ requirements: - 'r-xml >=3.98.0' - r-xml2 run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgabiolinksgui.data >=1.20.0,<1.21.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgabiolinksgui.data >=1.22.0,<1.23.0' - r-base - r-data.table - 'r-downloader >=0.4' diff --git a/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml b/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml index cf31353641906..a599989612e1c 100644 --- a/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml +++ b/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "TCGAbiolinksGUI.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d0764549e842b85e9ed17bb0e27b1c54 + md5: bd2042c0064583d666364a52ce3be17e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tcgabiolinksgui.data", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, readr, DT requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh b/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh index cd1bdb8413e09..3ce61f3013f98 100644 --- a/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh +++ b/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tcgabiolinksgui.data-1.20.0" +installBiocDataPackage.sh "tcgabiolinksgui.data-1.22.0" diff --git a/recipes/bioconductor-tcgacrcmirna/meta.yaml b/recipes/bioconductor-tcgacrcmirna/meta.yaml index 77c92d198b9ee..d5aa585eae22e 100644 --- a/recipes/bioconductor-tcgacrcmirna/meta.yaml +++ b/recipes/bioconductor-tcgacrcmirna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "TCGAcrcmiRNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a286cf4adf594bccf4910c3445e2901c + md5: 451d09b5ec341d7e92211a1d42c35947 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tcgacrcmirna", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tcgacrcmirna/post-link.sh b/recipes/bioconductor-tcgacrcmirna/post-link.sh index 5a4a98bea980a..8c432e9a0c322 100644 --- a/recipes/bioconductor-tcgacrcmirna/post-link.sh +++ b/recipes/bioconductor-tcgacrcmirna/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tcgacrcmirna-1.20.0" +installBiocDataPackage.sh "tcgacrcmirna-1.22.0" diff --git a/recipes/bioconductor-tcgacrcmrna/meta.yaml b/recipes/bioconductor-tcgacrcmrna/meta.yaml index f8b1e5d7b7be0..e4c24ff6fed90 100644 --- a/recipes/bioconductor-tcgacrcmrna/meta.yaml +++ b/recipes/bioconductor-tcgacrcmrna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "TCGAcrcmRNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d3f199714f9dba5ed0838af4e6646c7e + md5: bb9300e6ad6e4e5435a31487fdc22ed6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tcgacrcmrna", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tcgacrcmrna/post-link.sh b/recipes/bioconductor-tcgacrcmrna/post-link.sh index 5efda522e33cd..53b5ac1ad6709 100644 --- a/recipes/bioconductor-tcgacrcmrna/post-link.sh +++ b/recipes/bioconductor-tcgacrcmrna/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tcgacrcmrna-1.20.0" +installBiocDataPackage.sh "tcgacrcmrna-1.22.0" diff --git a/recipes/bioconductor-tcgamethylation450k/meta.yaml b/recipes/bioconductor-tcgamethylation450k/meta.yaml index 3bb05d8e97048..521516a508d02 100644 --- a/recipes/bioconductor-tcgamethylation450k/meta.yaml +++ b/recipes/bioconductor-tcgamethylation450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "TCGAMethylation450k" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d230a3e839f3ac33e404453c46dfa4f + md5: e913aa3b85d5cd1d0b27a346daf8c9ee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tcgamethylation450k", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tcgamethylation450k/post-link.sh b/recipes/bioconductor-tcgamethylation450k/post-link.sh index da7290bd32706..7b0a1b521a206 100644 --- a/recipes/bioconductor-tcgamethylation450k/post-link.sh +++ b/recipes/bioconductor-tcgamethylation450k/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tcgamethylation450k-1.36.0" +installBiocDataPackage.sh "tcgamethylation450k-1.38.0" diff --git a/recipes/bioconductor-tcgautils/meta.yaml b/recipes/bioconductor-tcgautils/meta.yaml index 946c3853a6883..472458d809d70 100644 --- a/recipes/bioconductor-tcgautils/meta.yaml +++ b/recipes/bioconductor-tcgautils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.2" %} +{% set version = "1.22.0" %} {% set name = "TCGAutils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,43 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61dc029c8eecfc34d14907b19d396360 + md5: 33d917253a210382a92537383bb4ee4f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tcgautils", max_pin="x.x") }}' noarch: generic -# Suggests: AnnotationHub, BiocFileCache, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, httr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, RColorBrewer, readr, rmarkdown, RTCGAToolbox (>= 2.17.4), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene +# Suggests: AnnotationHub, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, httr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, RColorBrewer, readr, rmarkdown, RTCGAToolbox (>= 2.17.4), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicdatacommons >=1.24.0,<1.25.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicdatacommons >=1.26.0,<1.27.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-rvest - r-stringr - r-xml2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicdatacommons >=1.24.0,<1.25.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicdatacommons >=1.26.0,<1.27.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-rvest - r-stringr diff --git a/recipes/bioconductor-tcgaworkflowdata/meta.yaml b/recipes/bioconductor-tcgaworkflowdata/meta.yaml index 4401e938f7cc9..8987d3058c1b2 100644 --- a/recipes/bioconductor-tcgaworkflowdata/meta.yaml +++ b/recipes/bioconductor-tcgaworkflowdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "TCGAWorkflowData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 12be13d34d28928864db32c639257777 + md5: cbba498f1922aeedadf96a1911a81751 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tcgaworkflowdata", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, pander, testthat +# Suggests: knitr, rmarkdown, pander, testthat, BiocStyle requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tcgaworkflowdata/post-link.sh b/recipes/bioconductor-tcgaworkflowdata/post-link.sh index 66078bdc1c486..1f5635c08afec 100644 --- a/recipes/bioconductor-tcgaworkflowdata/post-link.sh +++ b/recipes/bioconductor-tcgaworkflowdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tcgaworkflowdata-1.24.0" +installBiocDataPackage.sh "tcgaworkflowdata-1.26.0" diff --git a/recipes/bioconductor-tcseq/meta.yaml b/recipes/bioconductor-tcseq/meta.yaml index bd5393e7d4a55..59a57399ee0d5 100644 --- a/recipes/bioconductor-tcseq/meta.yaml +++ b/recipes/bioconductor-tcseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.23.0" %} +{% set version = "1.26.0" %} {% set name = "TCseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0bd128ed62aa6f6d75ea1083747b9f60 + md5: f5b63a6d1b40c82f8ddc86cc2abdb89b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tcseq", max_pin="x.x") }}' noarch: generic # Suggests: testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-e1071 @@ -35,13 +36,13 @@ requirements: - r-locfit - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-e1071 @@ -55,6 +56,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Time course sequencing data analysis' - description: 'Quantitative and differential analysis of epigenomic and transcriptomic time course sequencing data, clustering analysis and visualization of temporal patterns of time course data.' + description: 'Quantitative and differential analysis of epigenomic and transcriptomic time course sequencing data, clustering analysis and visualization of the temporal patterns of time course data.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-tdbasedufe/meta.yaml b/recipes/bioconductor-tdbasedufe/meta.yaml index 0cc6b899026b0..52baeee1720db 100644 --- a/recipes/bioconductor-tdbasedufe/meta.yaml +++ b/recipes/bioconductor-tdbasedufe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "TDbasedUFE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b1e0064920f4edfe8d052c3db37c7b2f + md5: 5557e1128d1d6ffab09670bf90b8947c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tdbasedufe", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-mofadata >=1.16.0,<1.17.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' - - 'bioconductor-tximportdata >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-mofadata >=1.18.0,<1.19.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' + - 'bioconductor-tximportdata >=1.30.0,<1.31.0' - r-base - r-readr - r-rtensor - r-shiny run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-mofadata >=1.16.0,<1.17.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' - - 'bioconductor-tximportdata >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-mofadata >=1.18.0,<1.19.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' + - 'bioconductor-tximportdata >=1.30.0,<1.31.0' - r-base - r-readr - r-rtensor diff --git a/recipes/bioconductor-tdbasedufeadv/meta.yaml b/recipes/bioconductor-tdbasedufeadv/meta.yaml index 9cc8358eef686..3ec6ded747c03 100644 --- a/recipes/bioconductor-tdbasedufeadv/meta.yaml +++ b/recipes/bioconductor-tdbasedufeadv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "TDbasedUFEadv" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f2dc73b489be0993668b18e618fbb3d + md5: 6f873403b62f756c6b8424cfeb2409c9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tdbasedufeadv", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 3.0.0), RTCGA.rnaseq, RTCGA.clinical, BiocStyle, MOFAdata requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtcga >=1.30.0,<1.31.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' - - 'bioconductor-tdbasedufe >=1.0.0,<1.1.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' + - 'bioconductor-tdbasedufe >=1.2.0,<1.3.0' - r-base - r-enrichr - r-hash - r-rtensor - r-shiny run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtcga >=1.30.0,<1.31.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' - - 'bioconductor-tdbasedufe >=1.0.0,<1.1.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' + - 'bioconductor-tdbasedufe >=1.2.0,<1.3.0' - r-base - r-enrichr - r-hash diff --git a/recipes/bioconductor-tekrabber/meta.yaml b/recipes/bioconductor-tekrabber/meta.yaml index 4e1051f1e4808..14842af5d7cd6 100644 --- a/recipes/bioconductor-tekrabber/meta.yaml +++ b/recipes/bioconductor-tekrabber/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "TEKRABber" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20b586d92efd367abd9c29d48d4fb9c7 + md5: 145026d8a5e02ec94f8a2a1f5405851e build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, ggpubr, rmarkdown, shiny, knitr, testthat (>= 3.0.0) + run_exports: '{{ pin_subpackage("bioconductor-tekrabber", max_pin="x.x") }}' +# Suggests: BiocStyle, bslib, ggplot2, ggpubr, plotly, rmarkdown, shiny, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-scbn >=1.18.0,<1.19.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-scbn >=1.20.0,<1.21.0' - r-base - r-dplyr - r-magrittr @@ -32,11 +32,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-scbn >=1.18.0,<1.19.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-scbn >=1.20.0,<1.21.0' - r-base - r-dplyr - r-magrittr @@ -50,8 +49,8 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' + license: 'LGPL (>=3)' summary: 'An R package estimates the correlations of orthologs and transposable elements between two species' description: 'TEKRABber is made to provide a user-friendly pipeline for comparing orthologs and transposable elements (TEs) between two species. It considers the orthology confidence between two species from BioMart to normalize expression counts and detect differentially expressed orthologs/TEs. Then it provides one to one correlation analysis for desired orthologs and TEs. There is also an app function to have a first insight on the result. Users can prepare orthologs/TEs RNA-seq expression data by their own preference to run TEKRABber following the data structure mentioned in the vignettes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' diff --git a/recipes/bioconductor-tenxbraindata/meta.yaml b/recipes/bioconductor-tenxbraindata/meta.yaml index db75aa07a19f1..58bd199e51f1a 100644 --- a/recipes/bioconductor-tenxbraindata/meta.yaml +++ b/recipes/bioconductor-tenxbraindata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "TENxBrainData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 74f64ec6654482787dcdc4d6edf085c0 + md5: 1fa1b93ab8d144b860c83dc5741490a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tenxbraindata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel, data.table, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tenxbraindata/post-link.sh b/recipes/bioconductor-tenxbraindata/post-link.sh index a8864917b11ce..5358e416f4cff 100644 --- a/recipes/bioconductor-tenxbraindata/post-link.sh +++ b/recipes/bioconductor-tenxbraindata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tenxbraindata-1.20.0" +installBiocDataPackage.sh "tenxbraindata-1.22.0" diff --git a/recipes/bioconductor-tenxbusdata/meta.yaml b/recipes/bioconductor-tenxbusdata/meta.yaml index 6460871ebb1bd..6b7ec47703e37 100644 --- a/recipes/bioconductor-tenxbusdata/meta.yaml +++ b/recipes/bioconductor-tenxbusdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "TENxBUSData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ef9324a12e6e70e28a16def5f6e8f8f + md5: 35be2bd3c806b055fc9463e8f135dd32 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tenxbusdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tenxbusdata/post-link.sh b/recipes/bioconductor-tenxbusdata/post-link.sh index 097377fc14852..dc2ed75ffb6a5 100644 --- a/recipes/bioconductor-tenxbusdata/post-link.sh +++ b/recipes/bioconductor-tenxbusdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tenxbusdata-1.14.0" +installBiocDataPackage.sh "tenxbusdata-1.16.0" diff --git a/recipes/bioconductor-tenxio/meta.yaml b/recipes/bioconductor-tenxio/meta.yaml index 3b6ee3533653c..d48c1bc5f0f43 100644 --- a/recipes/bioconductor-tenxio/meta.yaml +++ b/recipes/bioconductor-tenxio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "TENxIO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 156715deb84301cc0c1deaf2bea74a59 + md5: 98a845f55877d89b82b9a153fe54a41f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tenxio", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, DropletTestFiles, ExperimentHub, HDF5Array, knitr, RaggedExperiment, rhdf5, rmarkdown, Rsamtools, tinytest requirements: host: - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-r.utils - r-rcurl - r-readr run: - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-r.utils diff --git a/recipes/bioconductor-tenxpbmcdata/meta.yaml b/recipes/bioconductor-tenxpbmcdata/meta.yaml index 0663453a17cb5..7b29159a6f5b5 100644 --- a/recipes/bioconductor-tenxpbmcdata/meta.yaml +++ b/recipes/bioconductor-tenxpbmcdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "TENxPBMCData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6902ddadd45f76cce7e73228ed4bdcaf + md5: 3e6c961a01998667f37de542858dbc09 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tenxpbmcdata", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, BiocStyle, snow, BiocFileCache, BiocParallel requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tenxpbmcdata/post-link.sh b/recipes/bioconductor-tenxpbmcdata/post-link.sh index 21c88cd40324e..eb9fbb18d674f 100644 --- a/recipes/bioconductor-tenxpbmcdata/post-link.sh +++ b/recipes/bioconductor-tenxpbmcdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tenxpbmcdata-1.18.0" +installBiocDataPackage.sh "tenxpbmcdata-1.20.0" diff --git a/recipes/bioconductor-tenxplore/meta.yaml b/recipes/bioconductor-tenxplore/meta.yaml index cc37d8d989d1f..f2c5019b0eebf 100644 --- a/recipes/bioconductor-tenxplore/meta.yaml +++ b/recipes/bioconductor-tenxplore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "tenXplore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96c18d808ccb0106111ce4bf1d00ec5c + md5: 13e1778f8b644661a521bb832af6e7d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tenxplore", max_pin="x.x") }}' noarch: generic # Suggests: org.Hs.eg.db, testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-ontoproc >=1.22.0,<1.23.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-restfulse >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-ontoproc >=1.24.0,<1.25.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-restfulse >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrixstats - r-shiny run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-ontoproc >=1.22.0,<1.23.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-restfulse >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-ontoproc >=1.24.0,<1.25.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-restfulse >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrixstats - r-shiny diff --git a/recipes/bioconductor-tenxvisiumdata/meta.yaml b/recipes/bioconductor-tenxvisiumdata/meta.yaml index 449adeb44e95b..6c8051114d57a 100644 --- a/recipes/bioconductor-tenxvisiumdata/meta.yaml +++ b/recipes/bioconductor-tenxvisiumdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "TENxVisiumData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd391f3b1849f658578a44cfe2aec13b + md5: f578add429847efff027a61b1749b9b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tenxvisiumdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tenxvisiumdata/post-link.sh b/recipes/bioconductor-tenxvisiumdata/post-link.sh index 2d628409ccf36..1921065bf2398 100644 --- a/recipes/bioconductor-tenxvisiumdata/post-link.sh +++ b/recipes/bioconductor-tenxvisiumdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tenxvisiumdata-1.8.0" +installBiocDataPackage.sh "tenxvisiumdata-1.10.0" diff --git a/recipes/bioconductor-teqc/meta.yaml b/recipes/bioconductor-teqc/meta.yaml index a85b72af6bb87..062c2e16d092a 100644 --- a/recipes/bioconductor-teqc/meta.yaml +++ b/recipes/bioconductor-teqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.22.0" %} +{% set version = "4.24.0" %} {% set name = "TEQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1972bf594cded1f47f9fe7d9e6c9e2a0 + md5: 02976837ccda44f13a0a43b9de17ea81 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-teqc", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-hwriter run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-hwriter test: diff --git a/recipes/bioconductor-ternarynet/meta.yaml b/recipes/bioconductor-ternarynet/meta.yaml index 629108221b0ee..bd39c481f7479 100644 --- a/recipes/bioconductor-ternarynet/meta.yaml +++ b/recipes/bioconductor-ternarynet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "ternarynet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1aa77c1b9619ead34f9b06e00d761028 + md5: 1ee0ac867354eedf8cf756d94be52589 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ternarynet", max_pin="x.x") }}' # Suggests: testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-igraph - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-igraph build: diff --git a/recipes/bioconductor-terratcgadata/meta.yaml b/recipes/bioconductor-terratcgadata/meta.yaml index 2cf2e42ef005b..d5498e1fc2f25 100644 --- a/recipes/bioconductor-terratcgadata/meta.yaml +++ b/recipes/bioconductor-terratcgadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "terraTCGAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fceb4c4282a26c126a6b91f30c130904 + md5: b5803a78627bbe874b8cd8ae0a147979 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-terratcgadata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, withr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-anvil >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tcgautils >=1.20.0,<1.21.0' + - 'bioconductor-anvil >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tcgautils >=1.22.0,<1.23.0' - r-base - r-dplyr - r-readr - r-tidyr run: - - 'bioconductor-anvil >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tcgautils >=1.20.0,<1.21.0' + - 'bioconductor-anvil >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tcgautils >=1.22.0,<1.23.0' - r-base - r-dplyr - r-readr diff --git a/recipes/bioconductor-test1cdf/meta.yaml b/recipes/bioconductor-test1cdf/meta.yaml index a2679d123c71d..9cf00a9e907da 100644 --- a/recipes/bioconductor-test1cdf/meta.yaml +++ b/recipes/bioconductor-test1cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "test1cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8c94708b49ccc7bbf127485155970b9b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-test1cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-test2cdf/meta.yaml b/recipes/bioconductor-test2cdf/meta.yaml index 4ac7f876c924e..74ae9fa6eb04c 100644 --- a/recipes/bioconductor-test2cdf/meta.yaml +++ b/recipes/bioconductor-test2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "test2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0d1c20d6450dfc83d62214be9dc46b5f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-test2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-test3cdf/meta.yaml b/recipes/bioconductor-test3cdf/meta.yaml index 9316b144dff78..4f62a9f138b91 100644 --- a/recipes/bioconductor-test3cdf/meta.yaml +++ b/recipes/bioconductor-test3cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "test3cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9904e7fa6599f68400a9b77d0caa159a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-test3cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-test3probe/meta.yaml b/recipes/bioconductor-test3probe/meta.yaml index 06620f2d8c54c..4cf7c7451737f 100644 --- a/recipes/bioconductor-test3probe/meta.yaml +++ b/recipes/bioconductor-test3probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "test3probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ffcbfee4e5c486fd03b2b9b64820340c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-test3probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tfarm/meta.yaml b/recipes/bioconductor-tfarm/meta.yaml index 05573723829ec..f68855b990209 100644 --- a/recipes/bioconductor-tfarm/meta.yaml +++ b/recipes/bioconductor-tfarm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "TFARM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8cd4be3928a6737c36ae2a17d8d52d3 + md5: bf2876d47da6baa42642dc5492ef7a94 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tfarm", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, plyr requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-arules - r-base - r-fields - r-gplots - r-stringr run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-arules - r-base - r-fields diff --git a/recipes/bioconductor-tfbstools/meta.yaml b/recipes/bioconductor-tfbstools/meta.yaml index 21998ea8662db..73200d3f9cb99 100644 --- a/recipes/bioconductor-tfbstools/meta.yaml +++ b/recipes/bioconductor-tfbstools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "TFBSTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d0973f29eb2d02f3bbcdf438e79b6414 + md5: f2395c8153c4820e3cebb53a9eda94d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tfbstools", max_pin="x.x") }}' # Suggests: BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr(>= 1.11), testthat, JASPAR2016(>= 1.0.0), JASPAR2018(>= 1.0.0), rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-cner >=1.36.0,<1.37.0' - - 'bioconductor-dirichletmultinomial >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-cner >=1.38.0,<1.39.0' + - 'bioconductor-dirichletmultinomial >=1.44.0,<1.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-catools >=1.17.1' - 'r-dbi >=0.6' @@ -44,20 +45,20 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-cner >=1.36.0,<1.37.0' - - 'bioconductor-dirichletmultinomial >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-cner >=1.38.0,<1.39.0' + - 'bioconductor-dirichletmultinomial >=1.44.0,<1.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-catools >=1.17.1' - 'r-dbi >=0.6' diff --git a/recipes/bioconductor-tfea.chip/meta.yaml b/recipes/bioconductor-tfea.chip/meta.yaml index b3dc30610b2c9..de5695cd80ca7 100644 --- a/recipes/bioconductor-tfea.chip/meta.yaml +++ b/recipes/bioconductor-tfea.chip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "TFEA.ChIP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9c3bebfd9a9424c0585ba6351e1ebfca + md5: 86f7ae5bb16ceaf9fbdc01d0cc606c42 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tfea.chip", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2, DESeq2, BiocGenerics, ggrepel, rcompanion, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-dplyr - r-r.utils run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-dplyr - r-r.utils diff --git a/recipes/bioconductor-tfhaz/meta.yaml b/recipes/bioconductor-tfhaz/meta.yaml index 95a094ff1d190..62729c28422f7 100644 --- a/recipes/bioconductor-tfhaz/meta.yaml +++ b/recipes/bioconductor-tfhaz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "TFHAZ" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c80ec5e4711cc07bf27ff180942cc78c + md5: 4befbb77bb7eb52b220a2472010cab25 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tfhaz", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-orfik >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-orfik >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-orfik >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-orfik >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-tfutils/meta.yaml b/recipes/bioconductor-tfutils/meta.yaml index c5d9167c87b4c..e81f9833f5aea 100644 --- a/recipes/bioconductor-tfutils/meta.yaml +++ b/recipes/bioconductor-tfutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "TFutils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f91497509b64adadcb5babf7a2cc2f86 + md5: a2e83bbaafa0e47d7dbbd17385bd15fb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tfutils", max_pin="x.x") }}' noarch: generic # Suggests: knitr, data.table, testthat, AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges, S4Vectors, EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, GenomicFiles, GenomeInfoDb, SummarizedExperiment, UpSetR, ggplot2, png, gwascat, MotifDb, motifStack, RColorBrewer, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-dplyr - r-dt @@ -36,11 +37,11 @@ requirements: - r-rjson - r-shiny run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-dplyr - r-dt diff --git a/recipes/bioconductor-tidybulk/meta.yaml b/recipes/bioconductor-tidybulk/meta.yaml index 0840813a280b1..af300d3308e74 100644 --- a/recipes/bioconductor-tidybulk/meta.yaml +++ b/recipes/bioconductor-tidybulk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.2" %} {% set name = "tidybulk" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bdaa13b16dbafba7b0bbcc13ff4d810f + md5: e1a43f9392049059ec6b67930277df16 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tidybulk", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, testthat, vctrs, AnnotationDbi, BiocManager, Rsubread, e1071, edgeR, limma, org.Hs.eg.db, org.Mm.eg.db, sva, GGally, knitr, qpdf, covr, Seurat, KernSmooth, Rtsne, ggplot2, widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel, devtools, functional, survminer, tidySummarizedExperiment, markdown, uwot, matrixStats, igraph, EGSEA +# Suggests: BiocStyle, testthat, vctrs, AnnotationDbi, BiocManager, Rsubread, e1071, edgeR, limma, org.Hs.eg.db, org.Mm.eg.db, sva, GGally, knitr, qpdf, covr, Seurat, KernSmooth, Rtsne, ggplot2, widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel, devtools, functional, survminer, tidySummarizedExperiment, markdown, uwot, matrixStats, igraph, EGSEA, IRanges, here, glmmSeq, pbapply, pbmcapply, lme4, glmmTMB, MASS requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-crayon - - r-dplyr + - 'r-dplyr >=1.1.0' - r-lifecycle - r-magrittr + - r-matrix - r-purrr - r-readr - r-rlang @@ -39,16 +41,18 @@ requirements: - r-tibble - r-tidyr - r-tidyselect + - 'r-ttservice >=0.3.6' run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-crayon - - r-dplyr + - 'r-dplyr >=1.1.0' - r-lifecycle - r-magrittr + - r-matrix - r-purrr - r-readr - r-rlang @@ -58,6 +62,7 @@ requirements: - r-tibble - r-tidyr - r-tidyselect + - 'r-ttservice >=0.3.6' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tidysinglecellexperiment/meta.yaml b/recipes/bioconductor-tidysinglecellexperiment/meta.yaml index b73d09371bcbe..e37d659138088 100644 --- a/recipes/bioconductor-tidysinglecellexperiment/meta.yaml +++ b/recipes/bioconductor-tidysinglecellexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "tidySingleCellExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6cf2a2b42418731f758bce9df31de473 + md5: 4f0e61cb23c56df988e1a731a452eb2d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tidysinglecellexperiment", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, testthat, knitr, markdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, uwot, celldex, dittoSeq, EnsDb.Hsapiens.v86 +# Suggests: BiocStyle, testthat, knitr, rmarkdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, uwot, celldex, dittoSeq requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-dplyr @@ -34,6 +35,7 @@ requirements: - r-magrittr - r-matrix - r-pillar + - r-pkgconfig - r-plotly - r-purrr - r-rlang @@ -41,12 +43,12 @@ requirements: - r-tibble - r-tidyr - r-tidyselect - - r-ttservice + - 'r-ttservice >=0.3.8' - r-vctrs run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-dplyr @@ -57,6 +59,7 @@ requirements: - r-magrittr - r-matrix - r-pillar + - r-pkgconfig - r-plotly - r-purrr - r-rlang @@ -64,7 +67,7 @@ requirements: - r-tibble - r-tidyr - r-tidyselect - - r-ttservice + - 'r-ttservice >=0.3.8' - r-vctrs test: commands: @@ -73,6 +76,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Brings SingleCellExperiment to the Tidyverse' - description: 'tidySingleCellExperiment is an adapter that abstracts the ''SingleCellExperiment'' container in the form of a tibble and allows the data manipulation, plotting and nesting using ''tidyverse''.' + description: '''tidySingleCellExperiment'' is an adapter that abstracts the ''SingleCellExperiment'' container in the form of a ''tibble''. This allows *tidy* data manipulation, nesting, and plotting. For example, a ''tidySingleCellExperiment'' is directly compatible with functions from ''tidyverse'' packages `dplyr` and `tidyr`, as well as plotting with `ggplot2` and `plotly`. In addition, the package provides various utility functions specific to single-cell omics data analysis (e.g., aggregation of cell-level data to pseudobulks).' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-tidysummarizedexperiment/meta.yaml b/recipes/bioconductor-tidysummarizedexperiment/meta.yaml index 9f720354b8f60..e1c10a2c75d43 100644 --- a/recipes/bioconductor-tidysummarizedexperiment/meta.yaml +++ b/recipes/bioconductor-tidysummarizedexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "tidySummarizedExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4776d530e2487d78c6b502823d963c48 + md5: a7962f90a1d5e582e22a5c6e1f5e46da build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tidysummarizedexperiment", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, markdown requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-dplyr @@ -32,6 +33,7 @@ requirements: - r-lifecycle - r-magrittr - r-pillar + - r-pkgconfig - r-plotly - r-purrr - r-rlang @@ -39,10 +41,11 @@ requirements: - 'r-tibble >=3.0.4' - r-tidyr - r-tidyselect + - r-ttservice - r-vctrs run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-dplyr @@ -52,6 +55,7 @@ requirements: - r-lifecycle - r-magrittr - r-pillar + - r-pkgconfig - r-plotly - r-purrr - r-rlang @@ -59,6 +63,7 @@ requirements: - 'r-tibble >=3.0.4' - r-tidyr - r-tidyselect + - r-ttservice - r-vctrs test: commands: @@ -67,6 +72,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Brings SummarizedExperiment to the Tidyverse' - description: 'tidySummarizedExperiment is an adapter that abstracts the ''SummarizedExperiment'' container in the form of tibble and allows the data manipulation, plotting and nesting using ''tidyverse''' + description: 'The tidySummarizedExperiment package provides a set of tools for creating and manipulating tidy data representations of SummarizedExperiment objects. SummarizedExperiment is a widely used data structure in bioinformatics for storing high-throughput genomic data, such as gene expression or DNA sequencing data. The tidySummarizedExperiment package introduces a tidy framework for working with SummarizedExperiment objects. It allows users to convert their data into a tidy format, where each observation is a row and each variable is a column. This tidy representation simplifies data manipulation, integration with other tidyverse packages, and enables seamless integration with the broader ecosystem of tidy tools for data analysis.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-tigre/meta.yaml b/recipes/bioconductor-tigre/meta.yaml index eae63f5c1f1ff..3d755d26318d8 100644 --- a/recipes/bioconductor-tigre/meta.yaml +++ b/recipes/bioconductor-tigre/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "tigre" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0edc8e7589fc2380307610089d22178c + md5: d6bc46b9552c8c910c05c2ab705710d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tigre", max_pin="x.x") }}' # Suggests: drosgenome1.db, puma, lumi, BiocStyle, BiocManager requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dbi - r-gplots @@ -31,10 +32,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dbi - r-gplots diff --git a/recipes/bioconductor-tiledbarray/meta.yaml b/recipes/bioconductor-tiledbarray/meta.yaml index 2db05e47c4179..64c48ae9123a5 100644 --- a/recipes/bioconductor-tiledbarray/meta.yaml +++ b/recipes/bioconductor-tiledbarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "TileDBArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a54b516115c12a5cec2574c0b383f1a0 + md5: 7bb6ef67d882031ac2ebfcb3c1873dd2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tiledbarray", max_pin="x.x") }}' # Suggests: knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rcpp - r-tiledb - libblas - liblapack run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rcpp - r-tiledb diff --git a/recipes/bioconductor-tilingarray/meta.yaml b/recipes/bioconductor-tilingarray/meta.yaml index f34d6ad123d96..1cc59e0adddee 100644 --- a/recipes/bioconductor-tilingarray/meta.yaml +++ b/recipes/bioconductor-tilingarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "tilingArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3dad60f0e34a7b8edec674e76ef7373c + md5: ef9c26009f7990175b320386fcfeeb5c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tilingarray", max_pin="x.x") }}' requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-pixmap - r-rcolorbrewer @@ -30,10 +31,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-pixmap - r-rcolorbrewer diff --git a/recipes/bioconductor-timecourse/meta.yaml b/recipes/bioconductor-timecourse/meta.yaml index 58f5c9575973b..dac5e6130e637 100644 --- a/recipes/bioconductor-timecourse/meta.yaml +++ b/recipes/bioconductor-timecourse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "timecourse" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: feb399cff346d2361c9a1c47cc0df9e4 + md5: 4a760d4bcf875bb5c0069cbef4a1af32 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-timecourse", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-timecoursedata/meta.yaml b/recipes/bioconductor-timecoursedata/meta.yaml index c162f817abc10..96f0a9f45922b 100644 --- a/recipes/bioconductor-timecoursedata/meta.yaml +++ b/recipes/bioconductor-timecoursedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "timecoursedata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7f2ad9b14757098a934109a0597a630b + md5: a5b9f962c12d69003eff9b6949d2b0af build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-timecoursedata", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 1.0.0), knitr, rmarkdown, markdown, covr, BiocStyle requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-timecoursedata/post-link.sh b/recipes/bioconductor-timecoursedata/post-link.sh index b36c8fe9fe8cd..4e773c67621b2 100644 --- a/recipes/bioconductor-timecoursedata/post-link.sh +++ b/recipes/bioconductor-timecoursedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "timecoursedata-1.10.0" +installBiocDataPackage.sh "timecoursedata-1.12.0" diff --git a/recipes/bioconductor-timeomics/meta.yaml b/recipes/bioconductor-timeomics/meta.yaml index 79e6e5b19eaef..9c8c950e0f52f 100644 --- a/recipes/bioconductor-timeomics/meta.yaml +++ b/recipes/bioconductor-timeomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "timeOmics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd8990e7f9a92ec1208b598bc7091c37 + md5: ddea6709cf6d8d977b998f458e7938fb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-timeomics", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse, igraph, gplots requirements: host: - - 'bioconductor-mixomics >=6.24.0,<6.25.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' - r-base - r-dplyr - r-ggplot2 @@ -34,7 +35,7 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-mixomics >=6.24.0,<6.25.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-timerquant/meta.yaml b/recipes/bioconductor-timerquant/meta.yaml index 219c222b5396a..1a46726437cd3 100644 --- a/recipes/bioconductor-timerquant/meta.yaml +++ b/recipes/bioconductor-timerquant/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "TimerQuant" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8cbdff0672ae0d06372f36e5de1dc86c + md5: 7033d0ae9a0731af8bafecbbfa5398c8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-timerquant", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, reshape2, knitr, shinyBS requirements: @@ -37,7 +38,7 @@ requirements: - r-locfit - r-shiny - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-timerquant/post-link.sh b/recipes/bioconductor-timerquant/post-link.sh index 89a811d4052cc..c834f2b1641a0 100644 --- a/recipes/bioconductor-timerquant/post-link.sh +++ b/recipes/bioconductor-timerquant/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "timerquant-1.30.0" +installBiocDataPackage.sh "timerquant-1.32.0" diff --git a/recipes/bioconductor-timescape/meta.yaml b/recipes/bioconductor-timescape/meta.yaml index 4efb191116023..2b92ef17d1383 100644 --- a/recipes/bioconductor-timescape/meta.yaml +++ b/recipes/bioconductor-timescape/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "timescape" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3ed14459b64d92e1cb55934105941db0 + md5: 1a409bde946cb8ed4c7e8e6a334158de build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-timescape", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-timirgen/meta.yaml b/recipes/bioconductor-timirgen/meta.yaml index 41a7f31ddd10d..4e6c7b1d5d457 100644 --- a/recipes/bioconductor-timirgen/meta.yaml +++ b/recipes/bioconductor-timirgen/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.11.0" %} {% set name = "TimiRGeN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a5b8016f4edda9b0a5b863ce86204b98 + md5: 87bc148544059ef1b52ff839557d8a48 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-timirgen", max_pin="x.x") }}' noarch: generic # Suggests: BiocManager, kableExtra, knitr (>= 1.27), org.Hs.eg.db, org.Mm.eg.db, testthat, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-mfuzz >=2.60.0,<2.61.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' - - 'bioconductor-rwikipathways >=1.20.0,<1.21.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-mfuzz >=2.62.0,<2.63.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - 'bioconductor-rwikipathways >=1.22.0,<1.23.0' - r-base - 'r-dplyr >=0.8.4' - r-freqprof @@ -42,12 +43,12 @@ requirements: - 'r-stringr >=1.4.0' - 'r-tidyr >=1.0.2' run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-mfuzz >=2.60.0,<2.61.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' - - 'bioconductor-rwikipathways >=1.20.0,<1.21.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-mfuzz >=2.62.0,<2.63.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - 'bioconductor-rwikipathways >=1.22.0,<1.23.0' - r-base - 'r-dplyr >=0.8.4' - r-freqprof diff --git a/recipes/bioconductor-tin/meta.yaml b/recipes/bioconductor-tin/meta.yaml index 83630014fdd92..1acc38ee9a11d 100644 --- a/recipes/bioconductor-tin/meta.yaml +++ b/recipes/bioconductor-tin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "TIN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5693eb6bc1804b53b77dc4a3d58b14fb + md5: 33dbf5f6f5fada307f20f5a9b8d6f8a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tin", max_pin="x.x") }}' noarch: generic # Suggests: knitr, aroma.light, affxparser, RUnit, BiocGenerics requirements: host: - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-aroma.affymetrix - r-base - r-data.table @@ -29,7 +30,7 @@ requirements: - r-stringr - r-wgcna run: - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-aroma.affymetrix - r-base - r-data.table diff --git a/recipes/bioconductor-tinesath1cdf/meta.yaml b/recipes/bioconductor-tinesath1cdf/meta.yaml index cf5445ee14152..73e31ef2a3a0c 100644 --- a/recipes/bioconductor-tinesath1cdf/meta.yaml +++ b/recipes/bioconductor-tinesath1cdf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "tinesath1cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9e3235aa047fc3dc7d77437a0afa5b71 + md5: a58177f0ed4976f52370b35e13818ce3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tinesath1cdf", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tinesath1cdf/post-link.sh b/recipes/bioconductor-tinesath1cdf/post-link.sh index 5e3512aab7972..12e58ab694e6c 100644 --- a/recipes/bioconductor-tinesath1cdf/post-link.sh +++ b/recipes/bioconductor-tinesath1cdf/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tinesath1cdf-1.38.0" +installBiocDataPackage.sh "tinesath1cdf-1.40.0" diff --git a/recipes/bioconductor-tinesath1probe/meta.yaml b/recipes/bioconductor-tinesath1probe/meta.yaml index 894c1271e9b65..6f2f2c78341f2 100644 --- a/recipes/bioconductor-tinesath1probe/meta.yaml +++ b/recipes/bioconductor-tinesath1probe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "tinesath1probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d3dc0686f2651dff52a201923e73a751 + md5: abd9396a4f17a0044018702394b62933 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tinesath1probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tinesath1probe/post-link.sh b/recipes/bioconductor-tinesath1probe/post-link.sh index 116840a9029b2..1e35a8d90f622 100644 --- a/recipes/bioconductor-tinesath1probe/post-link.sh +++ b/recipes/bioconductor-tinesath1probe/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tinesath1probe-1.38.0" +installBiocDataPackage.sh "tinesath1probe-1.40.0" diff --git a/recipes/bioconductor-tissueenrich/meta.yaml b/recipes/bioconductor-tissueenrich/meta.yaml index e5835cf899280..e98619fb7169a 100644 --- a/recipes/bioconductor-tissueenrich/meta.yaml +++ b/recipes/bioconductor-tissueenrich/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "TissueEnrich" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 25b74b3d262fc3ccd8aded6ad6cc24c5 + md5: 5cc00925f523a6d82b216343e7f4b81a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tissueenrich", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-dplyr >=0.7.3' - 'r-ensurer >=1.1.0' - 'r-ggplot2 >=2.2.1' - 'r-tidyr >=0.8.0' run: - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-dplyr >=0.7.3' - 'r-ensurer >=1.1.0' diff --git a/recipes/bioconductor-tissuetreg/meta.yaml b/recipes/bioconductor-tissuetreg/meta.yaml index c8c75229a235e..78f702a37065e 100644 --- a/recipes/bioconductor-tissuetreg/meta.yaml +++ b/recipes/bioconductor-tissuetreg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "tissueTreg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9755c73b171a371afea8927b7d229a78 + md5: 5d975c08b7a19af832c4468ecb04c58b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tissuetreg", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq, SummarizedExperiment +# Suggests: BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq, SummarizedExperiment, ggplot2, reshape2 requirements: host: - r-base run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tissuetreg/post-link.sh b/recipes/bioconductor-tissuetreg/post-link.sh index 332df6472065a..407a1fd8a9db4 100644 --- a/recipes/bioconductor-tissuetreg/post-link.sh +++ b/recipes/bioconductor-tissuetreg/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tissuetreg-1.20.0" +installBiocDataPackage.sh "tissuetreg-1.22.0" diff --git a/recipes/bioconductor-titancna/meta.yaml b/recipes/bioconductor-titancna/meta.yaml index 3265c545f77b7..05bd29c21bf16 100644 --- a/recipes/bioconductor-titancna/meta.yaml +++ b/recipes/bioconductor-titancna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "TitanCNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9048b13844f8aa903f158f087e6199d5 + md5: ce40de587ae35a22c583019e6a85dbc6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-titancna", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-data.table >=1.10.4' - 'r-dplyr >=0.5.0' @@ -31,11 +32,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-data.table >=1.10.4' - 'r-dplyr >=0.5.0' diff --git a/recipes/bioconductor-tkwidgets/meta.yaml b/recipes/bioconductor-tkwidgets/meta.yaml index ddd9322e0b027..81145b1f4f180 100644 --- a/recipes/bioconductor-tkwidgets/meta.yaml +++ b/recipes/bioconductor-tkwidgets/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "tkWidgets" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b031940a2ac5599748b67348cc0c693 + md5: 044f7f3666426cbac3929eb9af1ce9d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tkwidgets", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, hgu95av2 requirements: host: - - 'bioconductor-dyndoc >=1.78.0,<1.79.0' - - 'bioconductor-widgettools >=1.78.0,<1.79.0' + - 'bioconductor-dyndoc >=1.80.0,<1.81.0' + - 'bioconductor-widgettools >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-dyndoc >=1.78.0,<1.79.0' - - 'bioconductor-widgettools >=1.78.0,<1.79.0' + - 'bioconductor-dyndoc >=1.80.0,<1.81.0' + - 'bioconductor-widgettools >=1.80.0,<1.81.0' - r-base test: commands: diff --git a/recipes/bioconductor-tloh/meta.yaml b/recipes/bioconductor-tloh/meta.yaml index abd9163085ee3..72917842a802d 100644 --- a/recipes/bioconductor-tloh/meta.yaml +++ b/recipes/bioconductor-tloh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "tLOH" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e6bea4dcf39c695fb5bc82f9be70e166 + md5: 1693fc28c2855f1af11159ec1051e2df build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tloh", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-bestnormalize - r-data.table @@ -35,9 +36,9 @@ requirements: - r-scales - r-stringr run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-bestnormalize - r-data.table diff --git a/recipes/bioconductor-tmexplorer/meta.yaml b/recipes/bioconductor-tmexplorer/meta.yaml index b009d57e535b4..016c668957311 100644 --- a/recipes/bioconductor-tmexplorer/meta.yaml +++ b/recipes/bioconductor-tmexplorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "TMExplorer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14411a5488789b44b63a2bc2b88cf33e + md5: 48b11be99739e61f54d9b442af739d49 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tmexplorer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-matrix run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-matrix - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tmexplorer/post-link.sh b/recipes/bioconductor-tmexplorer/post-link.sh index 5c6491ca754e0..7bb935ca65385 100644 --- a/recipes/bioconductor-tmexplorer/post-link.sh +++ b/recipes/bioconductor-tmexplorer/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tmexplorer-1.10.0" +installBiocDataPackage.sh "tmexplorer-1.12.0" diff --git a/recipes/bioconductor-tmixclust/meta.yaml b/recipes/bioconductor-tmixclust/meta.yaml index 5ab363076bb68..4542db2ccca41 100644 --- a/recipes/bioconductor-tmixclust/meta.yaml +++ b/recipes/bioconductor-tmixclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "TMixClust" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94b58831f2ce8e936e4c048369ce0bd6 + md5: 3e0e6852e806722f305ed45332c23179 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tmixclust", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-spem >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-spem >=1.42.0,<1.43.0' - r-base - r-cluster - r-flexclust @@ -31,9 +32,9 @@ requirements: - r-mvtnorm - r-zoo run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-spem >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-spem >=1.42.0,<1.43.0' - r-base - r-cluster - r-flexclust diff --git a/recipes/bioconductor-tnbc.cms/meta.yaml b/recipes/bioconductor-tnbc.cms/meta.yaml index 9a94c2592fff3..30db981ea98a1 100644 --- a/recipes/bioconductor-tnbc.cms/meta.yaml +++ b/recipes/bioconductor-tnbc.cms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "TNBC.CMS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46d15e4ca09ee831aff446cf62da575e + md5: a0cf09eed274d5cd812076d4f000e1bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tnbc.cms", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-forestplot @@ -36,8 +37,8 @@ requirements: - r-rcolorbrewer - r-survival run: - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-forestplot diff --git a/recipes/bioconductor-tnt/meta.yaml b/recipes/bioconductor-tnt/meta.yaml index 371856141ba03..eb73b9746ce6e 100644 --- a/recipes/bioconductor-tnt/meta.yaml +++ b/recipes/bioconductor-tnt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "TnT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e47b8605d300517fe691c3b8dc6c4124 + md5: 1afe4c0018eb0c5026c72dcfe2120045 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tnt", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures, shiny, BiocManager, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-htmlwidgets - r-jsonlite - r-knitr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-htmlwidgets diff --git a/recipes/bioconductor-toast/meta.yaml b/recipes/bioconductor-toast/meta.yaml index 8b3d92d6d7d5b..45a9580d13cd1 100644 --- a/recipes/bioconductor-toast/meta.yaml +++ b/recipes/bioconductor-toast/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "TOAST" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43fb520992045f40b5a505dcc9f20468 + md5: 7161d25bca2e95e8f83aea1f7d0bba6d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-toast", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix requirements: host: - - 'bioconductor-epidish >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-epidish >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-corpcor - r-doparallel @@ -33,9 +34,9 @@ requirements: - r-quadprog - r-tidyr run: - - 'bioconductor-epidish >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-epidish >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-corpcor - r-doparallel diff --git a/recipes/bioconductor-tofsimsdata/meta.yaml b/recipes/bioconductor-tofsimsdata/meta.yaml index 9e04978e4694b..d77787901bee4 100644 --- a/recipes/bioconductor-tofsimsdata/meta.yaml +++ b/recipes/bioconductor-tofsimsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "tofsimsData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5eccad99f9e3cdfb3813eb1243926142 + md5: 57fe35de7b03ee4f3ca07540949a6b5e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tofsimsdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, tools requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tofsimsdata/post-link.sh b/recipes/bioconductor-tofsimsdata/post-link.sh index 4d3ff1631bd37..2165ad029b1c3 100644 --- a/recipes/bioconductor-tofsimsdata/post-link.sh +++ b/recipes/bioconductor-tofsimsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tofsimsdata-1.28.0" +installBiocDataPackage.sh "tofsimsdata-1.30.0" diff --git a/recipes/bioconductor-tomatocdf/meta.yaml b/recipes/bioconductor-tomatocdf/meta.yaml index d6de1c8b55b55..18ad431e15afa 100644 --- a/recipes/bioconductor-tomatocdf/meta.yaml +++ b/recipes/bioconductor-tomatocdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "tomatocdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 200efc0637788d4bd3263fc9183c1aa6 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tomatocdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tomatoprobe/meta.yaml b/recipes/bioconductor-tomatoprobe/meta.yaml index b8621403ff105..da018906e552d 100644 --- a/recipes/bioconductor-tomatoprobe/meta.yaml +++ b/recipes/bioconductor-tomatoprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "tomatoprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 72020469f35c19399fd0be9eaffd8e77 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tomatoprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tomoda/meta.yaml b/recipes/bioconductor-tomoda/meta.yaml index 5dc661aa786e3..ef22967e0bd24 100644 --- a/recipes/bioconductor-tomoda/meta.yaml +++ b/recipes/bioconductor-tomoda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "tomoda" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9f15c43bd46119d2474f1224994e00b5 + md5: 49b8009bc1e0c7c7567b75be6fbde6c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tomoda", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggrepel @@ -30,7 +31,7 @@ requirements: - r-rtsne - r-umap run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-tomoseqr/meta.yaml b/recipes/bioconductor-tomoseqr/meta.yaml index 6d4c07423adc0..10dee3d515805 100644 --- a/recipes/bioconductor-tomoseqr/meta.yaml +++ b/recipes/bioconductor-tomoseqr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "tomoseqr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: abd0e85f5aaac89d5b86bd41a929b5df + md5: b881e4b272396cc4696d840658ec0ef5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tomoseqr", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-animation - r-base - r-dplyr @@ -33,7 +34,7 @@ requirements: - r-stringr - r-tibble run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-animation - r-base - r-dplyr diff --git a/recipes/bioconductor-top/meta.yaml b/recipes/bioconductor-top/meta.yaml index 2feec788acdb4..47810af59cec0 100644 --- a/recipes/bioconductor-top/meta.yaml +++ b/recipes/bioconductor-top/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "TOP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67cf959128704d96b21c8f04c0b94a2a + md5: af6712369d58630bdcc2b05d7dc06b52 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-top", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, Biobase, curatedOvarianData, ggbeeswarm, ggsci, survminer, tidyverse requirements: host: - - 'bioconductor-classifyr >=3.4.0,<3.5.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-classifyr >=3.6.0,<3.7.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-assertthat - r-base - r-caret @@ -50,8 +51,8 @@ requirements: - r-tidygraph - r-tidyr run: - - 'bioconductor-classifyr >=3.4.0,<3.5.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-classifyr >=3.6.0,<3.7.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-assertthat - r-base - r-caret diff --git a/recipes/bioconductor-topconfects/meta.yaml b/recipes/bioconductor-topconfects/meta.yaml index 9d70091f33ace..eb8e8b3ac1e1d 100644 --- a/recipes/bioconductor-topconfects/meta.yaml +++ b/recipes/bioconductor-topconfects/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "topconfects" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 30084c826e12d985bd00e1f4722ed54c + md5: 222a043b78c72f00d0dee0d6658d9284 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-topconfects", max_pin="x.x") }}' noarch: generic # Suggests: limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr, rmarkdown, BiocStyle requirements: diff --git a/recipes/bioconductor-topdownr/meta.yaml b/recipes/bioconductor-topdownr/meta.yaml index b7c363a52e8f7..ae46358e6c952 100644 --- a/recipes/bioconductor-topdownr/meta.yaml +++ b/recipes/bioconductor-topdownr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "topdownr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 51f610645fd9c00ef8b2719f9c16c476 + md5: 9aa08f9983d77f0794cd1cce6c1b8085 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-topdownr", max_pin="x.x") }}' noarch: generic # Suggests: topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat, BiocStyle, xml2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-ggplot2 >=2.2.1' - 'r-matrix >=1.4-2' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-ggplot2 >=2.2.1' - 'r-matrix >=1.4-2' diff --git a/recipes/bioconductor-topdownrdata/meta.yaml b/recipes/bioconductor-topdownrdata/meta.yaml index 6a7ed7f87e303..fd7e915295c84 100644 --- a/recipes/bioconductor-topdownrdata/meta.yaml +++ b/recipes/bioconductor-topdownrdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "topdownrdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c105c5a497f0270c574b757c55eea433 + md5: 28e746b858956bea0967344bfe363e7d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-topdownrdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-topdownr >=1.22.0,<1.23.0' + - 'bioconductor-topdownr >=1.24.0,<1.25.0' - r-base run: - - 'bioconductor-topdownr >=1.22.0,<1.23.0' + - 'bioconductor-topdownr >=1.24.0,<1.25.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-topdownrdata/post-link.sh b/recipes/bioconductor-topdownrdata/post-link.sh index 59251b5778340..b9614922d0e2b 100644 --- a/recipes/bioconductor-topdownrdata/post-link.sh +++ b/recipes/bioconductor-topdownrdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "topdownrdata-1.22.0" +installBiocDataPackage.sh "topdownrdata-1.24.0" diff --git a/recipes/bioconductor-topgo/meta.yaml b/recipes/bioconductor-topgo/meta.yaml index 1671a148aacec..1f934d3e45795 100644 --- a/recipes/bioconductor-topgo/meta.yaml +++ b/recipes/bioconductor-topgo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.52.0" %} +{% set version = "2.54.0" %} {% set name = "topGO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ca3c35559129d3dac81b5bbea27f1334 + md5: 62aeda25dfb89dfd466ddc749e52a422 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-topgo", max_pin="x.x") }}' noarch: generic # Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-dbi - r-lattice - r-matrixstats - 'r-sparsem >=0.73' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-dbi - r-lattice diff --git a/recipes/bioconductor-toxicogx/meta.yaml b/recipes/bioconductor-toxicogx/meta.yaml index 0c75eea26690c..94042954f8fd5 100644 --- a/recipes/bioconductor-toxicogx/meta.yaml +++ b/recipes/bioconductor-toxicogx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "ToxicoGx" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d6a576970e3646d89131996935da8c6 + md5: 2be22f48c0e155c94f9af6e6157a0333 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-toxicogx", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, testthat, BiocStyle, knitr, tinytex, devtools, PharmacoGx, xtable, markdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-coregx >=2.4.0,<2.5.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-catools @@ -42,13 +43,13 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-coregx >=2.4.0,<2.5.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-catools diff --git a/recipes/bioconductor-tpp/meta.yaml b/recipes/bioconductor-tpp/meta.yaml index 09ee0e38eb63d..573be703abd26 100644 --- a/recipes/bioconductor-tpp/meta.yaml +++ b/recipes/bioconductor-tpp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.28.0" %} +{% set version = "3.30.0" %} {% set name = "TPP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c1a08b79403e297acb280cf185a5855b + md5: 4a0ea50f7969045d710d3bfef371af62 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tpp", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biobroom >=1.32.0,<1.33.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biobroom >=1.34.0,<1.35.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-broom - r-data.table @@ -51,9 +52,9 @@ requirements: - r-venndiagram - r-vgam run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biobroom >=1.32.0,<1.33.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biobroom >=1.34.0,<1.35.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-broom - r-data.table diff --git a/recipes/bioconductor-tpp2d/meta.yaml b/recipes/bioconductor-tpp2d/meta.yaml index 906db98ec1583..c7c16fb5161cc 100644 --- a/recipes/bioconductor-tpp2d/meta.yaml +++ b/recipes/bioconductor-tpp2d/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "TPP2D" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c0319843d11772fdf950a5da576a4396 + md5: b10330822e1c629c04c568ab155b4ee1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tpp2d", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-doparallel - r-dplyr @@ -34,8 +35,8 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-doparallel - r-dplyr diff --git a/recipes/bioconductor-tracktables/meta.yaml b/recipes/bioconductor-tracktables/meta.yaml index b1b396afebb77..58b77cb8dd7a6 100644 --- a/recipes/bioconductor-tracktables/meta.yaml +++ b/recipes/bioconductor-tracktables/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "tracktables" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fddfa8e48265ccc4fa82c31e9a028457 + md5: 0726840a7d7c0252dc163cfe065cefa0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tracktables", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-rcolorbrewer - r-stringr - r-tractor.base - r-xml run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-rcolorbrewer - r-stringr diff --git a/recipes/bioconductor-trackviewer/meta.yaml b/recipes/bioconductor-trackviewer/meta.yaml index 9e959ab78163d..fa2657452ff77 100644 --- a/recipes/bioconductor-trackviewer/meta.yaml +++ b/recipes/bioconductor-trackviewer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.2" %} +{% set version = "1.38.1" %} {% set name = "trackViewer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a0be10d11abe74066bbfc8bd026c998a + md5: c0004e0bdb49b5d051e486f73a79a245 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-trackviewer", max_pin="x.x") }}' noarch: generic # Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown, motifStack requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-grimport - r-htmlwidgets @@ -43,21 +44,21 @@ requirements: - r-scales - r-strawr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-grimport - r-htmlwidgets diff --git a/recipes/bioconductor-tradeseq/meta.yaml b/recipes/bioconductor-tradeseq/meta.yaml index 1775b5406d426..cc3a8829e413c 100644 --- a/recipes/bioconductor-tradeseq/meta.yaml +++ b/recipes/bioconductor-tradeseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "tradeSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0bc724474103ac1b4f2f70e1bc65cda7 + md5: 5de25ecb5472b592837cd3937ff467c7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tradeseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, covr, clusterExperiment, DelayedMatrixStats requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-slingshot >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-slingshot >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' - r-base - r-ggplot2 - r-igraph @@ -43,14 +44,14 @@ requirements: - r-tibble - r-viridis run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-slingshot >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-slingshot >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' - r-base - r-ggplot2 - r-igraph diff --git a/recipes/bioconductor-trajectorygeometry/meta.yaml b/recipes/bioconductor-trajectorygeometry/meta.yaml index abd4de676597e..b8e7e01e6f772 100644 --- a/recipes/bioconductor-trajectorygeometry/meta.yaml +++ b/recipes/bioconductor-trajectorygeometry/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "TrajectoryGeometry" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 75158a6b92d1dc27580a4b7fd7ee6df1 + md5: a955410c20ec9cbae97e2d60a8c9b46f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-trajectorygeometry", max_pin="x.x") }}' noarch: generic # Suggests: dplyr, knitr, RColorBrewer, rmarkdown requirements: diff --git a/recipes/bioconductor-trajectoryutils/meta.yaml b/recipes/bioconductor-trajectoryutils/meta.yaml index dbac9c6191216..b5d17afac2d84 100644 --- a/recipes/bioconductor-trajectoryutils/meta.yaml +++ b/recipes/bioconductor-trajectoryutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "TrajectoryUtils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14277b55869f2bf8089e8608826b8f62 + md5: 8d29813e2befc86d418f15a3e594f37b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-trajectoryutils", max_pin="x.x") }}' noarch: generic # Suggests: BiocNeighbors, DelayedArray, DelayedMatrixStats, BiocParallel, testthat, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-matrix run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-matrix diff --git a/recipes/bioconductor-transcriptogramer/meta.yaml b/recipes/bioconductor-transcriptogramer/meta.yaml index 44fed3619f14a..987323d84bf10 100644 --- a/recipes/bioconductor-transcriptogramer/meta.yaml +++ b/recipes/bioconductor-transcriptogramer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "transcriptogramer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 98ed3dbfd9f93632f97f126df7db63cb + md5: 6c6b8c13ec29ef0e6e5552cbbd49f14d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-transcriptogramer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics # SystemRequirements: Java Runtime Environment (>= 6) requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-reder >=2.4.0,<2.5.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-data.table - r-dosnow @@ -37,10 +38,10 @@ requirements: - r-tidyr - openjdk run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-reder >=2.4.0,<2.5.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-data.table - r-dosnow diff --git a/recipes/bioconductor-transcriptr/meta.yaml b/recipes/bioconductor-transcriptr/meta.yaml index 61642c5bb8a20..9dbdcebc52b50 100644 --- a/recipes/bioconductor-transcriptr/meta.yaml +++ b/recipes/bioconductor-transcriptr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "transcriptR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 85c8f7e9e4267dc2fa7710e4db391144 + md5: a60b381f153539a74fa743f4f5edac43 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-transcriptr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chipseq >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chipseq >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - r-e1071 @@ -38,16 +39,16 @@ requirements: - r-proc - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chipseq >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chipseq >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - r-e1071 diff --git a/recipes/bioconductor-transformgampoi/meta.yaml b/recipes/bioconductor-transformgampoi/meta.yaml index 9e578d6873ee2..baecaa012883b 100644 --- a/recipes/bioconductor-transformgampoi/meta.yaml +++ b/recipes/bioconductor-transformgampoi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "transformGamPoi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 26f9f4a793ca9e8a3107831974857260 + md5: ec9683fa0efb74c2fae2e8721f265f0b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-transformgampoi", max_pin="x.x") }}' # Suggests: testthat, TENxPBMCData, scran, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-glmgampoi >=1.12.0,<1.13.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-glmgampoi >=1.14.0,<1.15.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-glmgampoi >=1.12.0,<1.13.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-glmgampoi >=1.14.0,<1.15.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-transite/meta.yaml b/recipes/bioconductor-transite/meta.yaml index 382d05db034b8..a5da73a5f57c1 100644 --- a/recipes/bioconductor-transite/meta.yaml +++ b/recipes/bioconductor-transite/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "transite" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fca53e0a3e5747c2fc0950fd8103234c + md5: 14ac71ed8ae01023f28aaed2d93f83b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-transite", max_pin="x.x") }}' # Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - 'r-dplyr >=0.7.6' - 'r-ggplot2 >=3.0.0' @@ -35,9 +36,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - 'r-dplyr >=0.7.6' - 'r-ggplot2 >=3.0.0' diff --git a/recipes/bioconductor-translatome/meta.yaml b/recipes/bioconductor-translatome/meta.yaml index 0087dc14cc434..500e767a03429 100644 --- a/recipes/bioconductor-translatome/meta.yaml +++ b/recipes/bioconductor-translatome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "tRanslatome" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a126654549808e184a6fd2b915bf8726 + md5: 6dabe57675cc4250a3b38f9d309a6816 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-translatome", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-anota >=1.48.0,<1.49.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-heatplus >=3.8.0,<3.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rankprod >=3.26.0,<3.27.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-anota >=1.50.0,<1.51.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-heatplus >=3.10.0,<3.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rankprod >=3.28.0,<3.29.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-gplots - r-plotrix run: - - 'bioconductor-anota >=1.48.0,<1.49.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-heatplus >=3.8.0,<3.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rankprod >=3.26.0,<3.27.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-anota >=1.50.0,<1.51.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-heatplus >=3.10.0,<3.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rankprod >=3.28.0,<3.29.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-gplots - r-plotrix diff --git a/recipes/bioconductor-transomics2cytoscape/meta.yaml b/recipes/bioconductor-transomics2cytoscape/meta.yaml index 82cdcca2598c5..656868a7687e9 100644 --- a/recipes/bioconductor-transomics2cytoscape/meta.yaml +++ b/recipes/bioconductor-transomics2cytoscape/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "transomics2cytoscape" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 19293f16a9fd2d5f64e7da38a9871ea0 + md5: 17325dd51ab6dfcc10dff97e98be6e91 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-transomics2cytoscape", max_pin="x.x") }}' noarch: generic # Suggests: testthat, roxygen2, knitr, BiocStyle, rmarkdown -# SystemRequirements: Cytoscape >= 3.9.1 +# SystemRequirements: Cytoscape >= 3.10.0 requirements: host: - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-dplyr + - r-pbapply - r-purrr - r-tibble run: - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-dplyr + - r-pbapply - r-purrr - r-tibble test: diff --git a/recipes/bioconductor-transview/meta.yaml b/recipes/bioconductor-transview/meta.yaml index 6dc1578b222ee..361542fb3d1c1 100644 --- a/recipes/bioconductor-transview/meta.yaml +++ b/recipes/bioconductor-transview/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "TransView" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a37e697eb98a5b1244563306577befb + md5: 39d2c9d2471bb732b294b68f3997eab2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-transview", max_pin="x.x") }}' # Suggests: RUnit, pasillaBamSubset, BiocManager # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-gplots - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-gplots build: diff --git a/recipes/bioconductor-traser/meta.yaml b/recipes/bioconductor-traser/meta.yaml index 3bba0ceecb4e6..cc53d2c42bb9d 100644 --- a/recipes/bioconductor-traser/meta.yaml +++ b/recipes/bioconductor-traser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "traseR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 472e1ac5ad2ccb5a07ea3b046a3727e8 + md5: 2af018d9562b672f6701de644617856b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-traser", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle,RUnit, BiocGenerics requirements: host: - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base run: - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base test: commands: diff --git a/recipes/bioconductor-traviz/build_failure.linux-64.yaml b/recipes/bioconductor-traviz/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..f1ffa5ab49f58 --- /dev/null +++ b/recipes/bioconductor-traviz/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 68cc108a4ebdc4305e3060a475e85276df2f244592455f0f29263f603f48ba51 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + libxdamage-cos6-x86_64: 1.1.3-h9b0a68f_1105 conda-forge + libxxf86vm-cos6-x86_64: 1.1.3-h9b0a68f_1105 conda-forge + mesa-dri-drivers-cos6-x86_64: 11.0.7-h9b0a68f_1105 conda-forge + mesa-dri1-drivers-cos6-x86_64: 7.11-h9b0a68f_1105 conda-forge + mesa-libgl-cos6-x86_64: 11.0.7-h9b0a68f_1105 conda-forge + mesa-libgl-devel-cos6-x86_64: 11.0.7-h9b0a68f_1105 conda-forge + pthread-stubs: 0.4-h36c2ea0_1001 conda-forge + sysroot_linux-64: 2.12-he073ed8_16 conda-forge + xorg-fixesproto: 5.0-h7f98852_1002 conda-forge + xorg-kbproto: 1.0.7-h7f98852_1002 conda-forge + xorg-libx11: 1.8.7-h8ee46fc_0 conda-forge + xorg-libxau: 1.0.11-hd590300_0 conda-forge + xorg-libxdmcp: 1.1.3-h7f98852_0 conda-forge + xorg-libxfixes: 5.0.3-h7f98852_1004 conda-forge + xorg-xextproto: 7.3.0-h0b41bf4_1003 conda-forge + xorg-xproto: 7.0.31-h7f98852_1007 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + INFO:conda_build.source:Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: traviz_1.8.0_65f0bdfccd.tar.gz + INFO:conda_build.source:Downloading source to cache: traviz_1.8.0_65f0bdfccd.tar.gz + Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/traviz_1.8.0.tar.gz + INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/traviz_1.8.0.tar.gz + Success + INFO:conda_build.source:Success + Extracting download + source tree in: /opt/conda/conda-bld/bioconductor-traviz_1703280230725/work + export PREFIX=/opt/conda/conda-bld/bioconductor-traviz_1703280230725/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-traviz_1703280230725/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-traviz_1703280230725/work + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-traviz_1703280230725/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library + * installing *source* package traviz ... + ** using staged installation + ** R + ** data + ** inst + ** byte-compile and prepare package for lazy loading + During startup - Warning message: + Setting LC_TIME failed, using "C" + Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. + ** help + *** installing help indices + ** building package indices + During startup - Warning message: + Setting LC_TIME failed, using "C" + ** installing vignettes + ** testing if installed package can be loaded from temporary location + During startup - Warning message: + Setting LC_TIME failed, using "C" + Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. + ** testing if installed package can be loaded from final location + During startup - Warning message: + Setting LC_TIME failed, using "C" + Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. + ** testing if installed package keeps a record of temporary installation path + * creating tarball + packaged installation of traviz as traviz_1.8.0_R_x86_64-conda-linux-gnu.tar.gz + * DONE (traviz) + + Resource usage statistics from building bioconductor-traviz: + Process count: 6 + CPU time: Sys=0:00:02.2, User=0:00:14.0 + Memory: 729.5M + Disk usage: 7.8K + Time elapsed: 0:00:19.3 + + + Packaging bioconductor-traviz + INFO:conda_build.build:Packaging bioconductor-traviz + Packaging bioconductor-traviz-1.8.0-r43hdfd78af_0 + INFO:conda_build.build:Packaging bioconductor-traviz-1.8.0-r43hdfd78af_0 + number of files: 32 + Fixing permissions + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2358, in build + newly_built_packages = bundlers[pkg_type](output_d, m, env, stats) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 1672, in bundle_conda + output['checksums'] = create_info_files(metadata, replacements, files, prefix=metadata.config.host_prefix) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 1272, in create_info_files + copy_license(m) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 762, in copy_license + generic_copy(m, "license", "license_file") + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 800, in generic_copy + raise ValueError( + ValueError: License file given in about/license_file (/opt/recipe/LICENSE) does not exist in source root dir or in recipe root dir (with meta.yaml) +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-traviz/meta.yaml b/recipes/bioconductor-traviz/meta.yaml index 893bd6a022e8c..dc8c8ce9fe896 100644 --- a/recipes/bioconductor-traviz/meta.yaml +++ b/recipes/bioconductor-traviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "traviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1958b9031af3abdc0e7018dc5a425cab + md5: 65f0bdfccd1faa4d9b61bef77e686155 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-traviz", max_pin="x.x") }}' noarch: generic # Suggests: scater, dplyr, testthat (>= 3.0.0), covr, S4Vectors, rmarkdown, knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-slingshot >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-slingshot >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-mgcv @@ -33,10 +34,10 @@ requirements: - r-rgl - r-viridis run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-slingshot >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-slingshot >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-mgcv @@ -59,6 +60,7 @@ about: license: 'MIT + file LICENSE' summary: 'Trajectory functions for visualization and interpretation.' description: 'traviz provides a suite of functions to plot trajectory related objects from Bioconductor packages. It allows plotting trajectories in reduced dimension, as well as averge gene expression smoothers as a function of pseudotime. Asides from general utility functions, traviz also allows plotting trajectories estimated by Slingshot, as well as smoothers estimated by tradeSeq. Furthermore, it allows for visualization of Slingshot trajectories using ggplot2.' + license_file: LICENSE extra: container: extended-base: true diff --git a/recipes/bioconductor-treeandleaf/meta.yaml b/recipes/bioconductor-treeandleaf/meta.yaml index 1e11fc2fd2bad..f5ae24bf9b602 100644 --- a/recipes/bioconductor-treeandleaf/meta.yaml +++ b/recipes/bioconductor-treeandleaf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "TreeAndLeaf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1e4076b533cb176f32d5498aa923752a + md5: 066beb0c7f15d3b6a853bcb68c682f73 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-treeandleaf", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr, geneplast, ggtree, ggplot2, dplyr, dendextend, RColorBrewer requirements: host: - - 'bioconductor-reder >=2.4.0,<2.5.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' - r-ape - r-base - r-igraph run: - - 'bioconductor-reder >=2.4.0,<2.5.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' - r-ape - r-base - r-igraph diff --git a/recipes/bioconductor-treeio/meta.yaml b/recipes/bioconductor-treeio/meta.yaml index 423d81525fb03..f7107d562170d 100644 --- a/recipes/bioconductor-treeio/meta.yaml +++ b/recipes/bioconductor-treeio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.1" %} +{% set version = "1.26.0" %} {% set name = "treeio" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b7d57a69b1ed07beec128f756261ff95 + md5: 583758f88bf0d8efa0749407f4183567 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-treeio", max_pin="x.x") }}' noarch: generic -# Suggests: Biostrings, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, testthat, tidyr, vroom, xml2, yaml, purrr +# Suggests: Biostrings, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, testthat, tidyr, vroom, xml2, yaml, purrr, cli requirements: host: - r-ape - r-base - - r-cli - r-dplyr - r-jsonlite - r-magrittr - r-rlang - r-tibble - - 'r-tidytree >=0.3.9' + - 'r-tidytree >=0.4.5' run: - r-ape - r-base - - r-cli - r-dplyr - r-jsonlite - r-magrittr - r-rlang - r-tibble - - 'r-tidytree >=0.3.9' + - 'r-tidytree >=0.4.5' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-treekor/meta.yaml b/recipes/bioconductor-treekor/meta.yaml index 62937050696a4..4eb3c5f1947e7 100644 --- a/recipes/bioconductor-treekor/meta.yaml +++ b/recipes/bioconductor-treekor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "treekoR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fdd0132593952c3eed82ef2d3c425d38 + md5: c1b9ce26aa6252f5cb1fe9cd07c3245f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-treekor", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-diffcyt >=1.20.0,<1.21.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-hopach >=2.60.0,<2.61.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-diffcyt >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-hopach >=2.62.0,<2.63.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-ape - r-base - r-data.table @@ -37,11 +38,11 @@ requirements: - r-patchwork - r-tidyr run: - - 'bioconductor-diffcyt >=1.20.0,<1.21.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-hopach >=2.60.0,<2.61.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-diffcyt >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-hopach >=2.62.0,<2.63.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-ape - r-base - r-data.table diff --git a/recipes/bioconductor-treesummarizedexperiment/meta.yaml b/recipes/bioconductor-treesummarizedexperiment/meta.yaml index a70dc907b0ff1..c507405f02a1b 100644 --- a/recipes/bioconductor-treesummarizedexperiment/meta.yaml +++ b/recipes/bioconductor-treesummarizedexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "TreeSummarizedExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a78e6a2d70a7fe7eaa12b1ca77bc832e + md5: 595842345af9cb4136aea17bdfdceb3f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-treesummarizedexperiment", max_pin="x.x") }}' noarch: generic # Suggests: ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treeio >=1.24.0,<1.25.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treeio >=1.26.0,<1.27.0' - r-ape - r-base - r-dplyr - r-rlang run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treeio >=1.24.0,<1.25.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treeio >=1.26.0,<1.27.0' - r-ape - r-base - r-dplyr diff --git a/recipes/bioconductor-treg/meta.yaml b/recipes/bioconductor-treg/meta.yaml index 29dffb113ff6f..dfeb2c614796a 100644 --- a/recipes/bioconductor-treg/meta.yaml +++ b/recipes/bioconductor-treg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "TREG" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90ee1d8dc737b34549f2ed915c97f833 + md5: d76ba3f3707e1810e6491d04013d6e7b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-treg", max_pin="x.x") }}' noarch: generic # Suggests: BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap, sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0), tibble, tidyr, SingleCellExperiment requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-purrr - r-rafalib run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-purrr diff --git a/recipes/bioconductor-trendy/meta.yaml b/recipes/bioconductor-trendy/meta.yaml index 61b8ce5881abe..aab3bd13ca6aa 100644 --- a/recipes/bioconductor-trendy/meta.yaml +++ b/recipes/bioconductor-trendy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.1" %} {% set name = "Trendy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ee8425a1de6db2081ac61e8252a6382 + md5: 00e5de9c46c116f4adc3caf3708608df build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-trendy", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, devtools requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dt - r-gplots @@ -32,9 +33,9 @@ requirements: - r-shiny - r-shinyfiles run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dt - r-gplots diff --git a/recipes/bioconductor-tress/meta.yaml b/recipes/bioconductor-tress/meta.yaml index 0af5bbd36984e..a3e9ebd429ed9 100644 --- a/recipes/bioconductor-tress/meta.yaml +++ b/recipes/bioconductor-tress/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "TRESS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b75e6e03b1b95b420e30bf9a7d8ed2d5 + md5: f0a0a2bbb1b989970231d8ac23ecfaaa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tress", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown,BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix - r-matrixstats run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix - r-matrixstats diff --git a/recipes/bioconductor-tricycle/meta.yaml b/recipes/bioconductor-tricycle/meta.yaml index c1b797eb2e8a2..e1fdcf85c0706 100644 --- a/recipes/bioconductor-tricycle/meta.yaml +++ b/recipes/bioconductor-tricycle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "tricycle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 33bba6617090b97414304b1b8697b0af + md5: 6a6a35c0a2cd9f279395e046b98a79f6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tricycle", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats, cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circular - r-dplyr @@ -36,13 +37,13 @@ requirements: - r-rcolorbrewer - r-scattermore run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circular - r-dplyr diff --git a/recipes/bioconductor-trigger/meta.yaml b/recipes/bioconductor-trigger/meta.yaml index c03ddcc99624f..e17c679057855 100644 --- a/recipes/bioconductor-trigger/meta.yaml +++ b/recipes/bioconductor-trigger/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "trigger" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7944a3dc498b593e76945f84bad02cfb + md5: d8cb2a76223f510ff08d9dcbf1d6210c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-trigger", max_pin="x.x") }}' requirements: host: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-corpcor - r-qtl - libblas - liblapack run: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-corpcor - r-qtl diff --git a/recipes/bioconductor-trio/meta.yaml b/recipes/bioconductor-trio/meta.yaml index 4170c29e5b51b..26c7056d86138 100644 --- a/recipes/bioconductor-trio/meta.yaml +++ b/recipes/bioconductor-trio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.38.0" %} +{% set version = "3.40.0" %} {% set name = "trio" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 659fd698018b3f4f5a9e7c6c56112ec4 + md5: cd87ad1a66fe181df937dd7a8edfda56 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-trio", max_pin="x.x") }}' noarch: generic # Suggests: haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation requirements: host: - - 'bioconductor-siggenes >=1.74.0,<1.75.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' - r-base - 'r-logicreg >=1.6.1' - r-survival run: - - 'bioconductor-siggenes >=1.74.0,<1.75.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' - r-base - 'r-logicreg >=1.6.1' - r-survival diff --git a/recipes/bioconductor-triplex/meta.yaml b/recipes/bioconductor-triplex/meta.yaml index 4954147c5afdf..008158d2d995b 100644 --- a/recipes/bioconductor-triplex/meta.yaml +++ b/recipes/bioconductor-triplex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "triplex" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 94c2754156770fdcc42d7ade7fe9b04c + md5: c66a6990486e7a4873b256d08eff9933 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-triplex", max_pin="x.x") }}' # Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-tripr/meta.yaml b/recipes/bioconductor-tripr/meta.yaml index d6d784902f055..727c7544b3cdb 100644 --- a/recipes/bioconductor-tripr/meta.yaml +++ b/recipes/bioconductor-tripr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "tripr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 115f039f182a6543c5bb99714e64401e + md5: 6682fcae99b44178612cdf8ebc48d045 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tripr", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, shinycssloaders, tidyverse, BiocManager, Biostrings, xtable, rlist, motifStack, knitr, rmarkdown, testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis, pryr requirements: diff --git a/recipes/bioconductor-trna/meta.yaml b/recipes/bioconductor-trna/meta.yaml index 9c111ee141651..1c6f912b7393d 100644 --- a/recipes/bioconductor-trna/meta.yaml +++ b/recipes/bioconductor-trna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "tRNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0870ee6c0b51fc8533a2128c939e9ec4 + md5: 52f5648075d6e9b6cb9ca2db65b5509f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-trna", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-modstrings >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structstrings >=1.16.0,<1.17.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-modstrings >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structstrings >=1.18.0,<1.19.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-ggplot2 - r-scales - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-modstrings >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structstrings >=1.16.0,<1.17.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-modstrings >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structstrings >=1.18.0,<1.19.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-ggplot2 - r-scales diff --git a/recipes/bioconductor-trnadbimport/meta.yaml b/recipes/bioconductor-trnadbimport/meta.yaml index f878de839dcbb..4306e7ec1e88a 100644 --- a/recipes/bioconductor-trnadbimport/meta.yaml +++ b/recipes/bioconductor-trnadbimport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "tRNAdbImport" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7fe475fbdfc05e6a9d1593d6289f3da + md5: 4610dcee69d8555572652b0193cc5cd3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-trnadbimport", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-modstrings >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structstrings >=1.16.0,<1.17.0' - - 'bioconductor-trna >=1.18.0,<1.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-modstrings >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structstrings >=1.18.0,<1.19.0' + - 'bioconductor-trna >=1.20.0,<1.21.0' - r-base - r-httr - r-stringr - r-xml2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-modstrings >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structstrings >=1.16.0,<1.17.0' - - 'bioconductor-trna >=1.18.0,<1.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-modstrings >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structstrings >=1.18.0,<1.19.0' + - 'bioconductor-trna >=1.20.0,<1.21.0' - r-base - r-httr - r-stringr diff --git a/recipes/bioconductor-trnascanimport/meta.yaml b/recipes/bioconductor-trnascanimport/meta.yaml index ce72bfc877041..87b8afa53958f 100644 --- a/recipes/bioconductor-trnascanimport/meta.yaml +++ b/recipes/bioconductor-trnascanimport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "tRNAscanImport" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,43 +11,44 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc67c78b9d8ec78f964b095933f36a30 + md5: 49f872c7de9b6cba139c7758330efa8c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-trnascanimport", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2, BSgenome.Scerevisiae.UCSC.sacCer3 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structstrings >=1.16.0,<1.17.0' - - 'bioconductor-trna >=1.18.0,<1.19.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structstrings >=1.18.0,<1.19.0' + - 'bioconductor-trna >=1.20.0,<1.21.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structstrings >=1.16.0,<1.17.0' - - 'bioconductor-trna >=1.18.0,<1.19.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structstrings >=1.18.0,<1.19.0' + - 'bioconductor-trna >=1.20.0,<1.21.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-stringr test: diff --git a/recipes/bioconductor-tronco/meta.yaml b/recipes/bioconductor-tronco/meta.yaml index 36d229b2a642e..58d3d0dadd395 100644 --- a/recipes/bioconductor-tronco/meta.yaml +++ b/recipes/bioconductor-tronco/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "TRONCO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80ed49d7d0ed5d5078c3029fdefed2e4 + md5: 0e137e734d0e5552bdcaa25ccdd4df08 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tronco", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways, magick requirements: host: - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-bnlearn - r-circlize @@ -37,7 +38,7 @@ requirements: - r-scales - r-xtable run: - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-bnlearn - r-circlize diff --git a/recipes/bioconductor-tsar/build.sh b/recipes/bioconductor-tsar/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tsar/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tsar/meta.yaml b/recipes/bioconductor-tsar/meta.yaml new file mode 100644 index 0000000000000..b6aae8910eb01 --- /dev/null +++ b/recipes/bioconductor-tsar/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.0.0" %} +{% set name = "TSAR" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7cc8589151c5b03e247590bbd7dc04dd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tsar", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - r-base + - 'r-dplyr >=1.0.7' + - 'r-ggplot2 >=3.3.5' + - 'r-ggpubr >=0.4.0' + - 'r-jsonlite >=1.8.7' + - 'r-magrittr >=2.0.3' + - 'r-mgcv >=1.8.38' + - 'r-minpack.lm >=1.2.3' + - 'r-openxlsx >=4.2.5.2' + - 'r-plotly >=4.10.2' + - 'r-readxl >=1.4.0' + - 'r-rhandsontable >=0.3.8' + - 'r-shiny >=1.7.4.1' + - 'r-shinyjs >=2.1.0' + - 'r-shinywidgets >=0.7.6' + - 'r-stringr >=1.4.0' + - 'r-tidyr >=1.1.4' + run: + - r-base + - 'r-dplyr >=1.0.7' + - 'r-ggplot2 >=3.3.5' + - 'r-ggpubr >=0.4.0' + - 'r-jsonlite >=1.8.7' + - 'r-magrittr >=2.0.3' + - 'r-mgcv >=1.8.38' + - 'r-minpack.lm >=1.2.3' + - 'r-openxlsx >=4.2.5.2' + - 'r-plotly >=4.10.2' + - 'r-readxl >=1.4.0' + - 'r-rhandsontable >=0.3.8' + - 'r-shiny >=1.7.4.1' + - 'r-shinyjs >=2.1.0' + - 'r-shinywidgets >=0.7.6' + - 'r-stringr >=1.4.0' + - 'r-tidyr >=1.1.4' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: AGPL-3 + summary: 'Thermal Shift Analysis in R' + description: 'This package automates analysis workflow for Thermal Shift Analysis (TSAS) data. Processing, analyzing, and visualizing data through both shiny applications and command lines. Package aims to simplify data analysis and offer front to end workflow, from raw data to multiple trial analysis.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + diff --git a/recipes/bioconductor-tscan/meta.yaml b/recipes/bioconductor-tscan/meta.yaml index 4cf037f190b49..2ea54e7791685 100644 --- a/recipes/bioconductor-tscan/meta.yaml +++ b/recipes/bioconductor-tscan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "TSCAN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ac450a8f8e95d90e0da330379af5bb0 + md5: 018be0d6197c80dbf2ce7832a3f9c49d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tscan", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' - r-base - r-combinat - r-fastica @@ -38,11 +39,11 @@ requirements: - r-plyr - r-shiny run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' - r-base - r-combinat - r-fastica diff --git a/recipes/bioconductor-ttgsea/meta.yaml b/recipes/bioconductor-ttgsea/meta.yaml index f9a1edcf172c9..9266a10fd6ed4 100644 --- a/recipes/bioconductor-ttgsea/meta.yaml +++ b/recipes/bioconductor-ttgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ttgsea" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 666f5cb46746a27a71312a8bedee2a49 + md5: 0b38c9baea88905217b9ed667c80c26f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ttgsea", max_pin="x.x") }}' noarch: generic # Suggests: fgsea, knitr, testthat, reticulate, rmarkdown requirements: diff --git a/recipes/bioconductor-ttmap/meta.yaml b/recipes/bioconductor-ttmap/meta.yaml index af509427b8eb8..bcb28bc41745f 100644 --- a/recipes/bioconductor-ttmap/meta.yaml +++ b/recipes/bioconductor-ttmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "TTMap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 053ab5b1d1b45af48c5338ebffb4eaf8 + md5: 9fb52b78486eff55cc91ef0f8116633b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ttmap", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, airway requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-colorramps - r-rgl run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-colorramps - r-rgl diff --git a/recipes/bioconductor-tuberculosis/meta.yaml b/recipes/bioconductor-tuberculosis/meta.yaml index b9e7d08b36705..019d16095c2ba 100644 --- a/recipes/bioconductor-tuberculosis/meta.yaml +++ b/recipes/bioconductor-tuberculosis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "tuberculosis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9f3fd16d5debb8705f56bf714fc3e860 + md5: 154cd343b8fba727ecf80a671a6a112d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tuberculosis", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, ggplot2, hrbrthemes, knitr, readr, rmarkdown, scater, usethis, utils requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-magrittr @@ -34,10 +35,10 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-magrittr @@ -47,7 +48,7 @@ requirements: - r-tibble - r-tidyr - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tuberculosis/post-link.sh b/recipes/bioconductor-tuberculosis/post-link.sh index 5d70a601472ac..387c3ba762b5d 100644 --- a/recipes/bioconductor-tuberculosis/post-link.sh +++ b/recipes/bioconductor-tuberculosis/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tuberculosis-1.6.0" +installBiocDataPackage.sh "tuberculosis-1.8.0" diff --git a/recipes/bioconductor-tumourmethdata/meta.yaml b/recipes/bioconductor-tumourmethdata/meta.yaml new file mode 100644 index 0000000000000..0258769ad47df --- /dev/null +++ b/recipes/bioconductor-tumourmethdata/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.0.0" %} +{% set name = "TumourMethData" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7b4ba6a8a59379a3b7f368e6c26fa0a6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tumourmethdata", max_pin="x.x") }}' + noarch: generic +# Suggests: ggplot2, knitr, rmarkdown +requirements: + host: + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-r.utils + run: + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-r.utils + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A Collection of DNA Methylation Datasets for Human Tumour Samples and Matching Normal Samples' + description: 'TumourMethData collects tumour methylation data from a variety of different tumour types (and also matching normal samples where available) and produced with different technologies (e.g. WGBS, RRBS and methylation arrays) and provides them as RangedSummarizedExperiments. This facilitates easy extraction of methylation data for regions of interest across different tumour types and studies.' + diff --git a/recipes/bioconductor-tumourmethdata/post-link.sh b/recipes/bioconductor-tumourmethdata/post-link.sh new file mode 100644 index 0000000000000..8e6c2a8a145a1 --- /dev/null +++ b/recipes/bioconductor-tumourmethdata/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "tumourmethdata-1.0.0" diff --git a/recipes/bioconductor-tumourmethdata/pre-unlink.sh b/recipes/bioconductor-tumourmethdata/pre-unlink.sh new file mode 100644 index 0000000000000..6eb78cbb96c43 --- /dev/null +++ b/recipes/bioconductor-tumourmethdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TumourMethData diff --git a/recipes/bioconductor-turbonorm/meta.yaml b/recipes/bioconductor-turbonorm/meta.yaml index e5b09163eae71..0818a2addd0ac 100644 --- a/recipes/bioconductor-turbonorm/meta.yaml +++ b/recipes/bioconductor-turbonorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "TurboNorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 82bdd2f9cb32c4366ba0c8983e31acc8 + md5: 6df6da83bc36e4ce202d91888feaafa7 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, affydata + run_exports: '{{ pin_subpackage("bioconductor-turbonorm", max_pin="x.x") }}' +# Suggests: BiocStyle, affydata, hgu95av2cdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-convert >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-convert >=1.78.0,<1.79.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-lattice - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-convert >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-convert >=1.78.0,<1.79.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-lattice build: diff --git a/recipes/bioconductor-tvtb/meta.yaml b/recipes/bioconductor-tvtb/meta.yaml index d7bcadb51de52..6955abe0f5030 100644 --- a/recipes/bioconductor-tvtb/meta.yaml +++ b/recipes/bioconductor-tvtb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "TVTB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,51 +11,52 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3e1e1dc3b593cb5f838eb3a40ffb59d0 + md5: 64da00f3c21bf3f9a82dc32e451395a1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tvtb", max_pin="x.x") }}' noarch: generic # Suggests: EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander requirements: host: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-ensemblvep >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-ensemblvep >=1.44.0,<1.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggally - r-ggplot2 - r-reshape2 run: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-ensemblvep >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-ensemblvep >=1.44.0,<1.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggally - r-ggplot2 diff --git a/recipes/bioconductor-tweedeseq/meta.yaml b/recipes/bioconductor-tweedeseq/meta.yaml index 646f74165d5b7..2005ab0221e0d 100644 --- a/recipes/bioconductor-tweedeseq/meta.yaml +++ b/recipes/bioconductor-tweedeseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.45.0" %} +{% set version = "1.48.0" %} {% set name = "tweeDEseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d9cc6b9ec2db1052d2ed270dbb1f6ec1 + md5: 1a919ba1b3c5709068bc126336b77826 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tweedeseq", max_pin="x.x") }}' # Suggests: tweeDEseqCountData, xtable requirements: host: - - 'bioconductor-cqn >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-cqn >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-mass + - 'r-rcpp >=1.0.10' - libblas - liblapack run: - - 'bioconductor-cqn >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-cqn >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-mass + - 'r-rcpp >=1.0.10' build: - {{ compiler('c') }} + - {{ compiler('cxx') }} - make test: commands: @@ -43,7 +47,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'RNA-seq data analysis using the Poisson-Tweedie family of distributions' - description: 'Differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions.' + description: 'Differential expression analysis of RNA-seq using the Poisson-Tweedie (PT) family of distributions. PT distributions are described by a mean, a dispersion and a shape parameter and include Poisson and NB distributions, among others, as particular cases. An important feature of this family is that, while the Negative Binomial (NB) distribution only allows a quadratic mean-variance relationship, the PT distributions generalizes this relationship to any orde.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: identifiers: diff --git a/recipes/bioconductor-tweedeseqcountdata/build_failure.linux-64.yaml b/recipes/bioconductor-tweedeseqcountdata/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..3e36ab5993f41 --- /dev/null +++ b/recipes/bioconductor-tweedeseqcountdata/build_failure.linux-64.yaml @@ -0,0 +1,44 @@ +recipe_sha: e9ea10dec9b205dbce587c85515bdb5db1c152a2def749ed83d0b124ea0cec27 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + WARNING:conda_build.build:No files or script found for output bioconductor-tweedeseqcountdata +category: |- + source download error +log: |- + 08:56:10 BIOCONDA INFO (OUT) Downloading https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tweeDEseqCountData_1.40.0.tar.gz + 08:56:10 BIOCONDA INFO (OUT) INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tweeDEseqCountData_1.40.0.tar.gz + 08:56:11 BIOCONDA INFO (OUT) Success + 08:56:11 BIOCONDA INFO (OUT) INFO:conda_build.source:Success + 08:56:11 BIOCONDA INFO (OUT) Extracting download + 08:56:11 BIOCONDA INFO (OUT) source tree in: /opt/conda/conda-bld/bioconductor-tweedeseqcountdata_1702025598887/work + 08:56:11 BIOCONDA INFO (OUT) Packaging bioconductor-tweedeseqcountdata + 08:56:11 BIOCONDA INFO (OUT) INFO:conda_build.build:Packaging bioconductor-tweedeseqcountdata + 08:56:11 BIOCONDA INFO (OUT) Packaging bioconductor-tweedeseqcountdata-1.40.0-r43hdfd78af_0 + 08:56:11 BIOCONDA INFO (OUT) INFO:conda_build.build:Packaging bioconductor-tweedeseqcountdata-1.40.0-r43hdfd78af_0 + 08:56:11 BIOCONDA INFO (OUT) No files or script found for output bioconductor-tweedeseqcountdata + 08:56:11 BIOCONDA INFO (OUT) WARNING:conda_build.build:No files or script found for output bioconductor-tweedeseqcountdata + 08:56:12 BIOCONDA INFO (OUT) number of files: 2 + 08:56:12 BIOCONDA INFO (OUT) Fixing permissions + 08:56:12 BIOCONDA INFO (OUT) Traceback (most recent call last): + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/bin/conda-mambabuild", line 10, in + 08:56:12 BIOCONDA INFO (OUT) sys.exit(main()) + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + 08:56:12 BIOCONDA INFO (OUT) call_conda_build(action, config) + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + 08:56:12 BIOCONDA INFO (OUT) result = api.build( + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + 08:56:12 BIOCONDA INFO (OUT) return build_tree( + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + 08:56:12 BIOCONDA INFO (OUT) packages_from_this = build(metadata, stats, + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2358, in build + 08:56:12 BIOCONDA INFO (OUT) newly_built_packages = bundlers[pkg_type](output_d, m, env, stats) + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 1672, in bundle_conda + 08:56:12 BIOCONDA INFO (OUT) output['checksums'] = create_info_files(metadata, replacements, files, prefix=metadata.config.host_prefix) + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 1272, in create_info_files + 08:56:12 BIOCONDA INFO (OUT) copy_license(m) + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 762, in copy_license + 08:56:12 BIOCONDA INFO (OUT) generic_copy(m, "license", "license_file") + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 800, in generic_copy + 08:56:12 BIOCONDA INFO (OUT) raise ValueError( + 08:56:12 BIOCONDA INFO (OUT) ValueError: License file given in about/license_file (/opt/recipe/LICENSE) does not exist in source root dir or in recipe root dir (with meta.yaml) + .08:56:20 BIOCONDA ERROR COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /tmp/tmpbp4seh01/build_script.bash:/opt/build_script.bash -v /opt/mambaforge/envs/bioconda/conda-bld/:/opt/host-conda-bld -v /home/runner/work/bioconda-recipes/bioconda-recipes/recipes/bioconductor-tweedeseqcountdata:/opt/recipe -e LANG=C.UTF-8 -e HOST_USER_ID=1001 quay.io/bioconda/bioconda-utils-build-env-cos7:2.11.0 /bin/bash /opt/build_script.bash diff --git a/recipes/bioconductor-tweedeseqcountdata/meta.yaml b/recipes/bioconductor-tweedeseqcountdata/meta.yaml index e98b6cb1fc0f6..4cec84b4097ed 100644 --- a/recipes/bioconductor-tweedeseqcountdata/meta.yaml +++ b/recipes/bioconductor-tweedeseqcountdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "tweeDEseqCountData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b48baebaa2abe35419bad4110d7523ec + md5: d63e819cedf93ffbe115ed518bc9feaf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tweedeseqcountdata", max_pin="x.x") }}' noarch: generic +# Suggests: knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>=2)' + license: 'MIT + file LICENSE' summary: 'RNA-seq count data employed in the vignette of the tweeDEseq package' description: 'RNA-seq count data from Pickrell et al. (2010) employed to illustrate the use of the Poisson-Tweedie family of distributions with the tweeDEseq package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + license_file: LICENSE diff --git a/recipes/bioconductor-tweedeseqcountdata/post-link.sh b/recipes/bioconductor-tweedeseqcountdata/post-link.sh index ee220691d0a70..5418d98cd3da2 100644 --- a/recipes/bioconductor-tweedeseqcountdata/post-link.sh +++ b/recipes/bioconductor-tweedeseqcountdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tweedeseqcountdata-1.38.0" +installBiocDataPackage.sh "tweedeseqcountdata-1.40.0" diff --git a/recipes/bioconductor-twilight/meta.yaml b/recipes/bioconductor-twilight/meta.yaml index 4c5e88db6a0e8..42a74a2994831 100644 --- a/recipes/bioconductor-twilight/meta.yaml +++ b/recipes/bioconductor-twilight/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "twilight" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9b97614549c3048f37ee8db280fe7602 + md5: fa6b01126ace9423edfc04757f6392b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-twilight", max_pin="x.x") }}' # Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-twoddpcr/meta.yaml b/recipes/bioconductor-twoddpcr/meta.yaml index 4a2997ce8842d..1de09201d6a1c 100644 --- a/recipes/bioconductor-twoddpcr/meta.yaml +++ b/recipes/bioconductor-twoddpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "twoddpcr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 598cbdea40a78c70568965c4a87019c4 + md5: bbdb2cd12a3bd6f756b700d1216043ee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-twoddpcr", max_pin="x.x") }}' noarch: generic # Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-class - r-ggplot2 @@ -30,7 +31,7 @@ requirements: - r-scales - r-shiny run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-class - r-ggplot2 diff --git a/recipes/bioconductor-txcutr/meta.yaml b/recipes/bioconductor-txcutr/meta.yaml index 708de4be2a766..0e45c92ea1d02 100644 --- a/recipes/bioconductor-txcutr/meta.yaml +++ b/recipes/bioconductor-txcutr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "txcutr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: da702f8e8c123e0745674ba4610a1a05 + md5: 10d81d02156a45cebc08845455180010 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txcutr", max_pin="x.x") }}' noarch: generic # Suggests: RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown, testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, BSgenome.Scerevisiae.UCSC.sacCer3 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml index 8011c9090a8ad..a6886a0920dd4 100644 --- a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.0.1" %} {% set name = "TxDb.Athaliana.BioMart.plantsmart22" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3bab54295e300fedba99eef521220e50 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.athaliana.biomart.plantsmart22", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml index 2ff8cad569c54..eda07b96d60d3 100644 --- a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.1.3" %} {% set name = "TxDb.Athaliana.BioMart.plantsmart25" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: eb007c07317b9717c76949e5ed999978 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.athaliana.biomart.plantsmart25", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml index 9aba3d36ac6ed..63dab73960eb5 100644 --- a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Athaliana.BioMart.plantsmart28" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9ed52284f01e08fc382db179b544bb17 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.athaliana.biomart.plantsmart28", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart51/meta.yaml b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart51/meta.yaml index 2e048e1293d01..d69be5548db43 100644 --- a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart51/meta.yaml +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart51/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.0" %} {% set name = "TxDb.Athaliana.BioMart.plantsmart51" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c623af555537bfd9958f8f9573308103 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.athaliana.biomart.plantsmart51", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml b/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml index 46d445c651fb0..4a642c4756fcb 100644 --- a/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Btaurus.UCSC.bosTau8.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2112b91fbecabf9c89d1b0a48d88ce03 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.btaurus.ucsc.bostau8.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.btaurus.ucsc.bostau9.refgene/meta.yaml b/recipes/bioconductor-txdb.btaurus.ucsc.bostau9.refgene/meta.yaml index 7f89af6557ccc..a6ba08db8eca3 100644 --- a/recipes/bioconductor-txdb.btaurus.ucsc.bostau9.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.btaurus.ucsc.bostau9.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "TxDb.Btaurus.UCSC.bosTau9.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fe443d123b0b788e1e450f4e60036788 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.btaurus.ucsc.bostau9.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/meta.yaml b/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/meta.yaml index 1db5d62f78fb1..b4921754ff83d 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.15.0" %} {% set name = "TxDb.Celegans.UCSC.ce11.ensGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1b4d61d06ac8acb27e57d1fafc5b79ce build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.celegans.ucsc.ce11.ensgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml index 28e829fb1aca1..25dfa74d6898a 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.6" %} {% set name = "TxDb.Celegans.UCSC.ce11.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3765169432e745aff5e85afd239066ca build: - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.celegans.ucsc.ce11.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml index 957e6b067aaf1..039511fff6c9e 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Celegans.UCSC.ce6.ensGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 215c2edd440a3df8229fe6a75b431aa8 build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.celegans.ucsc.ce6.ensgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml index c647963377fb5..18ad135c029fc 100644 --- a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.11.0" %} {% set name = "TxDb.Cfamiliaris.UCSC.canFam3.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: bf6af84c14a30ad5d01f3678246b1180 build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene/meta.yaml b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene/meta.yaml index c45c3264a26d4..b46d02cb2c06d 100644 --- a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.0" %} {% set name = "TxDb.Cfamiliaris.UCSC.canFam4.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0b47072fa79cf8e99f8563002a0998cb build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene/meta.yaml b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene/meta.yaml index 65c1b1d17f91e..ddec9ac42b39b 100644 --- a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.0" %} {% set name = "TxDb.Cfamiliaris.UCSC.canFam5.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fc3d84569c092b74e5e0bccb785db8b6 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene/meta.yaml b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene/meta.yaml index 1a6043e0ea30e..59b9744aeb5b0 100644 --- a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.17.0" %} {% set name = "TxDb.Cfamiliaris.UCSC.canFam6.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9279204329323191fbb72717a57b13aa build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml index c42688c4f3d01..d1f4e9fba8f5e 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Dmelanogaster.UCSC.dm3.ensGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 46b7ffe0c516edf8a2a3b5d78e0d8b67 build: - number: 16 + number: 17 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml index 4d1aafa9dbaa7..e336c647d474a 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Dmelanogaster.UCSC.dm6.ensGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: bec18a1fb2768347e907e3171d5332ca build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml index 6068ea11a32d2..fca8354c5912c 100644 --- a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.6" %} {% set name = "TxDb.Drerio.UCSC.danRer10.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fef9bbec3809e1b69991516988f146fb build: - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.drerio.ucsc.danrer10.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/meta.yaml b/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/meta.yaml index 24e329bb6164b..f95557448c480 100644 --- a/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.6" %} {% set name = "TxDb.Drerio.UCSC.danRer11.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3d4ded4cec068a807b8b86b31389b677 build: - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.drerio.ucsc.danrer11.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml b/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml index 0bcae1e37f595..a4d1e1a9d9a08 100644 --- a/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Ggallus.UCSC.galGal4.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: d50eb467227cd9077a7a690ae6934d11 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.ggallus.ucsc.galgal4.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml b/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml index a5619d77db894..c539c071a4343 100644 --- a/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Ggallus.UCSC.galGal5.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0df53cd4f8e29705df75867a427de56e build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.ggallus.ucsc.galgal5.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal6.refgene/meta.yaml b/recipes/bioconductor-txdb.ggallus.ucsc.galgal6.refgene/meta.yaml index 22dded94e5395..9a465cc414e93 100644 --- a/recipes/bioconductor-txdb.ggallus.ucsc.galgal6.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal6.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "TxDb.Ggallus.UCSC.galGal6.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4d81026ecb786abf1fe0cb548238214c build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.ggallus.ucsc.galgal6.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml b/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml index 68ed5a6e6c194..3dbd6d642a0c9 100644 --- a/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.3.2" %} {% set name = "TxDb.Hsapiens.BioMart.igis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 75b793928d29bcd3f069b5986bc2cfae build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.hsapiens.biomart.igis", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml index 766497a9f5d34..1e389329cbe79 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Hsapiens.UCSC.hg18.knownGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e8b32a672e87345c72bb30be73d1e2d6 build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.hsapiens.ucsc.hg18.knowngene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml index 664361974a4c3..09de8f7c38a1f 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Hsapiens.UCSC.hg19.knownGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 61be88a81433958571b57d0952be48a0 build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.hsapiens.ucsc.hg19.knowngene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml index 40debb03a2b43..4559792f7c905 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a0d61cd90639c40b3d0bb6bdb043cf12 build: - number: 17 + number: 18 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml index 4d52500d1e3c9..618385aa5a855 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "TxDb.Hsapiens.UCSC.hg38.knownGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a9b7cfbf5ed7d9ef129c84abdd7858dc + md5: 2344dbd2878c82c6c860ed6529a700b2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.hsapiens.ucsc.hg38.knowngene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh index 989c79064a838..7e845c2497808 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "txdb.hsapiens.ucsc.hg38.knowngene-3.17.0" +installBiocDataPackage.sh "txdb.hsapiens.ucsc.hg38.knowngene-3.18.0" diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/meta.yaml index 62180f04d9b91..fbea99b3dbea6 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.15.0" %} +{% set version = "3.18.0" %} {% set name = "TxDb.Hsapiens.UCSC.hg38.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 50e7c4ce068c4ca2d77a3c0b46a3ab45 + md5: 7ec982095ea795b99d53b6549d7ba4d4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.hsapiens.ucsc.hg38.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/post-link.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/post-link.sh index 0b664dac3262c..165899b5e92d6 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "txdb.hsapiens.ucsc.hg38.refgene-3.15.0" +installBiocDataPackage.sh "txdb.hsapiens.ucsc.hg38.refgene-3.18.0" diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene/meta.yaml b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene/meta.yaml index 22bf3eb855a3e..71ee0e7b1156c 100644 --- a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.0" %} {% set name = "TxDb.Mmulatta.UCSC.rheMac10.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 81b01b07d87ae91b4d9a269a2baf616e build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml index 4e21a38d6ccda..0534539bc09fe 100644 --- a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Mmulatta.UCSC.rheMac3.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: db84a9e85d613635d74002f11df41e1f build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml index 584c9a333cb06..bc41e0d7a744b 100644 --- a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Mmulatta.UCSC.rheMac8.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8437e0a05ffd28b667c7b740e0db68a7 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml index 459b32c3a98bb..d32fc6e7daded 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "TxDb.Mmusculus.UCSC.mm10.ensGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 88d65b714d1f86b456aee2b8524e9d84 build: - number: 16 + number: 17 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.mmusculus.ucsc.mm10.ensgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml index fa8fefd0a88e2..1466d7f497572 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "TxDb.Mmusculus.UCSC.mm10.knownGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 129b610bf05ec77451731196baa55bcc build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.mmusculus.ucsc.mm10.knowngene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/meta.yaml index d06a04e2188f3..7d5fc68376690 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "TxDb.Mmusculus.UCSC.mm39.knownGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ca2e9ed7dc7fe96ef98b18e3c7e3245a + md5: 5ceb110ce3327d44f45bf5118ec7f3af build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.mmusculus.ucsc.mm39.knowngene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/post-link.sh b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/post-link.sh index b53c424d92c0a..40c86bb8d84f5 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "txdb.mmusculus.ucsc.mm39.knowngene-3.17.0" +installBiocDataPackage.sh "txdb.mmusculus.ucsc.mm39.knowngene-3.18.0" diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/meta.yaml index 04ef013177696..9734f2b6f61c1 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.12.0" %} +{% set version = "3.18.0" %} {% set name = "TxDb.Mmusculus.UCSC.mm39.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2525799b85e0a52bf274ab5eed51cd84 + md5: 2fd64557d5f1bade11432b666c63f33a build: - number: 6 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.mmusculus.ucsc.mm39.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/post-link.sh b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/post-link.sh index 2fc5b5d65dd07..039d2293e91ed 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "txdb.mmusculus.ucsc.mm39.refgene-3.12.0" +installBiocDataPackage.sh "txdb.mmusculus.ucsc.mm39.refgene-3.18.0" diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml index a1ef79d8b7a66..4b3641897a188 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Mmusculus.UCSC.mm9.knownGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: cb72af039b011033477363bda8ed9104 build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.mmusculus.ucsc.mm9.knowngene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml index 93301e0d981e2..45f0301d0133b 100644 --- a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Ptroglodytes.UCSC.panTro4.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9bdd3ba81561550f50250368d7d52eaa build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml index 351b5edc41946..e46a4701dd0a3 100644 --- a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Ptroglodytes.UCSC.panTro5.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 76ee1d253d1c8e54c12e8d5b9db93303 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene/meta.yaml b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene/meta.yaml index f25065559cccb..7e50c87b44421 100644 --- a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "TxDb.Ptroglodytes.UCSC.panTro6.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 48a88973fe0e5117cadd5c816a46e6e9 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml index d1310743d20d7..072131a10520b 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.3.2" %} {% set name = "TxDb.Rnorvegicus.BioMart.igis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: eaf695f63cd021074d68c76d148cdfb7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.rnorvegicus.biomart.igis", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml index 8e1e7c08903b2..87c5843fcb54e 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn4.ensGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6bf2ebc522c2828c036e52b2028792c1 build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml index f9c1a81bab905..7a4c200fb093a 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn5.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8a93a15b37bf73e5c529c976c4561537 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq/meta.yaml index ac1b3853eb920..a891c74d515a3 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6660ee000fbc956541728c6dadf1fca7 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml index 4cc98f3db3ee6..18c8a1da4b97b 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.6" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn6.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ea525daa75bcf165eb24f6e93f4dbf6c build: - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene/meta.yaml index d383b75fe0cbd..50c4b8f2e2f3f 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.15.0" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn7.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 589dc0f8f4c6ee8f5ed11aeb95a74a7d build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml index 4a09a8c215b8e..15d753d9f15d2 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Scerevisiae.UCSC.sacCer2.sgdGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8ce83ef2ba6cfc69f9b4435a0a047819 build: - number: 18 + number: 19 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml index e84ce9f6c0dd3..c404797fc5a6d 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Scerevisiae.UCSC.sacCer3.sgdGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: afb23b3265730b9e59c2f07ab37cc3a0 build: - number: 21 + number: 22 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml index 58510c515e0d2..0aac7bae47394 100644 --- a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Sscrofa.UCSC.susScr11.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a6c5a2c402ad904a2f55099e391d18de build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.sscrofa.ucsc.susscr11.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml index 522da876b179d..dafdf280b2985 100644 --- a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Sscrofa.UCSC.susScr3.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 981602dc706e545d5acdf7590e222ca7 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.sscrofa.ucsc.susscr3.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tximeta/meta.yaml b/recipes/bioconductor-tximeta/meta.yaml index d1564f35f1dbd..f258f1c4275af 100644 --- a/recipes/bioconductor-tximeta/meta.yaml +++ b/recipes/bioconductor-tximeta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.1" %} {% set name = "tximeta" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0c1de1419dbe0b129421a1a7ada21fe8 + md5: 20a7fe1f7efc9be9ab420325932b8c0b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tximeta", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, fishpond, edgeR, limma, devtools requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-base - r-jsonlite - r-matrix - r-tibble run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-base - r-jsonlite - r-matrix @@ -61,7 +62,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Transcript Quantification Import with Automatic Metadata' - description: 'Transcript quantification import from Salmon and alevin with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.' + description: 'Transcript quantification import from Salmon and other quantifiers with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' extra: parent_recipe: diff --git a/recipes/bioconductor-tximport/meta.yaml b/recipes/bioconductor-tximport/meta.yaml index cdda57ad44ec5..0cac1468cec2d 100644 --- a/recipes/bioconductor-tximport/meta.yaml +++ b/recipes/bioconductor-tximport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "tximport" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,14 +11,15 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6b52b54d5477b1612e7be93cfd08d796 + md5: 8bbe549dafbf5b0dfe626f327910a893 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tximport", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds +# Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow, limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds requirements: host: - r-base diff --git a/recipes/bioconductor-tximportdata/meta.yaml b/recipes/bioconductor-tximportdata/meta.yaml index c468adfd7aa19..67efaa786b0ac 100644 --- a/recipes/bioconductor-tximportdata/meta.yaml +++ b/recipes/bioconductor-tximportdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "tximportData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b5ef0f4b63bcd11c21a8389af32fa1f + md5: 4494d764fc087333e5c04ee7977c85c8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tximportdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tximportdata/post-link.sh b/recipes/bioconductor-tximportdata/post-link.sh index 5ec2e04af174c..d17909a301ad8 100644 --- a/recipes/bioconductor-tximportdata/post-link.sh +++ b/recipes/bioconductor-tximportdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tximportdata-1.28.0" +installBiocDataPackage.sh "tximportdata-1.30.0" diff --git a/recipes/bioconductor-typeinfo/meta.yaml b/recipes/bioconductor-typeinfo/meta.yaml index 5b60c14bd9cf1..11ddbcbf2414b 100644 --- a/recipes/bioconductor-typeinfo/meta.yaml +++ b/recipes/bioconductor-typeinfo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "TypeInfo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 13936395f272715de70454397c80d7eb + md5: a2c4ab8a27a1d9c5a463a18cd0e37356 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-typeinfo", max_pin="x.x") }}' noarch: generic # Suggests: Biobase requirements: diff --git a/recipes/bioconductor-u133aaofav2cdf/meta.yaml b/recipes/bioconductor-u133aaofav2cdf/meta.yaml index 7f158e92ca7e6..68e66f5114324 100644 --- a/recipes/bioconductor-u133aaofav2cdf/meta.yaml +++ b/recipes/bioconductor-u133aaofav2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "u133aaofav2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 716483ddb6664b8b7f0c58cd21136e8b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-u133aaofav2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-u133x3p.db/meta.yaml b/recipes/bioconductor-u133x3p.db/meta.yaml index a315d9457b0e8..141cf64856d0d 100644 --- a/recipes/bioconductor-u133x3p.db/meta.yaml +++ b/recipes/bioconductor-u133x3p.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "u133x3p.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1a36a09dc64b94728bf6ac75600b40c6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-u133x3p.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-u133x3pcdf/meta.yaml b/recipes/bioconductor-u133x3pcdf/meta.yaml index 52b3580ddceb0..c14b372731fdb 100644 --- a/recipes/bioconductor-u133x3pcdf/meta.yaml +++ b/recipes/bioconductor-u133x3pcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "u133x3pcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ee4e62041bc8c63813e8cf8400ece2f3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-u133x3pcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-u133x3pprobe/meta.yaml b/recipes/bioconductor-u133x3pprobe/meta.yaml index 000ab40decaa2..2d940a22ec63b 100644 --- a/recipes/bioconductor-u133x3pprobe/meta.yaml +++ b/recipes/bioconductor-u133x3pprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "u133x3pprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 81e2b00985688160805147bef0c638be build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-u133x3pprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ucell/meta.yaml b/recipes/bioconductor-ucell/meta.yaml index e858d65a0d465..584900adb879c 100644 --- a/recipes/bioconductor-ucell/meta.yaml +++ b/recipes/bioconductor-ucell/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.2" %} {% set name = "UCell" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b3b3b2f541a098357e0d324a468cc5fa + md5: c02318fc6a9ac12b0d902460be5204d4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ucell", max_pin="x.x") }}' noarch: generic # Suggests: Seurat, scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-data.table >=1.13.6' - r-matrix run: - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-data.table >=1.13.6' - r-matrix diff --git a/recipes/bioconductor-ucscrepeatmasker/meta.yaml b/recipes/bioconductor-ucscrepeatmasker/meta.yaml index 2cec4f1d771cf..732e819f62c2b 100644 --- a/recipes/bioconductor-ucscrepeatmasker/meta.yaml +++ b/recipes/bioconductor-ucscrepeatmasker/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.15.2" %} {% set name = "UCSCRepeatMasker" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,27 +13,28 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ad19a6fbd936e478af88fa21bc918a29 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ucscrepeatmasker", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base - r-rcurl - r-xml run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base - r-rcurl - r-xml - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ularcirc/meta.yaml b/recipes/bioconductor-ularcirc/meta.yaml index 8ca10d19bda19..1007d484742c7 100644 --- a/recipes/bioconductor-ularcirc/meta.yaml +++ b/recipes/bioconductor-ularcirc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "Ularcirc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b82a3d2b16ce13cc2c3c354aec4f1e77 + md5: dee64401e02d9e5884a6399d7ab122b2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ularcirc", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-mirbase.db >=1.2.0,<1.3.0' - - 'bioconductor-organism.dplyr >=1.28.0,<1.29.0' - - 'bioconductor-plotgardener >=1.6.0,<1.7.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-organism.dplyr >=1.30.0,<1.31.0' + - 'bioconductor-plotgardener >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-data.table >=1.9.4' - r-dt @@ -49,20 +50,20 @@ requirements: - r-shinyjs - r-yaml run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-mirbase.db >=1.2.0,<1.3.0' - - 'bioconductor-organism.dplyr >=1.28.0,<1.29.0' - - 'bioconductor-plotgardener >=1.6.0,<1.7.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-organism.dplyr >=1.30.0,<1.31.0' + - 'bioconductor-plotgardener >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-data.table >=1.9.4' - r-dt diff --git a/recipes/bioconductor-umi4cats/meta.yaml b/recipes/bioconductor-umi4cats/meta.yaml index 3e76de3805dc8..caa73d85038c4 100644 --- a/recipes/bioconductor-umi4cats/meta.yaml +++ b/recipes/bioconductor-umi4cats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "UMI4Cats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84b4b4be278891d3503c78e20d3dfa6c + md5: bfadc67d7452919fe1e4a63684692442 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-umi4cats", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rbowtie2 >=2.6.0,<2.7.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - r-cowplot @@ -56,24 +57,24 @@ requirements: - r-stringr - r-zoo run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rbowtie2 >=2.6.0,<2.7.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - r-cowplot diff --git a/recipes/bioconductor-uncoverapplib/meta.yaml b/recipes/bioconductor-uncoverapplib/meta.yaml index 85e9b6269cd56..1a28223113b02 100644 --- a/recipes/bioconductor-uncoverapplib/meta.yaml +++ b/recipes/bioconductor-uncoverapplib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "uncoverappLib" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec3e240519cd29c9a91154e0c38bf211 + md5: 2aa395f92e95d5ff7e67612c6a2c0021 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-uncoverapplib", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat, rmarkdown, dplyr requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0' - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-condformat - r-dt @@ -48,18 +49,18 @@ requirements: - r-shinywidgets - r-stringr run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0' - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-condformat - r-dt diff --git a/recipes/bioconductor-undo/meta.yaml b/recipes/bioconductor-undo/meta.yaml index 30cd162fb9e37..f214965e0b298 100644 --- a/recipes/bioconductor-undo/meta.yaml +++ b/recipes/bioconductor-undo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "UNDO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a8de0b0595afb75551a7186b00b45bf + md5: a94665c036a09fbf3728f0a1ad220dfa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-undo", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-boot - r-mass - r-nnls run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-boot - r-mass diff --git a/recipes/bioconductor-unifiedwmwqpcr/meta.yaml b/recipes/bioconductor-unifiedwmwqpcr/meta.yaml index 92fae1b55a09a..9c7b8e08be53a 100644 --- a/recipes/bioconductor-unifiedwmwqpcr/meta.yaml +++ b/recipes/bioconductor-unifiedwmwqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "unifiedWMWqPCR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5014bd5d35c03623b142b02ac2599eaa + md5: d9a09d196f72dc2246328247851dd24a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-unifiedwmwqpcr", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-htqpcr >=1.54.0,<1.55.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-htqpcr >=1.56.0,<1.57.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-htqpcr >=1.54.0,<1.55.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-htqpcr >=1.56.0,<1.57.0' - r-base test: commands: diff --git a/recipes/bioconductor-uniprot.ws/meta.yaml b/recipes/bioconductor-uniprot.ws/meta.yaml index 095637e68a890..07e01957f1b4c 100644 --- a/recipes/bioconductor-uniprot.ws/meta.yaml +++ b/recipes/bioconductor-uniprot.ws/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.40.1" %} +{% set version = "2.42.0" %} {% set name = "UniProt.ws" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 19942d736d5f87dcb885720b524ce954 + md5: 47d9ee4038c5dcaf66229e4e1e07c052 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-uniprot.ws", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-httpcache - r-httr @@ -33,10 +34,10 @@ requirements: - r-rjsoncons - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-httpcache - r-httr diff --git a/recipes/bioconductor-uniprotkeywords/meta.yaml b/recipes/bioconductor-uniprotkeywords/meta.yaml index d14358fb3dfa3..e997cfd605a01 100644 --- a/recipes/bioconductor-uniprotkeywords/meta.yaml +++ b/recipes/bioconductor-uniprotkeywords/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.99.4" %} +{% set version = "0.99.7" %} {% set name = "UniProtKeywords" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f3f91ac1b8eca20fabcf46cae4348ea5 + md5: b2cda32dda256fb0d110192e194af838 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-uniprotkeywords", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, markdown, testthat requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-uniprotkeywords/post-link.sh b/recipes/bioconductor-uniprotkeywords/post-link.sh index 5a72202c55dd6..2f90ff95a700c 100644 --- a/recipes/bioconductor-uniprotkeywords/post-link.sh +++ b/recipes/bioconductor-uniprotkeywords/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "uniprotkeywords-0.99.4" +installBiocDataPackage.sh "uniprotkeywords-0.99.7" diff --git a/recipes/bioconductor-uniquorn/meta.yaml b/recipes/bioconductor-uniquorn/meta.yaml index 74ffa08b92ef2..3bcbea9f536d0 100644 --- a/recipes/bioconductor-uniquorn/meta.yaml +++ b/recipes/bioconductor-uniquorn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "Uniquorn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ca181ab420669fd785a9984d9c3a03e1 + md5: 63658e23af6991784cdd4b038f2d1268 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-uniquorn", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocGenerics requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-doparallel @@ -32,9 +33,9 @@ requirements: - r-stringr - r-writexls run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-universalmotif/meta.yaml b/recipes/bioconductor-universalmotif/meta.yaml index d828d62f4b536..3e87affe747df 100644 --- a/recipes/bioconductor-universalmotif/meta.yaml +++ b/recipes/bioconductor-universalmotif/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "universalmotif" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 53ef747289e457e4097ced1d46199854 + md5: fe680a8d988fce6bfde0af9fdce148de build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-universalmotif", max_pin="x.x") }}' # Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-mass @@ -35,11 +36,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-mass diff --git a/recipes/bioconductor-updateobject/meta.yaml b/recipes/bioconductor-updateobject/meta.yaml index e6901ad19b093..0ac250a75a4ef 100644 --- a/recipes/bioconductor-updateobject/meta.yaml +++ b/recipes/bioconductor-updateobject/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "updateObject" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d7a6ae09fcd22300d35d2ff503ce9f08 + md5: 0d69cbbcd4bd9c5f31d905a47f6af212 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-updateobject", max_pin="x.x") }}' noarch: generic # Suggests: GenomicRanges, SummarizedExperiment, InteractionSet, SingleCellExperiment, MultiAssayExperiment, TimiRGeN, testthat, knitr, rmarkdown, BiocStyle # SystemRequirements: git requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-digest run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-digest test: diff --git a/recipes/bioconductor-usort/meta.yaml b/recipes/bioconductor-usort/meta.yaml index c3367d77d2e81..5783b25934ca6 100644 --- a/recipes/bioconductor-usort/meta.yaml +++ b/recipes/bioconductor-usort/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "uSORT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0fb4c6b3706ad7e264a9f106c5519169 + md5: 0c89e7d86bb2f37b99ce32989b121110 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-usort", max_pin="x.x") }}' noarch: generic # Suggests: knitr, RUnit, testthat, ggplot2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-monocle >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-monocle >=2.30.0,<2.31.0' - r-base - r-cluster - r-fpc @@ -35,9 +36,9 @@ requirements: - r-rspectra - r-vgam run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-monocle >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-monocle >=2.30.0,<2.31.0' - r-base - r-cluster - r-fpc diff --git a/recipes/bioconductor-vaexprs/meta.yaml b/recipes/bioconductor-vaexprs/meta.yaml index 12718521e4783..41a54d8a833b0 100644 --- a/recipes/bioconductor-vaexprs/meta.yaml +++ b/recipes/bioconductor-vaexprs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "VAExprs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7f66a09bd4ecba61a3bb6a4931f9a2ff + md5: 6f9ed6eba476abd7908d6849381b545c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vaexprs", max_pin="x.x") }}' noarch: generic # Suggests: SC3, knitr, testthat, reticulate, rmarkdown requirements: host: - - 'bioconductor-deeppincs >=1.8.0,<1.9.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deeppincs >=1.10.0,<1.11.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-catencoders - r-diagrammer @@ -33,10 +34,10 @@ requirements: - r-purrr - r-tensorflow run: - - 'bioconductor-deeppincs >=1.8.0,<1.9.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deeppincs >=1.10.0,<1.11.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-catencoders - r-diagrammer diff --git a/recipes/bioconductor-vanillaice/meta.yaml b/recipes/bioconductor-vanillaice/meta.yaml index 0b037492191c2..ef2b66554d491 100644 --- a/recipes/bioconductor-vanillaice/meta.yaml +++ b/recipes/bioconductor-vanillaice/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "VanillaICE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e1544c4961ab0be39a24130c53fce392 + md5: 557131c410cc7474d15a4cc9a7d940de build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vanillaice", max_pin="x.x") }}' # Suggests: RUnit, human610quadv1bCrlmm requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' - - 'bioconductor-crlmm >=1.58.0,<1.59.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-crlmm >=1.60.0,<1.61.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-foreach @@ -39,17 +40,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' - - 'bioconductor-crlmm >=1.58.0,<1.59.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-crlmm >=1.60.0,<1.61.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-foreach diff --git a/recipes/bioconductor-varcon/meta.yaml b/recipes/bioconductor-varcon/meta.yaml index dd6f12bfb8cbe..409d0dc24a003 100644 --- a/recipes/bioconductor-varcon/meta.yaml +++ b/recipes/bioconductor-varcon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "VarCon" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b0ded1a90369093a4576e0d86660ca32 + md5: 843e95d7843d7611c222d8cbca8814b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-varcon", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-ggplot2 - r-shiny - r-shinycssloaders - r-shinyfiles run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-ggplot2 - r-shiny diff --git a/recipes/bioconductor-variancepartition/meta.yaml b/recipes/bioconductor-variancepartition/meta.yaml index 9e8cf690075ff..ff40c729611e6 100644 --- a/recipes/bioconductor-variancepartition/meta.yaml +++ b/recipes/bioconductor-variancepartition/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.2" %} +{% set version = "1.32.2" %} {% set name = "variancePartition" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,57 +11,58 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea2b29627ac9a4e7c039319af82a2caf + md5: 75a8e840769ba62b9f175c73aba9c99a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-variancepartition", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, Rfast, zenith, RUnit, statmod, BiocGenerics, r2glmm, readr +# Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, cowplot, Rfast, zenith, statmod, BiocGenerics, r2glmm, readr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-aod - r-base - - r-doparallel - - r-foreach + - r-corpcor + - r-fancova - r-ggplot2 - r-gplots - r-iterators - - 'r-lme4 >=1.1-10' + - 'r-lme4 >=1.1.33' - r-lmertest - r-mass - 'r-matrix >=1.4.0' + - r-matrixstats - 'r-pbkrtest >=0.4-4' - - r-progress - r-rdpack - - 'r-remacor >=0.0.11' + - 'r-remacor >=0.0.15' - r-reshape2 - r-rhpcblasctl - r-rlang - r-scales run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-aod - r-base - - r-doparallel - - r-foreach + - r-corpcor + - r-fancova - r-ggplot2 - r-gplots - r-iterators - - 'r-lme4 >=1.1-10' + - 'r-lme4 >=1.1.33' - r-lmertest - r-mass - 'r-matrix >=1.4.0' + - r-matrixstats - 'r-pbkrtest >=0.4-4' - - r-progress - r-rdpack - - 'r-remacor >=0.0.11' + - 'r-remacor >=0.0.15' - r-reshape2 - r-rhpcblasctl - r-rlang diff --git a/recipes/bioconductor-variantannotation/meta.yaml b/recipes/bioconductor-variantannotation/meta.yaml index 9751715d5559b..77114340c26da 100644 --- a/recipes/bioconductor-variantannotation/meta.yaml +++ b/recipes/bioconductor-variantannotation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.1" %} {% set name = "VariantAnnotation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,55 +11,56 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d297f17e9369a4e04d41b1fa86535f4c + md5: 39b6f4907fe37495a903c338e6d4cc73 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle + run_exports: '{{ pin_subpackage("bioconductor-variantannotation", max_pin="x.x") }}' +# Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle, knitr # SystemRequirements: GNU make requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-dbi - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-dbi build: diff --git a/recipes/bioconductor-variantexperiment/meta.yaml b/recipes/bioconductor-variantexperiment/meta.yaml index e0b33f5de1b02..d996d1d7f6948 100644 --- a/recipes/bioconductor-variantexperiment/meta.yaml +++ b/recipes/bioconductor-variantexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "VariantExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 307ba761619ec2eedb365f83b1e5950f + md5: cfa81c58331066ea4f23ce2ba29fa114 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-variantexperiment", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, markdown, BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayeddataframe >=1.16.0,<1.17.0' - - 'bioconductor-gdsarray >=1.20.0,<1.21.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayeddataframe >=1.18.0,<1.19.0' + - 'bioconductor-gdsarray >=1.22.0,<1.23.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayeddataframe >=1.16.0,<1.17.0' - - 'bioconductor-gdsarray >=1.20.0,<1.21.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayeddataframe >=1.18.0,<1.19.0' + - 'bioconductor-gdsarray >=1.22.0,<1.23.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-variantfiltering/meta.yaml b/recipes/bioconductor-variantfiltering/meta.yaml index 7d7cc657acfcc..339238b836f34 100644 --- a/recipes/bioconductor-variantfiltering/meta.yaml +++ b/recipes/bioconductor-variantfiltering/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.1" %} +{% set version = "1.38.0" %} {% set name = "VariantFiltering" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a5b2f20003b47121950dfbb60c9e95a8 + md5: af4ddac4cfb857eea4db9309da6de07d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-variantfiltering", max_pin="x.x") }}' # Suggests: RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-dt - r-shiny @@ -48,25 +49,25 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-dt - r-shiny diff --git a/recipes/bioconductor-varianttools/meta.yaml b/recipes/bioconductor-varianttools/meta.yaml index 42cd6b757219b..6a504d7d03da0 100644 --- a/recipes/bioconductor-varianttools/meta.yaml +++ b/recipes/bioconductor-varianttools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "VariantTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f6efd941310bd834bc9071454c65d5e + md5: 34afccb56ff143a33019bdd8f2e356ca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-varianttools", max_pin="x.x") }}' noarch: generic -# Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3) +# Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3), TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-matrix run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-varianttoolsdata/meta.yaml b/recipes/bioconductor-varianttoolsdata/meta.yaml index 26e84b603fd3e..a8a952360d6fc 100644 --- a/recipes/bioconductor-varianttoolsdata/meta.yaml +++ b/recipes/bioconductor-varianttoolsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "VariantToolsData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: abaad839d98a3c855cac80bd443fa9b6 + md5: a85757ce237b03b0480f01488a78879b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-varianttoolsdata", max_pin="x.x") }}' noarch: generic # Suggests: VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-varianttoolsdata/post-link.sh b/recipes/bioconductor-varianttoolsdata/post-link.sh index 9ff9ab2726d17..7c1ae1c238049 100644 --- a/recipes/bioconductor-varianttoolsdata/post-link.sh +++ b/recipes/bioconductor-varianttoolsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "varianttoolsdata-1.24.0" +installBiocDataPackage.sh "varianttoolsdata-1.26.0" diff --git a/recipes/bioconductor-vasp/meta.yaml b/recipes/bioconductor-vasp/meta.yaml index 0d8a475a7222e..b3e673476385f 100644 --- a/recipes/bioconductor-vasp/meta.yaml +++ b/recipes/bioconductor-vasp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "VaSP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c9272543d5387f9619fee22096af873 + md5: 5fddc833bc7dd84dfb16e030fe966cd3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vasp", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-ballgown >=2.32.0,<2.33.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-ballgown >=2.34.0,<2.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-matrixstats run: - - 'bioconductor-ballgown >=2.32.0,<2.33.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-ballgown >=2.34.0,<2.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-matrixstats diff --git a/recipes/bioconductor-vbmp/meta.yaml b/recipes/bioconductor-vbmp/meta.yaml index d0ae8c93023a7..ce99b5aa8630f 100644 --- a/recipes/bioconductor-vbmp/meta.yaml +++ b/recipes/bioconductor-vbmp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.0" %} {% set name = "vbmp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bbe85861887e0d02f6ab57203dfac89e + md5: b7d2a0a9950dd7ecdbcea5ffdfbd853c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vbmp", max_pin="x.x") }}' noarch: generic # Suggests: Biobase (>= 2.5.5), statmod requirements: diff --git a/recipes/bioconductor-vcfarray/meta.yaml b/recipes/bioconductor-vcfarray/meta.yaml index 5b3b0986decad..b97fe14953639 100644 --- a/recipes/bioconductor-vcfarray/meta.yaml +++ b/recipes/bioconductor-vcfarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "VCFArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ed57985f5b6fcd3e8221e75ae29ca65 + md5: 0e101fbb3c6c6b57d792527a6c720654 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vcfarray", max_pin="x.x") }}' noarch: generic # Suggests: SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-vdjdive/meta.yaml b/recipes/bioconductor-vdjdive/meta.yaml index b0ff3da36ebdf..9f4d20bf8610f 100644 --- a/recipes/bioconductor-vdjdive/meta.yaml +++ b/recipes/bioconductor-vdjdive/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "VDJdive" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,43 +11,47 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4900fdc58bbcb9fd6d36bf12379f671a + md5: 938051376344953e02e510f65d156939 build: number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic + run_exports: '{{ pin_subpackage("bioconductor-vdjdive", max_pin="x.x") }}' # Suggests: breakaway, covr, knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-ggplot2 - r-gridextra - r-matrix - r-rcolorbrewer - - r-reticulate + - r-rcpp + - libblas + - liblapack run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-ggplot2 - r-gridextra - r-matrix - r-rcolorbrewer - - r-reticulate + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-vectrapolarisdata/meta.yaml b/recipes/bioconductor-vectrapolarisdata/meta.yaml index 1a584263921ac..5c6b9f5915e33 100644 --- a/recipes/bioconductor-vectrapolarisdata/meta.yaml +++ b/recipes/bioconductor-vectrapolarisdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "VectraPolarisData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f427b5860f7e3498064deabff0328263 + md5: ea2006b85e374e76fbd70ca8b0819072 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vectrapolarisdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, dplyr requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-vectrapolarisdata/post-link.sh b/recipes/bioconductor-vectrapolarisdata/post-link.sh index 16113665d8f15..2f937fb860681 100644 --- a/recipes/bioconductor-vectrapolarisdata/post-link.sh +++ b/recipes/bioconductor-vectrapolarisdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "vectrapolarisdata-1.4.0" +installBiocDataPackage.sh "vectrapolarisdata-1.6.0" diff --git a/recipes/bioconductor-vegamc/meta.yaml b/recipes/bioconductor-vegamc/meta.yaml index 7c66f7ec08948..d21a2211e6724 100644 --- a/recipes/bioconductor-vegamc/meta.yaml +++ b/recipes/bioconductor-vegamc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.38.0" %} +{% set version = "3.40.0" %} {% set name = "VegaMC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 27fb05dee200093e81b0ad296ef9ce50 + md5: 0e02ae3375b7bed5ca1ed7011b60f180 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vegamc", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-velociraptor/meta.yaml b/recipes/bioconductor-velociraptor/meta.yaml index 9cff79fb403b4..85b401a821df5 100644 --- a/recipes/bioconductor-velociraptor/meta.yaml +++ b/recipes/bioconductor-velociraptor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "velociraptor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 725af79edbf1758273558a988c346605 + md5: d2c16e280b1957ef3989e5d02f4f0b5d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-velociraptor", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown, pkgdown, scran, scater, scRNAseq, Rtsne, graphics, grDevices, ggplot2, cowplot, GGally, patchwork, metR requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zellkonverter >=1.10.0,<1.11.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zellkonverter >=1.12.0,<1.13.0' - r-base - r-matrix - r-reticulate run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zellkonverter >=1.10.0,<1.11.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zellkonverter >=1.12.0,<1.13.0' - r-base - r-matrix - r-reticulate diff --git a/recipes/bioconductor-veloviz/meta.yaml b/recipes/bioconductor-veloviz/meta.yaml index dc09829f4b3ff..8fa3402c305e9 100644 --- a/recipes/bioconductor-veloviz/meta.yaml +++ b/recipes/bioconductor-veloviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "veloviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7c3af954c6be66f853f9aaf1a2f03d97 + md5: 54c6f9e5fd6275be8b999a2c949cf6bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-veloviz", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat requirements: host: diff --git a/recipes/bioconductor-venndetail/meta.yaml b/recipes/bioconductor-venndetail/meta.yaml index 2b46196c5960f..42c138436e3dd 100644 --- a/recipes/bioconductor-venndetail/meta.yaml +++ b/recipes/bioconductor-venndetail/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "VennDetail" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2da7c3ccb316ab6914812bedd8f351a5 + md5: be9c3506e9707fe42642ea413c0873a6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-venndetail", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, markdown requirements: diff --git a/recipes/bioconductor-verso/meta.yaml b/recipes/bioconductor-verso/meta.yaml index 359162175c5a3..f142090d335ed 100644 --- a/recipes/bioconductor-verso/meta.yaml +++ b/recipes/bioconductor-verso/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "VERSO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7cc88c9858954443ebd083f066aac93 + md5: dcc0220c3f10bb1efaaa360448547771 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-verso", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, testthat, knitr requirements: diff --git a/recipes/bioconductor-vidger/meta.yaml b/recipes/bioconductor-vidger/meta.yaml index 00d83b649aa7e..6104b533f8e4e 100644 --- a/recipes/bioconductor-vidger/meta.yaml +++ b/recipes/bioconductor-vidger/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "vidger" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d2674cb15af21919dfd378d5fa4ad4aa + md5: 01029a545153064095a804a7e9093231 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vidger", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggally - r-ggplot2 @@ -35,10 +36,10 @@ requirements: - r-scales - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggally - r-ggplot2 diff --git a/recipes/bioconductor-viper/meta.yaml b/recipes/bioconductor-viper/meta.yaml index 1d91ca6cb6844..d7cc28cd92f69 100644 --- a/recipes/bioconductor-viper/meta.yaml +++ b/recipes/bioconductor-viper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "viper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 68e8e97c7b733610c09e2938f9c1ac42 + md5: 0d7f13a212bc6fc5d7cf2213a1bfbdb0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-viper", max_pin="x.x") }}' noarch: generic # Suggests: bcellViper requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-e1071 - r-kernsmooth - r-mixtools run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-e1071 - r-kernsmooth diff --git a/recipes/bioconductor-viseago/meta.yaml b/recipes/bioconductor-viseago/meta.yaml index af9d0935c9c09..0ce17ff2718bd 100644 --- a/recipes/bioconductor-viseago/meta.yaml +++ b/recipes/bioconductor-viseago/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "ViSEAGO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ef6ab35f2558111c341ddabf7d69b3d + md5: 90f43624392275cbfbcd026e323769b9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-viseago", max_pin="x.x") }}' noarch: generic # Suggests: htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr, rmarkdown, corrplot, remotes, BiocManager requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationforge >=1.42.0,<1.43.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationforge >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-data.table - r-dendextend @@ -45,13 +46,13 @@ requirements: - r-scales - r-upsetr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationforge >=1.42.0,<1.43.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationforge >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-data.table - r-dendextend diff --git a/recipes/bioconductor-visse/meta.yaml b/recipes/bioconductor-visse/meta.yaml index 4d72ac521d56d..f9e749668920d 100644 --- a/recipes/bioconductor-visse/meta.yaml +++ b/recipes/bioconductor-visse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "vissE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3b75cc7ccad5e8341533a72d2c5449a + md5: 1c5018fd43f416ebc2d035a143877154 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-visse", max_pin="x.x") }}' noarch: generic # Suggests: testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore, knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr requirements: host: - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-msigdb >=1.8.0,<1.9.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-msigdb >=1.10.0,<1.11.0' - r-base - r-ggforce - r-ggplot2 @@ -39,8 +40,8 @@ requirements: - r-tidygraph - r-tm run: - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-msigdb >=1.8.0,<1.9.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-msigdb >=1.10.0,<1.11.0' - r-base - r-ggforce - r-ggplot2 diff --git a/recipes/bioconductor-vitisviniferacdf/meta.yaml b/recipes/bioconductor-vitisviniferacdf/meta.yaml index 618b415f6dceb..700763f7b9e4a 100644 --- a/recipes/bioconductor-vitisviniferacdf/meta.yaml +++ b/recipes/bioconductor-vitisviniferacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "vitisviniferacdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8eb491f3ffa3ff0814f5c155787ae160 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vitisviniferacdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-vitisviniferaprobe/meta.yaml b/recipes/bioconductor-vitisviniferaprobe/meta.yaml index 78c017c3278e5..6c147fb71d4de 100644 --- a/recipes/bioconductor-vitisviniferaprobe/meta.yaml +++ b/recipes/bioconductor-vitisviniferaprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "vitisviniferaprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 386c0d5e37896d073ac20970e88b3160 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vitisviniferaprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-voyager/meta.yaml b/recipes/bioconductor-voyager/meta.yaml index f18eed13d0105..805d9605955ad 100644 --- a/recipes/bioconductor-voyager/meta.yaml +++ b/recipes/bioconductor-voyager/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.3" %} +{% set version = "1.4.0" %} {% set name = "Voyager" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af8b62438ee17b2a3898ef9ee429a619 + md5: 1cc32e63cf1c410d82c2cd1a26f9f929 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-voyager", max_pin="x.x") }}' noarch: generic -# Suggests: adespatial, automap, BiocSingular, BiocStyle, cowplot, ExperimentHub, ggh4x, gstat, hexbin, knitr, pheatmap, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, vroom +# Suggests: automap, BiocSingular, BiocStyle, cowplot, ExperimentHub, ggh4x, gstat, hexbin, knitr, pheatmap, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, vroom requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bluster >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-spatialfeatureexperiment >=1.2.0,<1.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bluster >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-spatialfeatureexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggnewscale - 'r-ggplot2 >=3.4.0' - r-lifecycle - r-matrix + - r-matrixstats - r-patchwork - r-rlang - r-rspectra @@ -43,19 +44,19 @@ requirements: - r-spdep - r-terra run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bluster >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-spatialfeatureexperiment >=1.2.0,<1.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bluster >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-spatialfeatureexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggnewscale - 'r-ggplot2 >=3.4.0' - r-lifecycle - r-matrix + - r-matrixstats - r-patchwork - r-rlang - r-rspectra diff --git a/recipes/bioconductor-vplotr/meta.yaml b/recipes/bioconductor-vplotr/meta.yaml index c326702e06edc..60b10ff4e2b2e 100644 --- a/recipes/bioconductor-vplotr/meta.yaml +++ b/recipes/bioconductor-vplotr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.1" %} {% set name = "VplotR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a35b84246031a8a91934c6b0144d1c0d + md5: 91af0fd39cd72be94b7f5d674d9e494f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vplotr", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-ggplot2 @@ -35,12 +36,12 @@ requirements: - r-reshape2 - r-zoo run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-ggplot2 diff --git a/recipes/bioconductor-vsclust/meta.yaml b/recipes/bioconductor-vsclust/meta.yaml index f256165c67c44..7ba0555dd39b9 100644 --- a/recipes/bioconductor-vsclust/meta.yaml +++ b/recipes/bioconductor-vsclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "vsclust" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aa4f4df8fd8e0a96d3bce256e041f479 + md5: 0c492a6d65d0b230211a0f95706b51a4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vsclust", max_pin="x.x") }}' # Suggests: knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, clusterProfiler requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-matrixstats - r-rcpp @@ -30,9 +31,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-matrixstats - r-rcpp diff --git a/recipes/bioconductor-vsn/meta.yaml b/recipes/bioconductor-vsn/meta.yaml index 289e82fa4ce0a..f9f993fd76b95 100644 --- a/recipes/bioconductor-vsn/meta.yaml +++ b/recipes/bioconductor-vsn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.68.0" %} +{% set version = "3.70.0" %} {% set name = "vsn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cc5c43447e41dc37b1132a6407ba298b + md5: 1c9484f361b22f76135af5567306f0c6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vsn", max_pin="x.x") }}' # Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-lattice - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-lattice diff --git a/recipes/bioconductor-vtpnet/meta.yaml b/recipes/bioconductor-vtpnet/meta.yaml index 68ff7ed733dfe..5c0307387b96c 100644 --- a/recipes/bioconductor-vtpnet/meta.yaml +++ b/recipes/bioconductor-vtpnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.40.0" %} +{% set version = "0.42.0" %} {% set name = "vtpnet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cf95c0b39cbcd4f227c8b3e03c7d2906 + md5: a3a08b447e9ce26fafeed6fe2c515e10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vtpnet", max_pin="x.x") }}' noarch: generic # Suggests: MotifDb, VariantAnnotation, Rgraphviz requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gwascat >=2.32.0,<2.33.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gwascat >=2.34.0,<2.35.0' - r-base - r-doparallel - r-foreach run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gwascat >=2.32.0,<2.33.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gwascat >=2.34.0,<2.35.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-vulcan/meta.yaml b/recipes/bioconductor-vulcan/meta.yaml index e0d4a0fa3f9f5..37d48d05d6a20 100644 --- a/recipes/bioconductor-vulcan/meta.yaml +++ b/recipes/bioconductor-vulcan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "vulcan" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f526cacf3cf264b40ddb4f476a863e2c + md5: 0e0bf7a1e9b866d535489e7c37f2e19d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vulcan", max_pin="x.x") }}' noarch: generic # Suggests: vulcandata requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-diffbind >=3.10.0,<3.11.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-diffbind >=3.12.0,<3.13.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base - r-catools - r-gplots @@ -37,15 +38,15 @@ requirements: - r-wordcloud - r-zoo run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-diffbind >=3.10.0,<3.11.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-diffbind >=3.12.0,<3.13.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base - r-catools - r-gplots diff --git a/recipes/bioconductor-vulcandata/meta.yaml b/recipes/bioconductor-vulcandata/meta.yaml index c83ee258ad24a..c63ea516eec1c 100644 --- a/recipes/bioconductor-vulcandata/meta.yaml +++ b/recipes/bioconductor-vulcandata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "vulcandata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e51d04a9825be5fdb9591377095a0da9 + md5: cd95ea7ac7f2b9edfd46c1ffccb7c3c1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vulcandata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-vulcandata/post-link.sh b/recipes/bioconductor-vulcandata/post-link.sh index 9bf717d9b7e82..29950d9bb1d51 100644 --- a/recipes/bioconductor-vulcandata/post-link.sh +++ b/recipes/bioconductor-vulcandata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "vulcandata-1.22.0" +installBiocDataPackage.sh "vulcandata-1.24.0" diff --git a/recipes/bioconductor-waddr/meta.yaml b/recipes/bioconductor-waddr/meta.yaml index 9d0151af7f721..c7bc5ff14d5ed 100644 --- a/recipes/bioconductor-waddr/meta.yaml +++ b/recipes/bioconductor-waddr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "waddR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a4dd18e19d305d25e578016a82391c7 + md5: 97a692c918d531e3d872dc17141cd112 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-waddr", max_pin="x.x") }}' # Suggests: knitr, devtools, testthat, roxygen2, rprojroot, rmarkdown, scater requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - 'r-arm >=1.10-1' - r-base - r-eva @@ -31,9 +32,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - 'r-arm >=1.10-1' - r-base - r-eva diff --git a/recipes/bioconductor-watermelon/meta.yaml b/recipes/bioconductor-watermelon/meta.yaml index c52d665c14f60..b6fb1b65082bf 100644 --- a/recipes/bioconductor-watermelon/meta.yaml +++ b/recipes/bioconductor-watermelon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "wateRmelon" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4828a18835a1a56fde8a155a51452e7 + md5: dd08402958a5cc50170669a5f17e44f6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-watermelon", max_pin="x.x") }}' noarch: generic # Suggests: RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BiocStyle, knitr, rmarkdown, IlluminaHumanMethylationEPICmanifest, irlba, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-roc >=1.76.0,<1.77.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' - r-base - r-matrixstats run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-roc >=1.76.0,<1.77.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' - r-base - r-matrixstats test: diff --git a/recipes/bioconductor-wavcluster/meta.yaml b/recipes/bioconductor-wavcluster/meta.yaml index 9b019e5241b76..db62a8f56c5cf 100644 --- a/recipes/bioconductor-wavcluster/meta.yaml +++ b/recipes/bioconductor-wavcluster/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "wavClusteR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2894c6e0dbc3d6d968cf63dad83ab8e8 + md5: 9177c657b31b1abaac94079e658a9c18 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-wavcluster", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-foreach - r-ggplot2 @@ -37,14 +38,14 @@ requirements: - r-seqinr - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-foreach - r-ggplot2 diff --git a/recipes/bioconductor-weaver/meta.yaml b/recipes/bioconductor-weaver/meta.yaml index 735940fb2a99c..4eac9e85fb718 100644 --- a/recipes/bioconductor-weaver/meta.yaml +++ b/recipes/bioconductor-weaver/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "weaver" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 88b2dbb130fe48487b9f642f97475a3f + md5: 629d19681872923f14b50543d833c1ba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-weaver", max_pin="x.x") }}' noarch: generic # Suggests: codetools requirements: diff --git a/recipes/bioconductor-webbioc/meta.yaml b/recipes/bioconductor-webbioc/meta.yaml index 652c70188c9c3..2186052bfbd19 100644 --- a/recipes/bioconductor-webbioc/meta.yaml +++ b/recipes/bioconductor-webbioc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "webbioc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b1f539ec35de93f12f90c5432c7d30ea + md5: 59774accefb60098cdf15cfcd1cda508 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-webbioc", max_pin="x.x") }}' noarch: generic # SystemRequirements: Unix, Perl (>= 5.6.0), Netpbm requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annaffy >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annaffy >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-biocmanager run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annaffy >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annaffy >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-biocmanager test: diff --git a/recipes/bioconductor-weberdivechalcdata/meta.yaml b/recipes/bioconductor-weberdivechalcdata/meta.yaml index 44c9361352f19..c4b66627150c2 100644 --- a/recipes/bioconductor-weberdivechalcdata/meta.yaml +++ b/recipes/bioconductor-weberdivechalcdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "WeberDivechaLCdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f7b4867dc3ce8463050bd897209d00c4 + md5: 3b75c693f86ed228e2b7816872cfe4b7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-weberdivechalcdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-weberdivechalcdata/post-link.sh b/recipes/bioconductor-weberdivechalcdata/post-link.sh index cad6159f43b41..7776be0617620 100644 --- a/recipes/bioconductor-weberdivechalcdata/post-link.sh +++ b/recipes/bioconductor-weberdivechalcdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "weberdivechalcdata-1.2.0" +installBiocDataPackage.sh "weberdivechalcdata-1.4.0" diff --git a/recipes/bioconductor-weitrix/meta.yaml b/recipes/bioconductor-weitrix/meta.yaml index 9d4a0c43c50ef..eb99b763485c2 100644 --- a/recipes/bioconductor-weitrix/meta.yaml +++ b/recipes/bioconductor-weitrix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "weitrix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c32dce4e0730d66dd8757c78aadc44ad + md5: 101d61858d3d388a1396212f7ef5332e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-weitrix", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR, EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, ComplexHeatmap, patchwork, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topconfects >=1.16.0,<1.17.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topconfects >=1.18.0,<1.19.0' - r-assertthat - r-base - r-ckmeans.1d.dp @@ -41,14 +42,14 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topconfects >=1.16.0,<1.17.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topconfects >=1.18.0,<1.19.0' - r-assertthat - r-base - r-ckmeans.1d.dp diff --git a/recipes/bioconductor-wes.1kg.wugsc/meta.yaml b/recipes/bioconductor-wes.1kg.wugsc/meta.yaml index 5f537e13c5d7b..755106b9959f2 100644 --- a/recipes/bioconductor-wes.1kg.wugsc/meta.yaml +++ b/recipes/bioconductor-wes.1kg.wugsc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "WES.1KG.WUGSC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4037de5e802a16f5aae76eca264b0be7 + md5: a0a3d230e27342090638ec4868756e5a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-wes.1kg.wugsc", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-wes.1kg.wugsc/post-link.sh b/recipes/bioconductor-wes.1kg.wugsc/post-link.sh index ac9b442ef44fe..379916e93aea6 100644 --- a/recipes/bioconductor-wes.1kg.wugsc/post-link.sh +++ b/recipes/bioconductor-wes.1kg.wugsc/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "wes.1kg.wugsc-1.32.0" +installBiocDataPackage.sh "wes.1kg.wugsc-1.34.0" diff --git a/recipes/bioconductor-wgsmapp/meta.yaml b/recipes/bioconductor-wgsmapp/meta.yaml index 5761c6cc97e9d..004433757f803 100644 --- a/recipes/bioconductor-wgsmapp/meta.yaml +++ b/recipes/bioconductor-wgsmapp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "WGSmapp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e4b497bab5e73445e19a84f86e40888 + md5: dfc3f5a82d532551e2d6c21b11c99566 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-wgsmapp", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-wgsmapp/post-link.sh b/recipes/bioconductor-wgsmapp/post-link.sh index fa5f5b4d3d4ff..72a7d5958caa4 100644 --- a/recipes/bioconductor-wgsmapp/post-link.sh +++ b/recipes/bioconductor-wgsmapp/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "wgsmapp-1.12.0" +installBiocDataPackage.sh "wgsmapp-1.14.0" diff --git a/recipes/bioconductor-wheatcdf/meta.yaml b/recipes/bioconductor-wheatcdf/meta.yaml index ce66b53e4ba95..e48303b1fdecd 100644 --- a/recipes/bioconductor-wheatcdf/meta.yaml +++ b/recipes/bioconductor-wheatcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "wheatcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0abeeeb9700b8d93a1a83769bdd8480f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-wheatcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-wheatprobe/meta.yaml b/recipes/bioconductor-wheatprobe/meta.yaml index f662ba5fe5d20..a8a7d02b42958 100644 --- a/recipes/bioconductor-wheatprobe/meta.yaml +++ b/recipes/bioconductor-wheatprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "wheatprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b602d5050239850515be9dce12286360 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-wheatprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-widgettools/meta.yaml b/recipes/bioconductor-widgettools/meta.yaml index a649ad5806073..9bd762908f52b 100644 --- a/recipes/bioconductor-widgettools/meta.yaml +++ b/recipes/bioconductor-widgettools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "widgetTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d5d6e9f2d028392979502b0b07d13cb7 + md5: bb5358a7e064436aa744ffb098a9c0ec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-widgettools", max_pin="x.x") }}' noarch: generic # Suggests: Biobase requirements: diff --git a/recipes/bioconductor-wiggleplotr/meta.yaml b/recipes/bioconductor-wiggleplotr/meta.yaml index 21ba541310356..b8dcd748549bb 100644 --- a/recipes/bioconductor-wiggleplotr/meta.yaml +++ b/recipes/bioconductor-wiggleplotr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "wiggleplotr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 15aa40f6d6b29b4f43f76f818daac0ec + md5: 9e05d485ba51bf035918d23e686e60ba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-wiggleplotr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - r-cowplot @@ -33,11 +34,11 @@ requirements: - 'r-ggplot2 >=2.2.0' - r-purrr run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - r-cowplot diff --git a/recipes/bioconductor-worm.db0/meta.yaml b/recipes/bioconductor-worm.db0/meta.yaml index 98bdfb084ad56..18bb7a5e84082 100644 --- a/recipes/bioconductor-worm.db0/meta.yaml +++ b/recipes/bioconductor-worm.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "worm.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5ab9b7c14dafa60945e528fe7b940d42 + md5: 67be1277b5ae184558259ac720a5741e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-worm.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-worm.db0/post-link.sh b/recipes/bioconductor-worm.db0/post-link.sh index bbbb7b1411a33..58e6b26a5f6a0 100644 --- a/recipes/bioconductor-worm.db0/post-link.sh +++ b/recipes/bioconductor-worm.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "worm.db0-3.17.0" +installBiocDataPackage.sh "worm.db0-3.18.0" diff --git a/recipes/bioconductor-wpm/meta.yaml b/recipes/bioconductor-wpm/meta.yaml index 9da297b9934f8..38ed8c9815556 100644 --- a/recipes/bioconductor-wpm/meta.yaml +++ b/recipes/bioconductor-wpm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "wpm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1c516e008e79b67ff826cf796f4eeced + md5: 44df6efb278049a19cefea84cb8a8b64 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-wpm", max_pin="x.x") }}' noarch: generic # Suggests: MSnbase, testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-config @@ -39,8 +40,8 @@ requirements: - r-shinywidgets - r-stringr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-config diff --git a/recipes/bioconductor-wppi/meta.yaml b/recipes/bioconductor-wppi/meta.yaml index 7116847631e52..b3d8b9e3382a3 100644 --- a/recipes/bioconductor-wppi/meta.yaml +++ b/recipes/bioconductor-wppi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "wppi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6263659decef0f59841200d8558ec8a8 + md5: 1de428cfbb93be33d9e71b0415937cd9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-wppi", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-omnipathr >=3.8.0,<3.9.0' + - 'bioconductor-omnipathr >=3.10.0,<3.11.0' - r-base - r-dplyr - r-igraph @@ -35,7 +36,7 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-omnipathr >=3.8.0,<3.9.0' + - 'bioconductor-omnipathr >=3.10.0,<3.11.0' - r-base - r-dplyr - r-igraph @@ -57,4 +58,3 @@ about: summary: 'Weighting protein-protein interactions' description: 'Protein-protein interaction data is essential for omics data analysis and modeling. Database knowledge is general, not specific for cell type, physiological condition or any other context determining which connections are functional and contribute to the signaling. Functional annotations such as Gene Ontology and Human Phenotype Ontology might help to evaluate the relevance of interactions. This package predicts functional relevance of protein-protein interactions based on functional annotations such as Human Protein Ontology and Gene Ontology, and prioritizes genes based on network topology, functional scores and a path search algorithm.' license_file: LICENSE - diff --git a/recipes/bioconductor-wrench/meta.yaml b/recipes/bioconductor-wrench/meta.yaml index 6c7b3c52ded7b..8117dd068c109 100644 --- a/recipes/bioconductor-wrench/meta.yaml +++ b/recipes/bioconductor-wrench/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "Wrench" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c7e30debeed00e428d39c2b65fe51f8b + md5: 18e9fb2840f0002f41be3799688e2b1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-wrench", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-locfit - r-matrixstats run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-locfit - r-matrixstats diff --git a/recipes/bioconductor-xcms/meta.yaml b/recipes/bioconductor-xcms/meta.yaml index 8c2915782fe49..0db9d71304ea8 100644 --- a/recipes/bioconductor-xcms/meta.yaml +++ b/recipes/bioconductor-xcms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.22.0" %} +{% set version = "4.0.0" %} {% set name = "xcms" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,53 +11,60 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 044ad9c66603d6d269746262f72ba146 + md5: 194314f3a5b94121a4007b58b17182b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>= 0.25.1), ncdf4, testthat, pander, magrittr, rmarkdown, MALDIquant, pheatmap, Spectra (>= 1.1.17), MsBackendMgf, progress, signal + run_exports: '{{ pin_subpackage("bioconductor-xcms", max_pin="x.x") }}' +# Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>= 0.25.1), ncdf4, testthat, pander, rmarkdown, MALDIquant, pheatmap, MsBackendMgf, MetaboCoreUtils, signal requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-massspecwavelet >=1.66.0,<1.67.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-msfeatures >=1.8.0,<1.9.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-massspecwavelet >=1.68.0,<1.69.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-msexperiment >=1.4.0,<1.5.0' + - 'bioconductor-msfeatures >=1.10.0,<1.11.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-lattice - r-plyr + - r-progress - r-rann - r-rcolorbrewer - r-robustbase - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-massspecwavelet >=1.66.0,<1.67.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-msfeatures >=1.8.0,<1.9.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-massspecwavelet >=1.68.0,<1.69.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-msexperiment >=1.4.0,<1.5.0' + - 'bioconductor-msfeatures >=1.10.0,<1.11.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-lattice - r-plyr + - r-progress - r-rann - r-rcolorbrewer - r-robustbase diff --git a/recipes/bioconductor-xcore/meta.yaml b/recipes/bioconductor-xcore/meta.yaml index e84954b6e601d..f83edf02082ee 100644 --- a/recipes/bioconductor-xcore/meta.yaml +++ b/recipes/bioconductor-xcore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "xcore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5171f950290cc292a4878d982f241fa5 + md5: 4dd79b63bd7ff46aaa1b84dade889db2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xcore", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationHub (>= 3.0.2), BiocGenerics (>= 0.38.0), BiocParallel (>= 1.28), BiocStyle (>= 2.20.2), data.table (>= 1.14.0), devtools (>= 2.4.2), doParallel (>= 1.0.16), ExperimentHub (>= 2.2.0), knitr (>= 1.37), pheatmap (>= 1.0.12), proxy (>= 0.4.26), ridge (>= 3.0), rmarkdown (>= 2.11), rtracklayer (>= 1.52.0), testthat (>= 3.0.0), usethis (>= 2.0.1), xcoredata requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-foreach >=1.5.1' - 'r-glmnet >=4.1.2' @@ -34,12 +35,12 @@ requirements: - 'r-magrittr >=2.0.1' - 'r-matrix >=1.3.4' run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-foreach >=1.5.1' - 'r-glmnet >=4.1.2' diff --git a/recipes/bioconductor-xcoredata/meta.yaml b/recipes/bioconductor-xcoredata/meta.yaml index 121fd68bbdb97..d095f18812f83 100644 --- a/recipes/bioconductor-xcoredata/meta.yaml +++ b/recipes/bioconductor-xcoredata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "xcoredata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 172e8208ccf23b03ead836908e84522a + md5: 214626bfcbb5d66445324f6e367142c7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xcoredata", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics (>= 0.40.0), data.table (>= 1.14.2), GenomeInfoDb (>= 1.30.0), GenomicRanges (>= 1.46.1), IRanges (>= 2.28.0), knitr (>= 1.37), rmarkdown (>= 2.11), Matrix (>= 1.3.4), stringr (>= 1.4.0), S4Vectors (>= 0.32.3), TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.14.0), xcore requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xcoredata/post-link.sh b/recipes/bioconductor-xcoredata/post-link.sh index e6dff1b4de2c8..fc698f3463f09 100644 --- a/recipes/bioconductor-xcoredata/post-link.sh +++ b/recipes/bioconductor-xcoredata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "xcoredata-1.4.0" +installBiocDataPackage.sh "xcoredata-1.6.0" diff --git a/recipes/bioconductor-xde/meta.yaml b/recipes/bioconductor-xde/meta.yaml index 12e69037dc1f4..925ec6e74d9ad 100644 --- a/recipes/bioconductor-xde/meta.yaml +++ b/recipes/bioconductor-xde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "XDE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84d6c574373e0965f6bf5915f9771c11 + md5: aaf179de92edd3a7105c0fe20254f3d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xde", max_pin="x.x") }}' # Suggests: MASS, RUnit requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genemeta >=1.72.0,<1.73.0' - - 'bioconductor-siggenes >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genemeta >=1.74.0,<1.75.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' - r-base - r-gtools - r-mvtnorm @@ -32,11 +33,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genemeta >=1.72.0,<1.73.0' - - 'bioconductor-siggenes >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genemeta >=1.74.0,<1.75.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' - r-base - r-gtools - r-mvtnorm diff --git a/recipes/bioconductor-xenopus.db0/meta.yaml b/recipes/bioconductor-xenopus.db0/meta.yaml index 9d6ae3a8ab3d1..43ceb31511611 100644 --- a/recipes/bioconductor-xenopus.db0/meta.yaml +++ b/recipes/bioconductor-xenopus.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "xenopus.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cbdcc91045acef0ea9998f965b24dc2e + md5: 67b245b456f21672e70fa0690d7e8410 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xenopus.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xenopus.db0/post-link.sh b/recipes/bioconductor-xenopus.db0/post-link.sh index bb5200ffd15a8..f0f7cb9144929 100644 --- a/recipes/bioconductor-xenopus.db0/post-link.sh +++ b/recipes/bioconductor-xenopus.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "xenopus.db0-3.17.0" +installBiocDataPackage.sh "xenopus.db0-3.18.0" diff --git a/recipes/bioconductor-xenopuslaeviscdf/meta.yaml b/recipes/bioconductor-xenopuslaeviscdf/meta.yaml index 7b4c9e53adb36..567de4b026944 100644 --- a/recipes/bioconductor-xenopuslaeviscdf/meta.yaml +++ b/recipes/bioconductor-xenopuslaeviscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "xenopuslaeviscdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9d09ff76471ae60faf71090e0638f240 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xenopuslaeviscdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xenopuslaevisprobe/meta.yaml b/recipes/bioconductor-xenopuslaevisprobe/meta.yaml index 0853aa6c416f5..25b78155e0d34 100644 --- a/recipes/bioconductor-xenopuslaevisprobe/meta.yaml +++ b/recipes/bioconductor-xenopuslaevisprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "xenopuslaevisprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 06a25268a5ab57bddf28bbb364ea977b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xenopuslaevisprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xeva/meta.yaml b/recipes/bioconductor-xeva/meta.yaml index 6c08622a0c2a1..26be5b11abecf 100644 --- a/recipes/bioconductor-xeva/meta.yaml +++ b/recipes/bioconductor-xeva/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Xeva" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b765aa8d8e7a153fb73707c5f95c805 + md5: 94733e069395be524fa2d7254f9c2c5c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xeva", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-pharmacogx >=3.4.0,<3.5.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-pharmacogx >=3.6.0,<3.7.0' - r-base - r-bbmisc - r-doparallel @@ -33,9 +34,9 @@ requirements: - r-rmisc - r-scales run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-pharmacogx >=3.4.0,<3.5.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-pharmacogx >=3.6.0,<3.7.0' - r-base - r-bbmisc - r-doparallel diff --git a/recipes/bioconductor-xhybcasneuf/meta.yaml b/recipes/bioconductor-xhybcasneuf/meta.yaml index 487726e7771cb..82aa53006c4fa 100644 --- a/recipes/bioconductor-xhybcasneuf/meta.yaml +++ b/recipes/bioconductor-xhybcasneuf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "XhybCasneuf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9522270bba562cca4c2e5e2438294eca + md5: f3e6306b5c05fb026e36e4c60656e25a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xhybcasneuf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - 'bioconductor-ath1121501cdf >=2.18.0,<2.19.0' - - 'bioconductor-tinesath1cdf >=1.38.0,<1.39.0' + - 'bioconductor-tinesath1cdf >=1.40.0,<1.41.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - 'bioconductor-ath1121501cdf >=2.18.0,<2.19.0' - - 'bioconductor-tinesath1cdf >=1.38.0,<1.39.0' + - 'bioconductor-tinesath1cdf >=1.40.0,<1.41.0' - r-base - r-rcolorbrewer - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xhybcasneuf/post-link.sh b/recipes/bioconductor-xhybcasneuf/post-link.sh index 67bc5c34fecf6..40faf39513b0d 100644 --- a/recipes/bioconductor-xhybcasneuf/post-link.sh +++ b/recipes/bioconductor-xhybcasneuf/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "xhybcasneuf-1.38.0" +installBiocDataPackage.sh "xhybcasneuf-1.40.0" diff --git a/recipes/bioconductor-xina/meta.yaml b/recipes/bioconductor-xina/meta.yaml index c33500c40dac5..727ba242c837e 100644 --- a/recipes/bioconductor-xina/meta.yaml +++ b/recipes/bioconductor-xina/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "XINA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 82af22019aa44d3dc2afb08123721e80 + md5: f6a090d9e94032485c8c42a6c985b223 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xina", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-stringdb >=2.12.0,<2.13.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' - r-alluvial - r-base - r-ggplot2 @@ -30,7 +31,7 @@ requirements: - r-mclust - r-plyr run: - - 'bioconductor-stringdb >=2.12.0,<2.13.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' - r-alluvial - r-base - r-ggplot2 diff --git a/recipes/bioconductor-xlaevis.db/meta.yaml b/recipes/bioconductor-xlaevis.db/meta.yaml index 0cc840f89a298..cc34275d94283 100644 --- a/recipes/bioconductor-xlaevis.db/meta.yaml +++ b/recipes/bioconductor-xlaevis.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "xlaevis.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: deaffe47b4ee48a7edb159d8104dc241 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xlaevis.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.xl.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.xl.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.xl.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.xl.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xlaevis2cdf/meta.yaml b/recipes/bioconductor-xlaevis2cdf/meta.yaml index 8d60fc7d6bd5b..80adc6f158546 100644 --- a/recipes/bioconductor-xlaevis2cdf/meta.yaml +++ b/recipes/bioconductor-xlaevis2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "xlaevis2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9e4a80d66397299b4e66a8d6715ca4aa build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xlaevis2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xlaevis2probe/meta.yaml b/recipes/bioconductor-xlaevis2probe/meta.yaml index 8f8442f4e7479..1cba9aafeeb01 100644 --- a/recipes/bioconductor-xlaevis2probe/meta.yaml +++ b/recipes/bioconductor-xlaevis2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "xlaevis2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d86f8a05e106eb3123435da233ff851d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xlaevis2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xmapbridge/meta.yaml b/recipes/bioconductor-xmapbridge/meta.yaml index 880ef4a9d3fe4..8a8a6245590fd 100644 --- a/recipes/bioconductor-xmapbridge/meta.yaml +++ b/recipes/bioconductor-xmapbridge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "xmapbridge" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 69bd426f8a70da8f291689f424ba0ed5 + md5: 8b07bc6daa0d9dad8943ef442076eb5e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xmapbridge", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, RColorBrewer requirements: diff --git a/recipes/bioconductor-xnastring/meta.yaml b/recipes/bioconductor-xnastring/meta.yaml index e0246413138d7..b489f8d737902 100644 --- a/recipes/bioconductor-xnastring/meta.yaml +++ b/recipes/bioconductor-xnastring/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "XNAString" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a510ae3de3d9ac6d5a9bcb22c06a954 + md5: d09bf1b8eba2843f2b6285d353fb51bc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xnastring", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat, BSgenome.Hsapiens.UCSC.hg38, pander requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-formattable @@ -35,11 +36,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-formattable diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml index d66daca16a817..ebe23beba3511 100644 --- a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.12" %} {% set name = "XtraSNPlocs.Hsapiens.dbSNP144.GRCh37" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 758d024c50d2349036dc27cc689b4e5a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml index 1067bc0744ccc..ac390b39412d5 100644 --- a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.12" %} {% set name = "XtraSNPlocs.Hsapiens.dbSNP144.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c617aa805c7ecf60ee9283eb3c51b1c7 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38, SNPlocs.Hsapiens.dbSNP144.GRCh38 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xtropicaliscdf/meta.yaml b/recipes/bioconductor-xtropicaliscdf/meta.yaml index 2d5f6db6782db..117cb678fcdff 100644 --- a/recipes/bioconductor-xtropicaliscdf/meta.yaml +++ b/recipes/bioconductor-xtropicaliscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "xtropicaliscdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 253e3cde76a393789e124f395820e947 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xtropicaliscdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xtropicalisprobe/meta.yaml b/recipes/bioconductor-xtropicalisprobe/meta.yaml index d9e3ecbaf8a26..d9ebdd7601d4a 100644 --- a/recipes/bioconductor-xtropicalisprobe/meta.yaml +++ b/recipes/bioconductor-xtropicalisprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "xtropicalisprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 43d15a7e12edaec1bb5f24b87498b599 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xtropicalisprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xvector/meta.yaml b/recipes/bioconductor-xvector/meta.yaml index f9ccd9271755f..35aa815312336 100644 --- a/recipes/bioconductor-xvector/meta.yaml +++ b/recipes/bioconductor-xvector/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.40.0" %} +{% set version = "0.42.0" %} {% set name = "XVector" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c5b392028689bd387623344c3edc457d + md5: f126998c6b563132e51ea31c3995c6b9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xvector", max_pin="x.x") }}' # Suggests: Biostrings, drosophila2probe, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-yamss/meta.yaml b/recipes/bioconductor-yamss/meta.yaml index be366a95b73cb..7c64564193b38 100644 --- a/recipes/bioconductor-yamss/meta.yaml +++ b/recipes/bioconductor-yamss/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "yamss" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b3a62f39c6f009aac9c61d866e163eca + md5: a60cfddcf6749fc165badbe9a0f8a311 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yamss", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-matrix run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-matrix diff --git a/recipes/bioconductor-yapsa/meta.yaml b/recipes/bioconductor-yapsa/meta.yaml index 09e3ec2d5a308..ddef2c91d0bb8 100644 --- a/recipes/bioconductor-yapsa/meta.yaml +++ b/recipes/bioconductor-yapsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.25.0" %} +{% set version = "1.28.0" %} {% set name = "YAPSA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46e58d6b25038c9f501d67e67e49eac4 + md5: 7da75a0c0eabc79012aeb87c9a6e9582 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yapsa", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gtrellis >=1.32.0,<1.33.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-somaticsignatures >=2.36.0,<2.37.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gtrellis >=1.34.0,<1.35.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-somaticsignatures >=2.38.0,<2.39.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-circlize - r-corrplot @@ -46,15 +47,15 @@ requirements: - r-pracma - r-reshape2 run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gtrellis >=1.32.0,<1.33.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-somaticsignatures >=2.36.0,<2.37.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gtrellis >=1.34.0,<1.35.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-somaticsignatures >=2.38.0,<2.39.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-circlize - r-corrplot diff --git a/recipes/bioconductor-yarn/meta.yaml b/recipes/bioconductor-yarn/meta.yaml index 8253a3774aab2..2ac85ac689142 100644 --- a/recipes/bioconductor-yarn/meta.yaml +++ b/recipes/bioconductor-yarn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "yarn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 187cdd1c00ed2bad7d7378e1a14e10ca + md5: 90baa3de55a308d7deef0f913c6fdef8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yarn", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 0.8) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-quantro >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-quantro >=1.36.0,<1.37.0' - r-base - r-downloader - r-gplots @@ -34,12 +35,12 @@ requirements: - r-rcolorbrewer - r-readr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-quantro >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-quantro >=1.36.0,<1.37.0' - r-base - r-downloader - r-gplots diff --git a/recipes/bioconductor-ye6100subacdf/meta.yaml b/recipes/bioconductor-ye6100subacdf/meta.yaml index 3f2f1f1ecdd16..987121a33ff2b 100644 --- a/recipes/bioconductor-ye6100subacdf/meta.yaml +++ b/recipes/bioconductor-ye6100subacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ye6100subacdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 27bd71410956bfe8bffc8de14b85bdb0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ye6100subacdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ye6100subbcdf/meta.yaml b/recipes/bioconductor-ye6100subbcdf/meta.yaml index f854bb2a6c47e..e0bfba3fe6699 100644 --- a/recipes/bioconductor-ye6100subbcdf/meta.yaml +++ b/recipes/bioconductor-ye6100subbcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ye6100subbcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ee9ec4bd941940745bad538d79bfeab4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ye6100subbcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ye6100subccdf/meta.yaml b/recipes/bioconductor-ye6100subccdf/meta.yaml index 782299ff2634b..ff6863fba3546 100644 --- a/recipes/bioconductor-ye6100subccdf/meta.yaml +++ b/recipes/bioconductor-ye6100subccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ye6100subccdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fcdfed29a695fe53b62bacfe13dfe0c1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ye6100subccdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ye6100subdcdf/meta.yaml b/recipes/bioconductor-ye6100subdcdf/meta.yaml index b9ffb737415e4..03e5320b76673 100644 --- a/recipes/bioconductor-ye6100subdcdf/meta.yaml +++ b/recipes/bioconductor-ye6100subdcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ye6100subdcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 521b501ddbcdc680c3d27b5b201029b1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ye6100subdcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeast.db0/meta.yaml b/recipes/bioconductor-yeast.db0/meta.yaml index 5f538d60bb615..b98f59b289457 100644 --- a/recipes/bioconductor-yeast.db0/meta.yaml +++ b/recipes/bioconductor-yeast.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "yeast.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ce5a6e6febb6565c3a382d188d7652c0 + md5: 483043596daee94866843e6a43dcf538 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yeast.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeast.db0/post-link.sh b/recipes/bioconductor-yeast.db0/post-link.sh index 3c67745d538b4..84300e3c77c28 100644 --- a/recipes/bioconductor-yeast.db0/post-link.sh +++ b/recipes/bioconductor-yeast.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "yeast.db0-3.17.0" +installBiocDataPackage.sh "yeast.db0-3.18.0" diff --git a/recipes/bioconductor-yeast2.db/meta.yaml b/recipes/bioconductor-yeast2.db/meta.yaml index ad899e25c4fd4..8a430b81ad727 100644 --- a/recipes/bioconductor-yeast2.db/meta.yaml +++ b/recipes/bioconductor-yeast2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "yeast2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: add5784349cde4d01b75ea4472d25597 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yeast2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.sc.sgd.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.sc.sgd.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeast2cdf/meta.yaml b/recipes/bioconductor-yeast2cdf/meta.yaml index f7dfe00e0c340..af701c9f658c7 100644 --- a/recipes/bioconductor-yeast2cdf/meta.yaml +++ b/recipes/bioconductor-yeast2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "yeast2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0a718d78ae56bef9bad8168123038ac8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yeast2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeast2probe/meta.yaml b/recipes/bioconductor-yeast2probe/meta.yaml index 69700e2c68925..9e744a4c6cd0b 100644 --- a/recipes/bioconductor-yeast2probe/meta.yaml +++ b/recipes/bioconductor-yeast2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "yeast2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3f52a2b7bd379624bc2966ca28c9ddf9 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yeast2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeastcc/meta.yaml b/recipes/bioconductor-yeastcc/meta.yaml index 20948f279f447..51737465e21ea 100644 --- a/recipes/bioconductor-yeastcc/meta.yaml +++ b/recipes/bioconductor-yeastcc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "yeastCC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bf769fb99f3c5b763cc44fb25947231a + md5: 847d9bba73cb25f458f608c2cd6bf0e8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yeastcc", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeastcc/post-link.sh b/recipes/bioconductor-yeastcc/post-link.sh index de0088d2ddb2c..5cfa549de6683 100644 --- a/recipes/bioconductor-yeastcc/post-link.sh +++ b/recipes/bioconductor-yeastcc/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "yeastcc-1.40.0" +installBiocDataPackage.sh "yeastcc-1.42.0" diff --git a/recipes/bioconductor-yeastexpdata/meta.yaml b/recipes/bioconductor-yeastexpdata/meta.yaml index 41a56318dc5d8..e659778f8d1c3 100644 --- a/recipes/bioconductor-yeastexpdata/meta.yaml +++ b/recipes/bioconductor-yeastexpdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.46.0" %} +{% set version = "0.48.0" %} {% set name = "yeastExpData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 57c3359351ed64d39e2d8d82abe2d852 + md5: 7cd63808a957defe831bf3e9d3ef4789 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yeastexpdata", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeastexpdata/post-link.sh b/recipes/bioconductor-yeastexpdata/post-link.sh index 315ba75beea94..60ca33cf64171 100644 --- a/recipes/bioconductor-yeastexpdata/post-link.sh +++ b/recipes/bioconductor-yeastexpdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "yeastexpdata-0.46.0" +installBiocDataPackage.sh "yeastexpdata-0.48.0" diff --git a/recipes/bioconductor-yeastgsdata/meta.yaml b/recipes/bioconductor-yeastgsdata/meta.yaml index 0d48dd94a2999..ae9c7079330f7 100644 --- a/recipes/bioconductor-yeastgsdata/meta.yaml +++ b/recipes/bioconductor-yeastgsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "yeastGSData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09f1e0c194efae4d807ab0b3b14629a5 + md5: bc455a9ecd3eb2652f887026841b3c69 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yeastgsdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeastgsdata/post-link.sh b/recipes/bioconductor-yeastgsdata/post-link.sh index 412c2a9f44881..20a72ee7a6dc7 100644 --- a/recipes/bioconductor-yeastgsdata/post-link.sh +++ b/recipes/bioconductor-yeastgsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "yeastgsdata-0.38.0" +installBiocDataPackage.sh "yeastgsdata-0.40.0" diff --git a/recipes/bioconductor-yeastnagalakshmi/meta.yaml b/recipes/bioconductor-yeastnagalakshmi/meta.yaml index 585074839b144..1fdc69c9ba943 100644 --- a/recipes/bioconductor-yeastnagalakshmi/meta.yaml +++ b/recipes/bioconductor-yeastnagalakshmi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "yeastNagalakshmi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e9c196bfda6e0909a324d88a616dc992 + md5: ea5068bf2b4053452f416c56ab32736a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yeastnagalakshmi", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeastnagalakshmi/post-link.sh b/recipes/bioconductor-yeastnagalakshmi/post-link.sh index 21bc5072c30a3..38aeeac70d388 100644 --- a/recipes/bioconductor-yeastnagalakshmi/post-link.sh +++ b/recipes/bioconductor-yeastnagalakshmi/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "yeastnagalakshmi-1.36.0" +installBiocDataPackage.sh "yeastnagalakshmi-1.38.0" diff --git a/recipes/bioconductor-yeastrnaseq/meta.yaml b/recipes/bioconductor-yeastrnaseq/meta.yaml index 7136e8f15b98f..267ad94c02c79 100644 --- a/recipes/bioconductor-yeastrnaseq/meta.yaml +++ b/recipes/bioconductor-yeastrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "yeastRNASeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f8a8b1a80312aeac4d1676bc8adcb0ee + md5: 2344deacf993b96e1709ad96b710471f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yeastrnaseq", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, ShortRead, IRanges requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeastrnaseq/post-link.sh b/recipes/bioconductor-yeastrnaseq/post-link.sh index a897a1a63c2fb..5e55679c515cb 100644 --- a/recipes/bioconductor-yeastrnaseq/post-link.sh +++ b/recipes/bioconductor-yeastrnaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "yeastrnaseq-0.38.0" +installBiocDataPackage.sh "yeastrnaseq-0.40.0" diff --git a/recipes/bioconductor-ygs98.db/meta.yaml b/recipes/bioconductor-ygs98.db/meta.yaml index d4ae7caec47a2..a2127800e3fe5 100644 --- a/recipes/bioconductor-ygs98.db/meta.yaml +++ b/recipes/bioconductor-ygs98.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "ygs98.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d21c0dc1ee0f7512ae921a501b425fd3 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ygs98.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.sc.sgd.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.sc.sgd.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ygs98cdf/meta.yaml b/recipes/bioconductor-ygs98cdf/meta.yaml index e4d5474142f4d..3fe615142da63 100644 --- a/recipes/bioconductor-ygs98cdf/meta.yaml +++ b/recipes/bioconductor-ygs98cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ygs98cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ec7df7564cf28e093646325ec55baf1e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ygs98cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ygs98frmavecs/meta.yaml b/recipes/bioconductor-ygs98frmavecs/meta.yaml index 52208c458cde6..aa59611da9db5 100644 --- a/recipes/bioconductor-ygs98frmavecs/meta.yaml +++ b/recipes/bioconductor-ygs98frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.0" %} {% set name = "ygs98frmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e78c8447eb381b91dafb2f9688da39dc build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ygs98frmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ygs98probe/meta.yaml b/recipes/bioconductor-ygs98probe/meta.yaml index 9c19a6f150513..727f6b9cb5c26 100644 --- a/recipes/bioconductor-ygs98probe/meta.yaml +++ b/recipes/bioconductor-ygs98probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ygs98probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f40f21d7074818a4ee74a45b5533e89d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ygs98probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-zebrafish.db/meta.yaml b/recipes/bioconductor-zebrafish.db/meta.yaml index 41da05b397de1..a67f14aba8f67 100644 --- a/recipes/bioconductor-zebrafish.db/meta.yaml +++ b/recipes/bioconductor-zebrafish.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "zebrafish.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 64e40a61e81ac9397affb09880846559 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zebrafish.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.dr.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.dr.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.dr.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.dr.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-zebrafish.db0/meta.yaml b/recipes/bioconductor-zebrafish.db0/meta.yaml index e61006f4c9cc7..47615e4211032 100644 --- a/recipes/bioconductor-zebrafish.db0/meta.yaml +++ b/recipes/bioconductor-zebrafish.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "zebrafish.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bf2c5c9a8aaee76228e865cab2901cd2 + md5: 5da71e369e2b538fe276cd58b511ebab build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zebrafish.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-zebrafish.db0/post-link.sh b/recipes/bioconductor-zebrafish.db0/post-link.sh index df3ed7576fba4..9c2fee9d13f61 100644 --- a/recipes/bioconductor-zebrafish.db0/post-link.sh +++ b/recipes/bioconductor-zebrafish.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "zebrafish.db0-3.17.0" +installBiocDataPackage.sh "zebrafish.db0-3.18.0" diff --git a/recipes/bioconductor-zebrafishcdf/meta.yaml b/recipes/bioconductor-zebrafishcdf/meta.yaml index 228a47b0be6e1..fe5266cf6ca7e 100644 --- a/recipes/bioconductor-zebrafishcdf/meta.yaml +++ b/recipes/bioconductor-zebrafishcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "zebrafishcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 04edbb632600c97610b86423c2d850e7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zebrafishcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-zebrafishprobe/meta.yaml b/recipes/bioconductor-zebrafishprobe/meta.yaml index 07f967fbcbef9..a1f043e4c626b 100644 --- a/recipes/bioconductor-zebrafishprobe/meta.yaml +++ b/recipes/bioconductor-zebrafishprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "zebrafishprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: eea2747859afa763addc7313ab0a2452 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zebrafishprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-zebrafishrnaseq/meta.yaml b/recipes/bioconductor-zebrafishrnaseq/meta.yaml index d3c760874b7b2..64a3e534df264 100644 --- a/recipes/bioconductor-zebrafishrnaseq/meta.yaml +++ b/recipes/bioconductor-zebrafishrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "zebrafishRNASeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 06390452c93fde30918ee5c5a3f6e5f2 + md5: c1fcbadec1b25e4b28483c015f7ab35c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zebrafishrnaseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-zebrafishrnaseq/post-link.sh b/recipes/bioconductor-zebrafishrnaseq/post-link.sh index f93e198eb9261..48e9432717478 100644 --- a/recipes/bioconductor-zebrafishrnaseq/post-link.sh +++ b/recipes/bioconductor-zebrafishrnaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "zebrafishrnaseq-1.20.0" +installBiocDataPackage.sh "zebrafishrnaseq-1.22.0" diff --git a/recipes/bioconductor-zellkonverter/meta.yaml b/recipes/bioconductor-zellkonverter/meta.yaml index 20a3cc49e9795..779bd0a947f9a 100644 --- a/recipes/bioconductor-zellkonverter/meta.yaml +++ b/recipes/bioconductor-zellkonverter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.1" %} {% set name = "zellkonverter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1163d42795ee3d22169a0d6212a95c17 + md5: 5ba05cd62d95057a39c194a5084c551a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zellkonverter", max_pin="x.x") }}' noarch: generic -# Suggests: anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rmarkdown, rhdf5, scRNAseq, spelling, testthat, withr +# Suggests: anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rmarkdown, rhdf5 (>= 2.45.1), scRNAseq, spelling, testthat, withr requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-matrix - r-reticulate run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-matrix diff --git a/recipes/bioconductor-zenith/meta.yaml b/recipes/bioconductor-zenith/meta.yaml index 5df9b466a762e..20b3c23ba110d 100644 --- a/recipes/bioconductor-zenith/meta.yaml +++ b/recipes/bioconductor-zenith/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.2" %} {% set name = "zenith" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 92aec1931e3466b18edd951d9f2f1866 + md5: 60c9729fb2407d62a1ea15b1aa5ee0eb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zenith", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit requirements: host: - - 'bioconductor-enrichmentbrowser >=2.30.0,<2.31.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-variancepartition >=1.30.0,<1.31.0' + - 'bioconductor-enrichmentbrowser >=2.32.0,<2.33.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-variancepartition >=1.32.0,<1.33.0' - r-base - r-ggplot2 - 'r-msigdbr >=7.5.1' @@ -34,10 +35,10 @@ requirements: - r-rfast - r-tidyr run: - - 'bioconductor-enrichmentbrowser >=2.30.0,<2.31.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-variancepartition >=1.30.0,<1.31.0' + - 'bioconductor-enrichmentbrowser >=2.32.0,<2.33.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-variancepartition >=1.32.0,<1.33.0' - r-base - r-ggplot2 - 'r-msigdbr >=7.5.1' diff --git a/recipes/bioconductor-zfpkm/meta.yaml b/recipes/bioconductor-zfpkm/meta.yaml index e3d521f2c1214..0624f38a002d1 100644 --- a/recipes/bioconductor-zfpkm/meta.yaml +++ b/recipes/bioconductor-zfpkm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "zFPKM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6819aae4b24e1a3ff09b47137e6e9a8f + md5: a167e99447d7fd6b5081152a7d4472a4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zfpkm", max_pin="x.x") }}' noarch: generic # Suggests: knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-dplyr - r-ggplot2 - r-tidyr run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-dplyr diff --git a/recipes/bioconductor-zinbwave/meta.yaml b/recipes/bioconductor-zinbwave/meta.yaml index 48a73518b7173..2dec8b8225d7f 100644 --- a/recipes/bioconductor-zinbwave/meta.yaml +++ b/recipes/bioconductor-zinbwave/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "zinbwave" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eb568f3b13f70194dfbd6438d917b0d0 + md5: e909f5d76f0ce0b7d65358ee0f80b1f3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zinbwave", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-softimpute run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-softimpute diff --git a/recipes/bioconductor-zlibbioc/meta.yaml b/recipes/bioconductor-zlibbioc/meta.yaml index bf2395a8350b9..2434de1bccde7 100644 --- a/recipes/bioconductor-zlibbioc/meta.yaml +++ b/recipes/bioconductor-zlibbioc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "zlibbioc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1036b343d28d7fe87cd23543d6702425 + md5: babdaf77bc9e9e8218fa07d643f31730 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zlibbioc", max_pin="x.x") }}' # Suggests: BiocStyle requirements: host: diff --git a/recipes/bioconductor-zygositypredictor/meta.yaml b/recipes/bioconductor-zygositypredictor/meta.yaml index f304148a7bc32..6ed4225df0b9b 100644 --- a/recipes/bioconductor-zygositypredictor/meta.yaml +++ b/recipes/bioconductor-zygositypredictor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.3" %} +{% set version = "1.2.0" %} {% set name = "ZygosityPredictor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 08898751473ecbad4c0b07367b5b8cfc + md5: c201664f307a2cf422119e2fa87759cf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zygositypredictor", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-dplyr - r-igraph @@ -34,12 +35,12 @@ requirements: - r-stringr - r-tibble run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-dplyr - r-igraph diff --git a/recipes/expansionhunter/meta.yaml b/recipes/expansionhunter/meta.yaml index a0e856b6f9c2c..9e2552fbe11df 100644 --- a/recipes/expansionhunter/meta.yaml +++ b/recipes/expansionhunter/meta.yaml @@ -15,7 +15,7 @@ source: - 0004-add-fmt-formatters-for-classes.patch - 0005-apply-bioconda-4.0.2-patches.patch # [osx] build: - number: '0' + number: 1 run_exports: - {{ pin_subpackage('expansionhunter', max_pin="x") }} requirements: diff --git a/recipes/pxblat/build_failure.linux-64.yaml b/recipes/pxblat/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..5b942524e2cd1 --- /dev/null +++ b/recipes/pxblat/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 9910e8828c844b7213ab38c0600f3caa04cc87acd4497a3b3fbd44a337aefad8 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 169, in exc_logging_wrapper + status = run_func(*args) + ^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/cli/req_command.py", line 248, in wrapper + return func(self, options, args) + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/commands/install.py", line 377, in run + requirement_set = resolver.resolve( + ^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 73, in resolve + collected = self.factory.collect_root_requirements(root_reqs) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 491, in collect_root_requirements + req = self._make_requirement_from_install_req( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 453, in _make_requirement_from_install_req + cand = self._make_candidate_from_link( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 206, in _make_candidate_from_link + self._link_candidate_cache[link] = LinkCandidate( + ^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 293, in __init__ + super().__init__( + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__ + self.dist = self._prepare() + ^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 225, in _prepare + dist = self._prepare_distribution() + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in _prepare_distribution + return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/operations/prepare.py", line 516, in prepare_linked_requirement + return self._prepare_linked_requirement(req, parallel_builds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/operations/prepare.py", line 631, in _prepare_linked_requirement + dist = _get_prepared_distribution( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/operations/prepare.py", line 69, in _get_prepared_distribution + abstract_dist.prepare_distribution_metadata( + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/distributions/sdist.py", line 61, in prepare_distribution_metadata + self.req.prepare_metadata() + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/req/req_install.py", line 555, in prepare_metadata + self.metadata_directory = generate_metadata( + ^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/operations/build/metadata.py", line 35, in generate_metadata + distinfo_dir = backend.prepare_metadata_for_build_wheel(metadata_dir) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/utils/misc.py", line 713, in prepare_metadata_for_build_wheel + return super().prepare_metadata_for_build_wheel( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 186, in prepare_metadata_for_build_wheel + return self._call_hook('prepare_metadata_for_build_wheel', { + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 321, in _call_hook + raise BackendUnavailable(data.get('traceback', '')) + pip._vendor.pyproject_hooks._impl.BackendUnavailable: Traceback (most recent call last): + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 77, in _build_backend + obj = import_module(mod_path) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/importlib/__init__.py", line 126, in import_module + return _bootstrap._gcd_import(name[level:], package, level) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "", line 1204, in _gcd_import + File "", line 1176, in _find_and_load + File "", line 1126, in _find_and_load_unlocked + File "", line 241, in _call_with_frames_removed + File "", line 1204, in _gcd_import + File "", line 1176, in _find_and_load + File "", line 1126, in _find_and_load_unlocked + File "", line 241, in _call_with_frames_removed + File "", line 1204, in _gcd_import + File "", line 1176, in _find_and_load + File "", line 1126, in _find_and_load_unlocked + File "", line 241, in _call_with_frames_removed + File "", line 1204, in _gcd_import + File "", line 1176, in _find_and_load + File "", line 1140, in _find_and_load_unlocked + ModuleNotFoundError: No module named 'poetry' + [0m[31m + [0mRemoved file://$SRC_DIR from build tracker '/tmp/pip-build-tracker-jl36fbnx' + Removed build tracker: '/tmp/pip-build-tracker-jl36fbnx' + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build + utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, + File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/pxblat_1688740629379/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/pxblat/build_failure.osx-64.yaml b/recipes/pxblat/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..7cf5a245e3926 --- /dev/null +++ b/recipes/pxblat/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 9910e8828c844b7213ab38c0600f3caa04cc87acd4497a3b3fbd44a337aefad8 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 169, in exc_logging_wrapper + status = run_func(*args) + ^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/cli/req_command.py", line 248, in wrapper + return func(self, options, args) + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/commands/install.py", line 377, in run + requirement_set = resolver.resolve( + ^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 73, in resolve + collected = self.factory.collect_root_requirements(root_reqs) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 491, in collect_root_requirements + req = self._make_requirement_from_install_req( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 453, in _make_requirement_from_install_req + cand = self._make_candidate_from_link( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 206, in _make_candidate_from_link + self._link_candidate_cache[link] = LinkCandidate( + ^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 293, in __init__ + super().__init__( + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__ + self.dist = self._prepare() + ^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 225, in _prepare + dist = self._prepare_distribution() + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in _prepare_distribution + return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/operations/prepare.py", line 516, in prepare_linked_requirement + return self._prepare_linked_requirement(req, parallel_builds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/operations/prepare.py", line 631, in _prepare_linked_requirement + dist = _get_prepared_distribution( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/operations/prepare.py", line 69, in _get_prepared_distribution + abstract_dist.prepare_distribution_metadata( + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/distributions/sdist.py", line 61, in prepare_distribution_metadata + self.req.prepare_metadata() + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/req/req_install.py", line 555, in prepare_metadata + self.metadata_directory = generate_metadata( + ^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/operations/build/metadata.py", line 35, in generate_metadata + distinfo_dir = backend.prepare_metadata_for_build_wheel(metadata_dir) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/utils/misc.py", line 713, in prepare_metadata_for_build_wheel + return super().prepare_metadata_for_build_wheel( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 186, in prepare_metadata_for_build_wheel + return self._call_hook('prepare_metadata_for_build_wheel', { + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 321, in _call_hook + raise BackendUnavailable(data.get('traceback', '')) + pip._vendor.pyproject_hooks._impl.BackendUnavailable: Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 77, in _build_backend + obj = import_module(mod_path) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/importlib/__init__.py", line 126, in import_module + return _bootstrap._gcd_import(name[level:], package, level) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "", line 1204, in _gcd_import + File "", line 1176, in _find_and_load + File "", line 1126, in _find_and_load_unlocked + File "", line 241, in _call_with_frames_removed + File "", line 1204, in _gcd_import + File "", line 1176, in _find_and_load + File "", line 1126, in _find_and_load_unlocked + File "", line 241, in _call_with_frames_removed + File "", line 1204, in _gcd_import + File "", line 1176, in _find_and_load + File "", line 1126, in _find_and_load_unlocked + File "", line 241, in _call_with_frames_removed + File "", line 1204, in _gcd_import + File "", line 1176, in _find_and_load + File "", line 1140, in _find_and_load_unlocked + ModuleNotFoundError: No module named 'poetry' + + Removed file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-m00ixlfd' + Removed build tracker: '/private/tmp/pip-build-tracker-m00ixlfd' + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build + utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/r-acidbase/meta.yaml b/recipes/r-acidbase/meta.yaml index bf7918867c609..bd6a6b423c173 100644 --- a/recipes/r-acidbase/meta.yaml +++ b/recipes/r-acidbase/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 104b8c7907375ef5943217aa1565ef8fd01ac8bed4e4d9addc2aa489195b172d build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-acidbase', max_pin="x.x") }} diff --git a/recipes/r-basejump/meta.yaml b/recipes/r-basejump/meta.yaml index 8e6d80ca32c6f..6fe0a1493ed18 100644 --- a/recipes/r-basejump/meta.yaml +++ b/recipes/r-basejump/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 06b216c539d112468172d021ba9445b8d98918609319fb34c200093fa052cbb9 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-basejump', max_pin="x.x") }} diff --git a/recipes/r-biomartr/meta.yaml b/recipes/r-biomartr/meta.yaml index 350413e5b3959..a4fbd52da4fc5 100644 --- a/recipes/r-biomartr/meta.yaml +++ b/recipes/r-biomartr/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-chromium/meta.yaml b/recipes/r-chromium/meta.yaml index 323e18c9b526c..0c8141d3d61c6 100644 --- a/recipes/r-chromium/meta.yaml +++ b/recipes/r-chromium/meta.yaml @@ -10,7 +10,7 @@ source: sha256: e2f58a6141ce55b73d631323360d86d3713bf7870476c2505f457c61f41a3d0b build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-chromium', max_pin="x.x") }} diff --git a/recipes/r-goalie/meta.yaml b/recipes/r-goalie/meta.yaml index ad0ccf22a5c52..166ff214cc367 100644 --- a/recipes/r-goalie/meta.yaml +++ b/recipes/r-goalie/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 58e751134e5b0431a3a8fee58eefdef2b169e782f1a6eea623c6c9e7fadcd937 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-goalie', max_pin="x.x") }} diff --git a/recipes/r-interpretmsspectrum/meta.yaml b/recipes/r-interpretmsspectrum/meta.yaml new file mode 100644 index 0000000000000..40d0de68aa104 --- /dev/null +++ b/recipes/r-interpretmsspectrum/meta.yaml @@ -0,0 +1,43 @@ +{% set version = '1.3.3' %} + +package: + name: r-interpretmsspectrum + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/InterpretMSSpectrum_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/InterpretMSSpectrum/InterpretMSSpectrum_{{ version }}.tar.gz + sha256: 306a1541504088a05636f49e71a12d806f32fcaaa2d0622a58288452012d71db + +build: + number: 1 + noarch: generic + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + host: + - r-base + - bioconductor-rdisop + - r-envipat + - r-plyr + run: + - r-base + - bioconductor-rdisop + - r-envipat + - r-plyr + +test: + commands: + - $R -e "library('InterpretMSSpectrum')" + +about: + home: http://dx.doi.org/10.1021/acs.analchem.6b02743 + license: GPL-3.0-only + summary: Annotate and interpret deconvoluted mass spectra (mass*intensity pairs) from high + resolution mass spectrometry devices. + license_family: GPL3 + license_file: + - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/r-pipette/meta.yaml b/recipes/r-pipette/meta.yaml index 0a64d3387eaec..3c673788c57bd 100644 --- a/recipes/r-pipette/meta.yaml +++ b/recipes/r-pipette/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 80298775063372e1275191ff800ec00b7feb9cc33fdb9afb453826499e3b54c0 build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-ramclustr/meta.yaml b/recipes/r-ramclustr/meta.yaml index bdaafa9cc6768..ac3e72aa6403e 100644 --- a/recipes/r-ramclustr/meta.yaml +++ b/recipes/r-ramclustr/meta.yaml @@ -11,7 +11,7 @@ source: sha256: cd1154bb1411346a5426a919b2d374daedaabc08ce094b6ebed5a897c1fc9156 build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-tinyarray/meta.yaml b/recipes/r-tinyarray/meta.yaml index dc511cf128aee..1a61d8ba0282c 100644 --- a/recipes/r-tinyarray/meta.yaml +++ b/recipes/r-tinyarray/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 68ea15eb8d726368919faa54c89e2d18806b94e73e21fdee365c350b7ee79eb3 build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/ultraplex/meta.yaml b/recipes/ultraplex/meta.yaml index 68e00272ed7de..86c0708b1c4f0 100644 --- a/recipes/ultraplex/meta.yaml +++ b/recipes/ultraplex/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 7b1efa09a421590907c7e5177eb9e4837deade89c237b961bcf2f7edfa9f2e90 build: - number: 0 + number: 1 skip: True # [py < 37 or py > 39] script: - "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --use-pep517 -vvv" From 6e3ed1753da8984d6f1f46c8906bbf956c00c523 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Dec 2023 15:49:02 -0500 Subject: [PATCH 026/121] Update deeplc to 2.2.26 (#44238) * Update deeplc to 2.2.23 * Update deeplc to 2.2.24 * add pyopenms * Update deeplc to 2.2.25 * Update deeplc to 2.2.26 * try extended base * revert extended base --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/deeplc/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/deeplc/meta.yaml b/recipes/deeplc/meta.yaml index ad2ebc4a427b0..51849c0d6507f 100644 --- a/recipes/deeplc/meta.yaml +++ b/recipes/deeplc/meta.yaml @@ -1,6 +1,6 @@ {% set name = "DeepLC" %} -{% set version = "2.2.22" %} -{% set sha256 = "82049484d907a410ed8cdf27711af90a7a372adeb53fc8a2d2e0917109c4e611" %} +{% set version = "2.2.26" %} +{% set sha256 = "b4cbb3612a89fe82ddac6149a261f7440c721f4b87235ce534c4cbd95d424e1b" %} package: name: {{ name|lower }} @@ -13,7 +13,7 @@ source: build: number: 0 noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv run_exports: - {{ pin_subpackage("deeplc", max_pin="x") }} entry_points: @@ -40,6 +40,7 @@ requirements: - deeplcretrainer - psm-utils - hdf5plugin + - pyopenms test: imports: @@ -49,7 +50,8 @@ about: home: "https://compomics.github.io/projects/DeepLC" summary: 'DeepLC: Retention time prediction for (modified) peptides using Deep Learning.' dev_url: "https://github.com/compomics/DeepLC" - license: APACHE + license: Apache-2.0 + license_family: APACHE license_file: LICENSE extra: From fe74e96d7c4b100fccf2be422a83364aeb641ade Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 29 Dec 2023 15:57:53 -0600 Subject: [PATCH 027/121] Add recipe for CellBender v0.3.0 (#45024) * Add recipe for CellBender v0.3.0 * add run_exports --- recipes/cellbender/meta.yaml | 64 ++++++++++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 recipes/cellbender/meta.yaml diff --git a/recipes/cellbender/meta.yaml b/recipes/cellbender/meta.yaml new file mode 100644 index 0000000000000..68183da020015 --- /dev/null +++ b/recipes/cellbender/meta.yaml @@ -0,0 +1,64 @@ +{% set name = "cellbender" %} +{% set version = "0.3.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cellbender-{{ version }}.tar.gz + sha256: 94a46fb2b5921414ea86213cfdebca267b9ba6ba02df854cbd353980ab3aff42 + +build: + number: 0 + noarch: python + entry_points: + - cellbender = cellbender.base_cli:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('cellbender', max_pin="x.x") }} + +requirements: + host: + - python 3.7 + - setuptools >=61.2 + - pip + run: + - python 3.7 + - numpy + - scipy + - pytables + - pandas + - pyro-ppl >=1.8.4 + - pytorch + - matplotlib-base + - anndata >=0.7 + - loompy + - ipython + - jupyter + - jupyter_contrib_nbextensions + - notebook <7.0.0 + - nbconvert <7.0.0 + - psutil + +test: + imports: + - cellbender + commands: + - cellbender --help + +about: + home: https://github.com/broadinstitute/CellBender + summary: "A software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data" + license: BSD-3-Clause + license_family: BSD + license_file: LICENSE + doc_url: https://cellbender.readthedocs.io/en/latest/ + dev_url: https://github.com/broadinstitute/CellBender + +extra: + recipe-maintainers: + - mencian + identifiers: + - biotools:CellBender + - doi:10.1038/s41592-023-01943-7 From 49baea5c2b1614c7e2e91fe9bad597ce2011c8fd Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 29 Dec 2023 18:46:16 -0600 Subject: [PATCH 028/121] Fix nrpys to build on python 3.8+ (#45025) --- recipes/nrpys/build.sh | 2 +- recipes/nrpys/cargo.patch | 9 +++++++++ recipes/nrpys/meta.yaml | 15 ++++++++------- recipes/nrpys/{patch => pyproject.patch} | 11 ++++++++--- 4 files changed, 26 insertions(+), 11 deletions(-) create mode 100644 recipes/nrpys/cargo.patch rename recipes/nrpys/{patch => pyproject.patch} (50%) diff --git a/recipes/nrpys/build.sh b/recipes/nrpys/build.sh index c08897288c011..6c41a389a5494 100644 --- a/recipes/nrpys/build.sh +++ b/recipes/nrpys/build.sh @@ -11,4 +11,4 @@ mkdir -p ${PREFIX}/bin # build shared Python module with Rust maturin build --release --strip -f -${PYTHON} -m pip install -vv . +${PYTHON} -m pip install -vvv --no-deps --no-build-isolation . diff --git a/recipes/nrpys/cargo.patch b/recipes/nrpys/cargo.patch new file mode 100644 index 0000000000000..71fb4191700c6 --- /dev/null +++ b/recipes/nrpys/cargo.patch @@ -0,0 +1,9 @@ +--- a/Cargo.toml ++++ b/Cargo.toml +@@ -14,5 +14,5 @@ crate-type = ["cdylib"] + + [dependencies] + nrps-rs = "0.2.1" +-pyo3 = { version = "0.18.0", features = ["extension-module"] } ++pyo3 = { version = "0.19.0", features = ["abi3-py38"] } + thiserror = "1.0.38" diff --git a/recipes/nrpys/meta.yaml b/recipes/nrpys/meta.yaml index 497aba8dd7f46..e1a1b94498112 100644 --- a/recipes/nrpys/meta.yaml +++ b/recipes/nrpys/meta.yaml @@ -7,26 +7,27 @@ package: version: {{ version }} build: - number: 2 - noarch: generic + number: 3 + noarch: python run_exports: - {{ pin_subpackage(name|lower, max_pin="x.x") }} source: url: https://github.com/kblin/nrpys/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} - patch: - - patch + patches: + - cargo.patch + - pyproject.patch requirements: host: - - python >=3.7 + - python >=3.8 - pip - rust - maturin - zlib run: - - python >=3.7 + - python >=3.8 test: imports: @@ -34,6 +35,6 @@ test: about: home: "https://github.com/kblin/nrpys" - license: GPL3 + license: AGPL-3.0-or-later license_file: LICENSE.txt summary: "Python language bindings for nrps-rs substrate specificity predictor." diff --git a/recipes/nrpys/patch b/recipes/nrpys/pyproject.patch similarity index 50% rename from recipes/nrpys/patch rename to recipes/nrpys/pyproject.patch index 99ab333ca033e..2a8640ef4169d 100644 --- a/recipes/nrpys/patch +++ b/recipes/nrpys/pyproject.patch @@ -1,15 +1,20 @@ --- a/pyproject.toml +++ b/pyproject.toml -@@ -1,5 +1,5 @@ +@@ -1,10 +1,10 @@ [build-system] -requires = ["maturin>=0.14,<0.15"] +requires = ["maturin>=1.0,<2.0"] build-backend = "maturin" [project] -@@ -13,3 +13,5 @@ classifiers = [ + name = "nrpys" +-requires-python = ">=3.7" ++requires-python = ">=3.8" + classifiers = [ + "Programming Language :: Rust", + "Programming Language :: Python :: Implementation :: CPython", +@@ -13,3 +13,4 @@ classifiers = [ [tool.maturin] python-source = "python" +features = ["pyo3/extension-module"] -+cargo-extra-args = "--features extension-module" From b8779fb45f5dee2e48f30cf1c88fd843022e9229 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Dec 2023 19:46:30 -0500 Subject: [PATCH 029/121] Update oakvar to 2.9.83 (#45026) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index f4b045bd05e12..3980d2f261a57 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.82" %} -{% set sha256 = "77865978a9b646ce02a6e728f3f74f203a801bb4cf3df816badaca46d71ab4d2" %} +{% set version = "2.9.83" %} +{% set sha256 = "b7157f768ee6b631a202ac50a05a6b69c233320c036437f484ebeb2660422f77" %} package: name: {{ name|lower }} From df4f00e3b0c0829772acf5c4fc702851db635ed2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Dec 2023 21:08:55 -0500 Subject: [PATCH 030/121] Update foldcomp to 0.0.6 (#45018) * Update foldcomp to 0.0.6 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/foldcomp/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/foldcomp/meta.yaml b/recipes/foldcomp/meta.yaml index e27989971aa76..f645e6e9482ca 100644 --- a/recipes/foldcomp/meta.yaml +++ b/recipes/foldcomp/meta.yaml @@ -1,12 +1,14 @@ -{% set version = "0.0.5" %} -{% set sha256 = "f4997c67023946287a3958866a75a9776978d533ec8cbcb1b6ccc8b2c081d0b2" %} +{% set version = "0.0.6" %} +{% set sha256 = "7f77fded798ea711f816220e4ca20fe4a9fed9917b9b2d3f7eba22ad5e1aa7f5" %} package: name: foldcomp version: {{ version }} build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('foldcomp', max_pin="x.x") }} source: url: https://github.com/steineggerlab/foldcomp/archive/v{{ version }}.tar.gz @@ -31,10 +33,11 @@ test: about: home: https://github.com/steineggerlab/foldcomp - license: GPLv3 + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE.txt summary: "Foldcomp: a library and format for compressing and indexing large protein structure sets" extra: identifiers: - - doi:10.1101/2022.12.09.519715 + - doi:10.1093/bioinformatics/btad153 From 4d075ab4db5f31b8164ac97bdd997cbc62fa3e50 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 29 Dec 2023 21:35:58 -0600 Subject: [PATCH 031/121] Update antismash-lite to 7.1.0 (#45027) --- recipes/antismash-lite/build.sh | 4 +-- recipes/antismash-lite/meta.yaml | 55 ++++++++++++++++++-------------- 2 files changed, 33 insertions(+), 26 deletions(-) diff --git a/recipes/antismash-lite/build.sh b/recipes/antismash-lite/build.sh index 9b87424be5101..3ad1536ca047f 100644 --- a/recipes/antismash-lite/build.sh +++ b/recipes/antismash-lite/build.sh @@ -1,5 +1,5 @@ #!/bin/bash echo "include antismash/detection/genefinding/data/train_crypto" >> MANIFEST.in -df -h -$PYTHON -m pip install . --ignore-installed --no-deps -vv \ No newline at end of file +df -h +$PYTHON -m pip install . --no-build-isolation --no-deps --no-cache-dir -vvv diff --git a/recipes/antismash-lite/meta.yaml b/recipes/antismash-lite/meta.yaml index 2e3d43924775c..a41431b1a3b3f 100644 --- a/recipes/antismash-lite/meta.yaml +++ b/recipes/antismash-lite/meta.yaml @@ -1,59 +1,65 @@ -{% set name = "antiSMASH-lite" %} -{% set version = "6.1.1" %} -{% set sha256 = "38c9fa8d34dea2552d3b21e3cb2ca293864f2f53d381764de9dd3d5f0b40139e" %} +{% set name = "antismash-lite" %} +{% set version = "7.1.0" %} +{% set sha256 = "5c01cce48ef5cc2bc60bfd2e185a5937e731e86a711c4c822a336640984e9b48" %} package: name: {{ name|lower }} version: {{ version }} -build: - number: 1 - noarch: python - source: url: https://dl.secondarymetabolites.org/releases/{{ version }}/antismash-{{ version }}.tar.gz sha256: {{ sha256 }} +build: + number: 0 + noarch: python + entry_points: + - download-antismash-databases=antismash.download_databases:_main + - antismash=antismash.__main__:entrypoint + run_exports: + - {{ pin_subpackage('antismash-lite', max_pin="x") }} + requirements: host: - - python >=3.7 + - python >=3.9 - pip run: - - python >=3.7 + - python >=3.9 + - brawn >=1.0.1 - numpy - - biopython 1.78 - - helperlibs >=0.2.0 + - biopython 1.78.* + - helperlibs >=0.2.1 - jinja2 - joblib - jsonschema - - markupsafe >=2.0 + - markupsafe >=2.1.0 + - nrpys >=0.1.1 - pysvg-py3 - bcbio-gff - - pyscss + - libsass - matplotlib-base - scipy - - openjdk - - scikit-learn >=0.19 - - diamond >=0.9,<=2.0.15 + - scikit-learn >=1.3.2 + - moods >=1.9.4 + - diamond - fasttree 2.1.* - - glimmerhmm ==3.0.* + - glimmerhmm 3.0.* - hmmer2 - hmmer >=3.1b2 - - meme <=4.11.2 - - muscle 3.8.* + - meme 4.11.2 - blast - prodigal test: + imports: + - antismash commands: - - antismash -h - - blastp -help - - fasttree -help - - diamond --help 2>&1 > /dev/null + - antismash --help + - download-antismash-databases --help about: home: https://docs.antismash.secondarymetabolites.org/intro/ - license: AGPL-3.0 + license: AGPL-3.0-or-later license_family: AGPL license_file: LICENSE.txt summary: antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell @@ -72,4 +78,5 @@ extra: - doi:10.1093/nar/gkx319 - doi:10.1093/nar/gkz310 - doi:10.1093/nar/gkab335 + - doi:10.1093/nar/gkad344 - usegalaxy-eu:antismash From f4db81c8029887f6651171a14c10e70c769e937a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 30 Dec 2023 09:10:50 -0500 Subject: [PATCH 032/121] Update jcvi to 1.3.9 (#45029) * Update jcvi to 1.3.9 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/jcvi/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/jcvi/meta.yaml b/recipes/jcvi/meta.yaml index d563589238e5b..fff106f59101f 100644 --- a/recipes/jcvi/meta.yaml +++ b/recipes/jcvi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "jcvi" %} -{% set version = "1.3.8" %} +{% set version = "1.3.9" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: f193f93b0a967ab6b6e940645f68e7ab640f2838973d270a0aa8662fe3f774ae + sha256: 495940ed40e419a32c8b9dc9582fe64e233edf8d796fca71422223c3494ceaa8 build: skip: True # [py2k or osx] @@ -77,5 +77,6 @@ about: home: http://github.com/tanghaibao/jcvi license: BSD-2-Clause license_family: BSD + license_file: LICENSE summary: Python utility libraries on genome assembly, annotation and comparative genomics description: "JCVI utility libraries" From 313b18cd013654b75df72801035e6c597e901ddd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 30 Dec 2023 12:34:04 -0500 Subject: [PATCH 033/121] Update recognizer to 1.10.1 (#45031) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: João Sequeira --- recipes/recognizer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/recognizer/meta.yaml b/recipes/recognizer/meta.yaml index c8acd63dc115b..efcc7fb27632f 100644 --- a/recipes/recognizer/meta.yaml +++ b/recipes/recognizer/meta.yaml @@ -1,6 +1,6 @@ {% set name = "recognizer" %} -{% set version = "1.10.0" %} -{% set sha256 = "7f001a4fb888777a7b14707f76458f25fc98fe14299d1bdcbf2452eba7cab75f" %} +{% set version = "1.10.1" %} +{% set sha256 = "1d97b521a5b8660e5dd1726c95b885bcdce53654d01a001d8e6522a9c76d81c2" %} package: name: {{ name|lower }} From bf44da8d2db2c8e4977e2e019c67020775dd13dd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 31 Dec 2023 11:51:27 -0500 Subject: [PATCH 034/121] Update midsv to 0.11.0 (#45028) * Update midsv to 0.11.0 * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/midsv/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/midsv/meta.yaml b/recipes/midsv/meta.yaml index 653a9df45db78..7193ae74b64af 100644 --- a/recipes/midsv/meta.yaml +++ b/recipes/midsv/meta.yaml @@ -1,5 +1,5 @@ {% set name = "midsv" %} -{% set version = "0.10.2" %} +{% set version = "0.11.0" %} package: name: {{ name|lower }} @@ -7,12 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/midsv-{{ version }}.tar.gz - sha256: 5ead1213b3f34f3a4a676ddb5e88cf7bc63ae2aac1226afe735bc46a7602e559 + sha256: 713a164c4bce68f1caa72d50f7b7eef7a62b869bd65f2aebf8024d33ba6cc5b8 build: noarch: python script: {{ PYTHON }} -m pip install . -vv number: 0 + run_exports: + - {{ pin_subpackage('midsv', max_pin="x") }} requirements: host: From abd5f7b596736fea39eb2a9f2cf1f4128fffa3cf Mon Sep 17 00:00:00 2001 From: Carl Mathias Kobel Date: Wed, 3 Jan 2024 10:05:07 +0100 Subject: [PATCH 035/121] Update meta.yaml (#45041) Snakemake refactored in newer version. --- recipes/assemblycomparator2/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml index 350463aca94b1..f0d50c8973c9b 100644 --- a/recipes/assemblycomparator2/meta.yaml +++ b/recipes/assemblycomparator2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.14" %} +{% set version = "2.5.15" %} package: name: assemblycomparator2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz - sha256: d95f39d996330ab72ceffc5e8aa17b9348b39478fd2a4bfd01ca960adff2d20e + sha256: 9605f4021710e975365090fba1c13c2005c46978cec48c6cabe678167c86d33e build: @@ -17,7 +17,7 @@ build: requirements: run: - - snakemake >=7.32.3 + - snakemake =7.32.4 - mamba >=1.4.9 # Necessary for snakemake to install child environments during development. From fac515c4a64bbc159c86171fa9139f698952c318 Mon Sep 17 00:00:00 2001 From: John Lees Date: Wed, 3 Jan 2024 09:05:40 +0000 Subject: [PATCH 036/121] Rebuild unitig caller for new bifrost version (#45035) * Rebuild unitig caller for new bifrost version * Add run_exports * Fix string interpolation in pinning --- recipes/unitig-caller/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/unitig-caller/meta.yaml b/recipes/unitig-caller/meta.yaml index 66a861b27b3ad..67bcd0abf6cb4 100644 --- a/recipes/unitig-caller/meta.yaml +++ b/recipes/unitig-caller/meta.yaml @@ -12,10 +12,12 @@ source: - 0001-No-experimental.patch build: - number: 2 + number: 3 skip: True # [py27] entry_points: - unitig-caller = unitig_caller.__main__:main + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: @@ -29,12 +31,12 @@ requirements: - pybind11 - zlib - bzip2 - - bifrost >=1.2.0 + - bifrost >=1.3.0 - libgomp # [linux64] - llvm-openmp # [osx] run: - python - - bifrost >=1.2.0 + - bifrost >=1.3.0 test: imports: From 5a3a493b6d8a54905e9d3d686bf54a604f51104f Mon Sep 17 00:00:00 2001 From: Ray <851836818@qq.com> Date: Wed, 3 Jan 2024 17:09:09 +0800 Subject: [PATCH 037/121] Update annosine2 build (#45033) * Update meta.yaml * Update meta.yaml --- recipes/annosine2/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/annosine2/meta.yaml b/recipes/annosine2/meta.yaml index 9c474c8c73b80..98c711f9ab79d 100644 --- a/recipes/annosine2/meta.yaml +++ b/recipes/annosine2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: c9d12adec9875c4a429c6e9da5b76d31c760ef7474635caf742d25592378f34c build: - number: 0 + number: 1 entry_points: - annosine2 = AnnoSINE.AnnoSINE_v2:main script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " @@ -27,6 +27,7 @@ requirements: - kiwisolver - matplotlib-base - numpy + - pandas - pillow - pyparsing - python From e36c4c5ad18fd50b07d2852279677f92171a0f58 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 3 Jan 2024 04:09:55 -0500 Subject: [PATCH 038/121] Update rasusa to 0.8.0 (#45042) * Update rasusa to 0.8.0 * add run_export * bump msrv --------- Co-authored-by: Michael Hall --- recipes/rasusa/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/rasusa/meta.yaml b/recipes/rasusa/meta.yaml index 0bd1e57489918..b61dc1feb6422 100644 --- a/recipes/rasusa/meta.yaml +++ b/recipes/rasusa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.1" %} +{% set version = "0.8.0" %} {% set name = "rasusa" %} package: @@ -7,14 +7,16 @@ package: source: url: https://github.com/mbhall88/{{ name }}/archive/{{ version }}.tar.gz - sha256: 7a7e3f2f2038b3fd3ce112fa7264ef8cbd91c2aa14fe60d8be1be1bb13416a56 + sha256: 903fa09fd7f7cc92880953131487186c3fbf539a127dc82f502559f9c1e9c11a build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('rasusa', max_pin="x.x") }} requirements: build: - - rust >=1.53 + - rust >=1.70 - {{ compiler('c') }} # [not win] test: From 418fbdabc38d59053287d13cde899d02a4bd1973 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 3 Jan 2024 07:52:25 -0500 Subject: [PATCH 039/121] Update annonars to 0.33.0 (#45043) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 7cd859e346249..d7d44551f9f50 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.32.0" %} +{% set version = "0.33.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 467ebd15737c4a6451f5993fa1e93f52c5ecb4a1cdf0b0cd754b414261730f37 + sha256: 258cfc2aee680718fc1acc8bccddb571416e425198ca258ee295cdc42cc19f71 requirements: build: From bf501ad446c790877543dcb1a512cf58b083fd21 Mon Sep 17 00:00:00 2001 From: Florian Zwagemaker <49153065+florianzwagemaker@users.noreply.github.com> Date: Wed, 3 Jan 2024 14:33:27 +0100 Subject: [PATCH 040/121] patch viroconstrictor snakemake requirements to not use version 8.x (#45036) --- recipes/viroconstrictor/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/viroconstrictor/meta.yaml b/recipes/viroconstrictor/meta.yaml index aed7470960f98..a1f44a2d6cd3d 100644 --- a/recipes/viroconstrictor/meta.yaml +++ b/recipes/viroconstrictor/meta.yaml @@ -17,7 +17,7 @@ build: - viroConstrictor = ViroConstrictor.__main__:main - Viroconstrictor = ViroConstrictor.__main__:main script: {{ PYTHON }} -m pip install . --no-deps -vvv - number: 0 + number: 1 run_exports: - {{ pin_subpackage('viroconstrictor', max_pin="x") }} @@ -25,7 +25,7 @@ requirements: host: - python >=3.10 - pip - - snakemake >=7.15.2 + - snakemake >=7.15.2, < 8 - conda run: - python >=3.10 @@ -37,7 +37,7 @@ requirements: - openpyxl - pyyaml ==6.0 - rich ==13.* - - snakemake >=7.15.2 + - snakemake >=7.15.2, < 8 - aminoextract ==0.3.1 - conda - mamba From e99ba8fa7b2c89c7011456d63c2fff11f6747a5d Mon Sep 17 00:00:00 2001 From: Kanglu123 <64641114+Kanglu123@users.noreply.github.com> Date: Wed, 3 Jan 2024 21:35:21 +0800 Subject: [PATCH 041/121] Add Deepmei version 1.0.0 recipes (#45005) --- recipes/deepmei/build.sh | 4 + recipes/deepmei/license.txt | 674 ++++++++++++++++++++++++++++++++++++ recipes/deepmei/meta.yaml | 35 ++ 3 files changed, 713 insertions(+) create mode 100644 recipes/deepmei/build.sh create mode 100644 recipes/deepmei/license.txt create mode 100644 recipes/deepmei/meta.yaml diff --git a/recipes/deepmei/build.sh b/recipes/deepmei/build.sh new file mode 100644 index 0000000000000..1b8b9158061ef --- /dev/null +++ b/recipes/deepmei/build.sh @@ -0,0 +1,4 @@ +mkdir -p $PREFIX/bin +ls $PREFIX/bin/ +cp -r * $PREFIX/bin/ +chmod +x $PREFIX/bin/* diff --git a/recipes/deepmei/license.txt b/recipes/deepmei/license.txt new file mode 100644 index 0000000000000..f288702d2fa16 --- /dev/null +++ b/recipes/deepmei/license.txt @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/deepmei/meta.yaml b/recipes/deepmei/meta.yaml new file mode 100644 index 0000000000000..ab40e3175008d --- /dev/null +++ b/recipes/deepmei/meta.yaml @@ -0,0 +1,35 @@ +package: + name: deepmei + version: 1.0.0 + +source: + url: https://raw.githubusercontent.com/kanglu123/deepmei_v1.0.0/master/DeepMEI.without_models_and_files.tar.gz + sha256: 6af31abb690b3ba209d719a1e924baaab725760deb47a69319c171308d095269 +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage('deepmei', max_pin="x.x") }} + +requirements: + run: + # List dependencies here. e.g.: + # ... any other dependencies + - bedtools =2.30.0 + - bwa + - pysam =0.17.0 + - repeatmasker + - tensorflow =2.7.0 + - python >=3.8,<=3.9 + - perl =5.32.1 + - samtools + +test: + commands: + - deepmeiv1 + +about: + home: https://github.com/Kanglu123/deepmei + license: GPL-3.0 + license_file: license.txt + summary: A pipeline to detect mobile elements insertion in human genome From d50e17a610b513fb5fe697b097ae56cb39782071 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 3 Jan 2024 14:27:42 -0500 Subject: [PATCH 042/121] Update keggcharter to 1.1.0 (#45046) --- recipes/keggcharter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/keggcharter/meta.yaml b/recipes/keggcharter/meta.yaml index b4284f829e7c1..a77bcf562f63d 100644 --- a/recipes/keggcharter/meta.yaml +++ b/recipes/keggcharter/meta.yaml @@ -1,6 +1,6 @@ {% set name = "keggcharter" %} -{% set version = "1.0.2" %} -{% set sha256 = "605795641af04a7045cc92b6f37ee0b0c0b8e508b85fb70bcc6c00234b9d5d89" %} +{% set version = "1.1.0" %} +{% set sha256 = "092622dd992432e18d650be0f36572a3285ebb4f18703fca21d2161af9e272ff" %} package: name: {{ name|lower }} From d556ca973af0a65baf38db18b64efaaf52d506b7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 06:53:23 -0500 Subject: [PATCH 043/121] Update mosca to 2.2.0 (#45054) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update mosca to 2.2.0 * Update meta.yaml Added run_exports Added pandas as dependency Fixed python version to <3.12 Fixed snakemake version to <8 --------- Co-authored-by: João Sequeira --- recipes/mosca/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/mosca/meta.yaml b/recipes/mosca/meta.yaml index 11788ab31187e..eec8c3b69c882 100644 --- a/recipes/mosca/meta.yaml +++ b/recipes/mosca/meta.yaml @@ -1,6 +1,6 @@ {% set name = "mosca" %} -{% set version = "2.1.0" %} -{% set sha256 = "823bffe56b298505136d7cbad3ab0cca526736edeba4458bc3dbb0b4450ab132" %} +{% set version = "2.2.0" %} +{% set sha256 = "575d17f70b7ff1860789bc352055d32af06b6c5fbe16e2169d762ae3d49a7ca2" %} package: name: {{ name|lower }} @@ -13,11 +13,14 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage("mosca", max_pin="x.x") }} requirements: run: - - python >=3.9 - - snakemake + - python >=3.9, <3.12 + - pandas + - snakemake <8 test: commands: @@ -47,4 +50,4 @@ about: extra: recipe-maintainers: - - iquasere \ No newline at end of file + - iquasere From 9b07186820646cd7ba3c2c15f3435582303c625e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 06:55:33 -0500 Subject: [PATCH 044/121] Update fgbio to 2.2.1 (#45050) --- recipes/fgbio/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fgbio/meta.yaml b/recipes/fgbio/meta.yaml index e48a484303a73..ee2047de82028 100644 --- a/recipes/fgbio/meta.yaml +++ b/recipes/fgbio/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.2.0" %} +{% set version = "2.2.1" %} package: name: fgbio @@ -6,7 +6,7 @@ package: source: url: https://github.com/fulcrumgenomics/fgbio/releases/download/{{ version }}/fgbio-{{ version }}.jar - sha256: e3907b0edf525f9becc69472f843fa3bf5a5fd6e2e03b88532d6622aa264ed3d + sha256: bb875e9a9218b841f39bdd007492b56be25b4d112ef7c22311c554b7b60fcd2c build: noarch: generic From 5d541006e4d8652a9ba2743777070942054c94a6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 06:56:00 -0500 Subject: [PATCH 045/121] Update fgbio-minimal to 2.2.1 (#45051) --- recipes/fgbio-minimal/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fgbio-minimal/meta.yaml b/recipes/fgbio-minimal/meta.yaml index c1588facf506d..23242dc27e036 100644 --- a/recipes/fgbio-minimal/meta.yaml +++ b/recipes/fgbio-minimal/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.2.0" %} +{% set version = "2.2.1" %} package: name: fgbio-minimal @@ -6,7 +6,7 @@ package: source: url: https://github.com/fulcrumgenomics/fgbio/releases/download/{{ version }}/fgbio-{{ version }}.jar - sha256: e3907b0edf525f9becc69472f843fa3bf5a5fd6e2e03b88532d6622aa264ed3d + sha256: bb875e9a9218b841f39bdd007492b56be25b4d112ef7c22311c554b7b60fcd2c build: noarch: generic From 71a9eff39be529360b2fd121b17606a52bdee061 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 10:22:25 -0500 Subject: [PATCH 046/121] Update viralmsa to 1.1.41 (#45047) --- recipes/viralmsa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/viralmsa/meta.yaml b/recipes/viralmsa/meta.yaml index 1a41b2d896121..78d60f0913045 100644 --- a/recipes/viralmsa/meta.yaml +++ b/recipes/viralmsa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.40" %} +{% set version = "1.1.41" %} package: name: viralmsa @@ -12,7 +12,7 @@ build: source: url: https://github.com/niemasd/ViralMSA/archive/refs/tags/{{ version }}.tar.gz - sha256: eb61ebad514448b5eebb675a19bfe91b622c7d825fb11528c8331aa9d3d7222d + sha256: 1475eb3497823fd85febd5bb983c919b830b1e367aa7cf21af19fb33d437404b requirements: run: From c7d15efcddd9d8e1879ef426739a0d55998bc6bb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 10:22:48 -0500 Subject: [PATCH 047/121] Update ndex2 to 3.7.0 (#45049) --- recipes/ndex2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ndex2/meta.yaml b/recipes/ndex2/meta.yaml index de8e93c6e67c0..223be915ae200 100644 --- a/recipes/ndex2/meta.yaml +++ b/recipes/ndex2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ndex2" %} -{% set version = "3.6.0" %} +{% set version = "3.7.0" %} package: @@ -8,7 +8,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ndex2-{{ version }}.tar.gz" - sha256: "d6e95ba33747c59ae47d32ebce55837f17d001f776ea811a70b9e716592d2d1e" + sha256: "5fed3b6c204275fd75724f7d609823f9f6e249b3d468fdd8b0a1f7a9be7a294f" build: noarch: python From 1bdd02af8ba71b134f13312d32f1537b8a5749b5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 10:22:59 -0500 Subject: [PATCH 048/121] Update expam to 1.2.2.5 (#45053) --- recipes/expam/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/expam/meta.yaml b/recipes/expam/meta.yaml index 01df06215fcbd..6ca6b72a1a13b 100644 --- a/recipes/expam/meta.yaml +++ b/recipes/expam/meta.yaml @@ -1,5 +1,5 @@ {% set name = "expam" %} -{% set version = "1.2.2.4" %} +{% set version = "1.2.2.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: c33b249351c13fd3cfcbd0b2411a9d61e5e1e6239d5b841c2d980dcb9a88debc + sha256: 4a102a67da23c37598c0a0778d0caf99d4c6c0ea4286aff7ca0ab360dc5cda09 build: number: 0 From 8406aac0fdf35c122fe182093f7be865ded61021 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 10:23:11 -0500 Subject: [PATCH 049/121] Update bustools to 0.43.2 (#45055) --- recipes/bustools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bustools/meta.yaml b/recipes/bustools/meta.yaml index 331adae0b3b1a..1e1cf6991bd0f 100644 --- a/recipes/bustools/meta.yaml +++ b/recipes/bustools/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.43.1" %} +{% set version = "0.43.2" %} package: name: bustools @@ -6,7 +6,7 @@ package: source: url: https://github.com/BUStools/bustools/archive/v{{ version }}.tar.gz - sha256: ac94a33ca459de81c5756825a7a7f8daeae357fc6bf0ef88d4900e77b70f2b90 + sha256: ad5816152644ee615316daecf5883183994bd7cc96e6c008439123f4cd750b1f build: number: 0 From 1d738249f2a203b76c6cfffed27d83c3b4eda233 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 10:23:38 -0500 Subject: [PATCH 050/121] Update kb-python to 0.28.1 (#45056) --- recipes/kb-python/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/kb-python/meta.yaml b/recipes/kb-python/meta.yaml index 9cc58afa65d9a..9838dbed1aff6 100644 --- a/recipes/kb-python/meta.yaml +++ b/recipes/kb-python/meta.yaml @@ -1,5 +1,5 @@ {% set name = "kb-python" %} -{% set version = "0.28.0" %} +{% set version = "0.28.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/pachterlab/kb_python/archive/v{{ version }}.tar.gz - sha256: ed3d655f6e60d87be5b5b013ffc54e68a943f2997b70ba4f7b3e8a1c83bd2b8a + sha256: a45f396046f544326089c0c25deabcca254989eebab040b12e07114e6d87a09d patches: config.py.patch build: From c47ceb7763d958df13844b3989367355675be685 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 10:24:41 -0500 Subject: [PATCH 051/121] Update xengsort to 2.0.5 (#44888) * Update xengsort to 2.0.4 * pin python to 3.11 * Update xengsort to 2.0.5 --------- Co-authored-by: joshuazhuang7 --- recipes/xengsort/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/xengsort/meta.yaml b/recipes/xengsort/meta.yaml index 0c8ea25b50318..64fbad850f790 100644 --- a/recipes/xengsort/meta.yaml +++ b/recipes/xengsort/meta.yaml @@ -1,5 +1,5 @@ {% set name = "xengsort" %} -{% set version = "2.0.3" %} +{% set version = "2.0.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 4783b53d4641b053f928994c9c316962b6cb1604ed7de0853aa3aa3e339e7e76 + sha256: 243567ee3bdb7111ca7294c5979c2cd9ab5e76fdeefd30b7e27a177c839b33c9 build: number: 0 @@ -16,14 +16,14 @@ build: run_exports: - {{ pin_subpackage(name, max_pin="x") }} noarch: python - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" requirements: host: - pip - - python >=3.10 + - python ==3.11 run: - - python >=3.10 + - python ==3.11 - numpy >=1.22 - numba >=0.56 - zarr @@ -48,6 +48,6 @@ about: extra: identifiers: - - doi:10.4230/LIPIcs.WABI.2020.4 + - doi:10.4230/LIPIcs.WABI.2020.4 recipe-maintainers: - JZentgraf From 475838804203768184399a26b080b73f82139f78 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 10:49:40 -0500 Subject: [PATCH 052/121] Update ena-webin-cli to 6.8.0 (#45059) --- recipes/ena-webin-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ena-webin-cli/meta.yaml b/recipes/ena-webin-cli/meta.yaml index 249da97616a98..582fa0f98d569 100644 --- a/recipes/ena-webin-cli/meta.yaml +++ b/recipes/ena-webin-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "6.7.2" %} -{% set sha256 = "f45f9e54813711b6ea57130efae83a3381b2a3c66debd6d941fc1d9a85c69c6e" %} +{% set version = "6.8.0" %} +{% set sha256 = "08d39ed646f00d2e682ea83849c04e0665106af9f7ae25ca04c07bdd086c91ef" %} package: name: ena-webin-cli From df6303c8027ad797b36e6d01e52fdbc5ae8d5e29 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 16:26:04 -0500 Subject: [PATCH 053/121] Update zol to 1.3.17 (#45067) --- recipes/zol/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index c1af50a0bcea9..ce26b14a3821b 100644 --- a/recipes/zol/meta.yaml +++ b/recipes/zol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zol" %} -{% set version = "1.3.16" %} +{% set version = "1.3.17" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz - sha256: 1b881771eac51bfcf0b58ea13b090514e3f0ed1e1d4d0a252709881ffc46730f + sha256: 71205d5144d4489d863d63dd0e4eb5b4341e66b71bf4bc7fc186e9bed98fa17b build: number: 0 From cf99e57f8235f40b4a95c26abf7ebea824486677 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 17:49:39 -0500 Subject: [PATCH 054/121] Update pybiolib to 1.1.1673 (#45057) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index d1e5bb09bb712..92e71dea5060c 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1666" %} +{% set version = "1.1.1673" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 71888c84f4ad3cf97f461d2fc5e9955560d131e0c74d9a453e378d5d80262442 + sha256: cb62441a9fabcab0a8cb1d1a541936ee90e39599a51e55ddd87d963a0499ff02 build: noarch: python From ea2bd23d97ab830d0296a1a009942070e38b96e6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 18:39:40 -0500 Subject: [PATCH 055/121] Update pybiolib to 1.1.1682 (#45072) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 92e71dea5060c..135ea9c49e89f 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1673" %} +{% set version = "1.1.1682" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: cb62441a9fabcab0a8cb1d1a541936ee90e39599a51e55ddd87d963a0499ff02 + sha256: 3bb0789aea5e55cf7fc33f41e898e6d3abb05adbafd870ba6be1c761e762c105 build: noarch: python From 37d344ca0ad53a8ed07ab4297ea4d0faeeeaf41d Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Fri, 5 Jan 2024 03:30:49 -0600 Subject: [PATCH 056/121] Update adam to 1.0.1 (#45069) * Update adam to 1.0.1 * add pin_subpackage --- recipes/adam/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/adam/meta.yaml b/recipes/adam/meta.yaml index c29df2abaf583..51700f7519ec5 100644 --- a/recipes/adam/meta.yaml +++ b/recipes/adam/meta.yaml @@ -1,4 +1,4 @@ -{% set version="1.0" %} +{% set version="1.0.1" %} package: name: adam @@ -6,7 +6,7 @@ package: source: url: https://search.maven.org/remotecontent?filepath=org/bdgenomics/adam/adam-distribution-spark3_2.12/{{ version }}/adam-distribution-spark3_2.12-{{ version }}-bin.tar.gz - sha256: 1c1d91ccb42d2faaefb075f93a11bfb5a8c6dd575c7f01d21842a8957204f705 + sha256: cd6259148a2d9d8bf10549cedd09fe5b12d9f34a25e80a4025f96d60e50be807 patches: - adam-shell.patch - adam-submit.patch @@ -14,6 +14,8 @@ source: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('adam', max_pin="1") }} requirements: run: From b9eb742523fe3f23535c0246635d49d69ac83d45 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Fri, 5 Jan 2024 03:31:25 -0600 Subject: [PATCH 057/121] Update cannoli to 1.0.1 (#45070) * Update cannoli to 1.0.1. * add pin_subpackage --- recipes/cannoli/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/cannoli/meta.yaml b/recipes/cannoli/meta.yaml index 37e73896b7434..e4b3a7739a686 100644 --- a/recipes/cannoli/meta.yaml +++ b/recipes/cannoli/meta.yaml @@ -1,4 +1,4 @@ -{% set version="1.0" %} +{% set version="1.0.1" %} package: name: cannoli @@ -6,11 +6,13 @@ package: source: url: https://search.maven.org/remotecontent?filepath=org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/{{ version }}/cannoli-distribution-spark3_2.12-{{ version }}-bin.tar.gz - sha256: 28c076ebd64278c07e9169e5b5de13ea5fd30a1f68daffbe551518092089ef6a + sha256: 4cfbbe1d2085298e62d4143116f8776ef2c91854f36a0803c27164c51b541e12 build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('cannoli', max_pin="1") }} requirements: run: From dc57e3335004dbc4070db18c442864a259f9d161 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 09:36:41 -0500 Subject: [PATCH 058/121] Update keggcharter to 1.1.1 (#45079) --- recipes/keggcharter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/keggcharter/meta.yaml b/recipes/keggcharter/meta.yaml index a77bcf562f63d..aa9fb12f6ef41 100644 --- a/recipes/keggcharter/meta.yaml +++ b/recipes/keggcharter/meta.yaml @@ -1,6 +1,6 @@ {% set name = "keggcharter" %} -{% set version = "1.1.0" %} -{% set sha256 = "092622dd992432e18d650be0f36572a3285ebb4f18703fca21d2161af9e272ff" %} +{% set version = "1.1.1" %} +{% set sha256 = "66e33b222572eaa38b37ce0e04f844550b505c78e05533cbcaead31053c3fc69" %} package: name: {{ name|lower }} From 964ae0bdd1e3b57b0e52b7098a671fded3c8e2ec Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 10:11:31 -0500 Subject: [PATCH 059/121] Update galaxy-objectstore to 23.1.4 (#45061) --- recipes/galaxy-objectstore/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/galaxy-objectstore/meta.yaml b/recipes/galaxy-objectstore/meta.yaml index ac332bc820da2..148329751bff0 100644 --- a/recipes/galaxy-objectstore/meta.yaml +++ b/recipes/galaxy-objectstore/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.1.3" %} -{% set sha256 = "52b9b213e15f1e219a25304f616e44f29f0ac52b61c753a6e89fac9d5c2a0fa2" %} +{% set version = "23.1.4" %} +{% set sha256 = "548af50412cac61a38299b5ab6a7e9b787afc51db43370e058e4e58f2d10706b" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: From a5778f2c4c749253de738eaaaa217f259154d355 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 10:11:40 -0500 Subject: [PATCH 060/121] Update galaxy-files to 23.1.4 (#45062) --- recipes/galaxy-files/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/galaxy-files/meta.yaml b/recipes/galaxy-files/meta.yaml index 0a61489a554ce..ffe4ded18d97d 100644 --- a/recipes/galaxy-files/meta.yaml +++ b/recipes/galaxy-files/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.1.3" %} -{% set sha256 = "0facf5bfe8573a6e1a576d4e4b7f0ad7fa7924a1291111b9dfc1714520e1d559" %} +{% set version = "23.1.4" %} +{% set sha256 = "9d36250e580a29c8982904e90b1ad89b1712de0743750e72bea3f740960a6524" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: From 569d13f03324bd7ca9f8fc9d5e607f42fcfc5905 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 10:43:05 -0500 Subject: [PATCH 061/121] Update mashmap to 3.1.3 (#45064) --- recipes/mashmap/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mashmap/meta.yaml b/recipes/mashmap/meta.yaml index 672f557d6afef..86acff531bec5 100644 --- a/recipes/mashmap/meta.yaml +++ b/recipes/mashmap/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "3.1.2" %} +{% set version = "3.1.3" %} {% set github = "https://github.com/marbl/MashMap" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: cf9bb085cc85b0f1b91f4fc45a907cff536099a4a82031f1e112259e24ba5976 + sha256: 7719dd6b3c25e650e16218252eaae7dbf424a10890d717ec3ad0920b102fd05a build: number: 0 From 17adb3055a01e97d68f22d96c22708b7f8eeac53 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 10:46:31 -0500 Subject: [PATCH 062/121] Update rosella to 0.5.3 (#45075) --- recipes/rosella/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/rosella/meta.yaml b/recipes/rosella/meta.yaml index bcc70f4e4c7a5..090fd11d0e2ac 100644 --- a/recipes/rosella/meta.yaml +++ b/recipes/rosella/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.5.2" %} +{% set version = "0.5.3" %} {% set name = "rosella" %} -{% set hash = "7f0851bbeef7e694983b3002a06c4cc1346544818a532373ca63dab14fa0245a" %} +{% set hash = "a7a07f3217c40bc0308eb2fb964092662d6c99f4093e68e96c9575bce208d214" %} package: name: rosella From d6e67032f251f30a4c5844c064e5c2107159c35b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 10:55:48 -0500 Subject: [PATCH 063/121] Update snakemake-executor-plugin-googlebatch to 0.2.0 (#45039) * Update snakemake-executor-plugin-googlebatch to 0.2.0 * add summary --------- Co-authored-by: mencian --- .../snakemake-executor-plugin-googlebatch/meta.yaml | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/recipes/snakemake-executor-plugin-googlebatch/meta.yaml b/recipes/snakemake-executor-plugin-googlebatch/meta.yaml index 06a457c3e614b..2b428cb274a58 100644 --- a/recipes/snakemake-executor-plugin-googlebatch/meta.yaml +++ b/recipes/snakemake-executor-plugin-googlebatch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-googlebatch" %} -{% set version = "0.1.1" %} +{% set version = "0.2.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_googlebatch-{{ version }}.tar.gz - sha256: 12a25a51f4471d6fb774ed0e837a49c8f3cebbe5a6494a5b2daf96146df87925 + sha256: 3cccef6db07f47d53c0863db960c36d24c6336caabbea2b7fd3f2fc42c95edc4 build: noarch: python @@ -35,15 +35,12 @@ requirements: test: imports: - snakemake_executor_plugin_googlebatch - commands: - - pip check - requires: - - pip about: home: https://github.com/snakemake/snakemake-executor-plugin-googlebatch - summary: '' + summary: 'Snakemake executor plugin for Google Batch' license: MIT + license_family: MIT license_file: LICENSE extra: From a7ee16ee8974b8e918eb4ecdf967f52351e4a624 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 10:56:34 -0500 Subject: [PATCH 064/121] Update hifihla to 0.2.3 (#45066) --- recipes/hifihla/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hifihla/meta.yaml b/recipes/hifihla/meta.yaml index c0eedd01c0050..df508026a76a4 100644 --- a/recipes/hifihla/meta.yaml +++ b/recipes/hifihla/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hifihla" %} -{% set version = "0.2.2" %} -{% set hifihla_sha256 = "3de4f6166f7a253571a6feeeed17fc38a53f274881757c883204c7c3963de5cc" %} +{% set version = "0.2.3" %} +{% set hifihla_sha256 = "f2c3cf24ca12b1bf1bec88dae6a30089c702077e683eb01451f216b3ee93bbe0" %} package: name: {{ name }} From 28278722cc8dc8696e566100ed3936fe153ef399 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 10:56:45 -0500 Subject: [PATCH 065/121] Update micom to 0.33.1 (#45071) --- recipes/micom/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/micom/meta.yaml b/recipes/micom/meta.yaml index 2e740c6af928e..cd53b1a6dd737 100644 --- a/recipes/micom/meta.yaml +++ b/recipes/micom/meta.yaml @@ -1,5 +1,5 @@ {% set name = "micom" %} -{% set version = "0.33.0" %} +{% set version = "0.33.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 489d15dd2b7aa14db6c2c2887069f3ef5588df95c06a2b397bd81bb8b8970604 + sha256: 75e8a1fe8f1535d12a466a028cd4e3caa7c199788b02c18d1bff9f03ae1d92ec build: number: 0 From 3f1e5dd13af4caac7c2ba662bdbe9b9203ec65f0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 10:57:08 -0500 Subject: [PATCH 066/121] Update flight-genome to 1.6.3 (#45073) --- recipes/flight-genome/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/flight-genome/meta.yaml b/recipes/flight-genome/meta.yaml index 98ec30f242755..cbad38fef8043 100644 --- a/recipes/flight-genome/meta.yaml +++ b/recipes/flight-genome/meta.yaml @@ -1,5 +1,5 @@ {% set name = "flight-genome" %} -{% set version = "1.6.2" %} +{% set version = "1.6.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: d07b920f3a6bfabb6190d27eb2cbe8ad8a1ddb40b0cbf62104d3adbb71c484a2 + sha256: 48a450da686d634aaed5d223d79481876836929892a5b730e42610d9b741dc6e build: number: 0 From cbb6ecd076af3fa791d3d87b44ea8a99b63e2875 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 10:57:32 -0500 Subject: [PATCH 067/121] Update bioframe to 0.6.0 (#45076) --- recipes/bioframe/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioframe/meta.yaml b/recipes/bioframe/meta.yaml index 3dd3614557adf..0cd0bbd8b9c45 100644 --- a/recipes/bioframe/meta.yaml +++ b/recipes/bioframe/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bioframe" %} -{% set version = "0.5.1" %} +{% set version = "0.6.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 416132f14334f3921d700a692bf94ea21161ca608e5e3b9a119f97c01012d578 + sha256: 7998f6aa072ab9655354b64c511a093c9f1a181f2d994f0e884b9c48c4d0c313 build: noarch: python From cd220c7c290f30b02ba4ea981ed155bcc40a9fa6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 11:32:38 -0500 Subject: [PATCH 068/121] Update metdatamodel to 0.5.5 (#45082) --- recipes/metdatamodel/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/metdatamodel/meta.yaml b/recipes/metdatamodel/meta.yaml index bfd1858956799..e83742363e601 100644 --- a/recipes/metdatamodel/meta.yaml +++ b/recipes/metdatamodel/meta.yaml @@ -1,5 +1,5 @@ {% set name = "metdatamodel" %} -{% set version = "0.4.14" %} +{% set version = "0.5.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/metDataModel-{{ version }}.tar.gz - sha256: 49583289a596934204f458c4464579d3b58e18765ae97d283b32b58028de0fbc + sha256: 8ed0c978ffe4e1a75d169ae58687cb86f15c991d05529748791c554c9f1103a9 build: noarch: python From 56f5416744184ee3e4cc961cfba5f3f53e026728 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 12:25:23 -0500 Subject: [PATCH 069/121] Update odgi to 0.8.4 (#45077) * Update odgi to 0.8.4 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/odgi/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/odgi/meta.yaml b/recipes/odgi/meta.yaml index 43c3c89859e29..44d9dfd0ea1b0 100644 --- a/recipes/odgi/meta.yaml +++ b/recipes/odgi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "odgi" %} -{% set version = "0.8.3" %} +{% set version = "0.8.4" %} package: name: "{{ name }}" @@ -7,11 +7,13 @@ package: source: url: https://github.com/pangenome/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - sha256: 13a63b8ada79851fd8ce5e7638dda1a8b75ef0346a5d93552ee2179256eb81bf + sha256: bc656e541a42c890f71e748e4420215e1efba5b7b890d8c009bfef114c811f47 build: skip: True # [osx or py27] number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: From 99201d0449cb4000da440afd7442b99d8615f125 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 12:59:33 -0500 Subject: [PATCH 070/121] Update nanovar to 1.5.1 (#45084) --- recipes/nanovar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanovar/meta.yaml b/recipes/nanovar/meta.yaml index d0b873ee9c1ff..9d412711b5581 100644 --- a/recipes/nanovar/meta.yaml +++ b/recipes/nanovar/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.5.0" %} +{% set version = "1.5.1" %} package: name: nanovar @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nanovar/nanovar-{{ version }}.tar.gz - sha256: cca25fde5da27bd5497e80c3a2bfd5eb6bffa46d348d30682bbe4cca20ed767f + sha256: 5b189ff18958be0e7406752f7700e0c70d464ae64b70ed278fd32a2fe61280a4 build: skip: True # [py2k or osx or py > 39] From af69b0a9b393acb3ac84955661fcc460f74465cd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 15:59:45 -0500 Subject: [PATCH 071/121] Update r-ldweaver to 1.4 (#45058) * Update r-ldweaver to 1.4 * drop genbankr dependency * it seems genbankr is still needed --------- Co-authored-by: mencian --- recipes/r-ldweaver/meta.yaml | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) diff --git a/recipes/r-ldweaver/meta.yaml b/recipes/r-ldweaver/meta.yaml index f5c10cbc6684e..26d05b5b7316e 100644 --- a/recipes/r-ldweaver/meta.yaml +++ b/recipes/r-ldweaver/meta.yaml @@ -1,6 +1,6 @@ {% set name = "r-ldweaver" %} -{% set version = "1.3.1" %} -{% set sha256 = "a926d946b4fea6abdc2e7fdcc3ac8a55865da0403d45180eeb60cda0b92d3de0" %} +{% set version = "1.4" %} +{% set sha256 = "8fca169dbf073a280cb47d1352fbb1a49b7f0b4daeba146928705def61650608" %} package: name: {{ name }} @@ -23,10 +23,10 @@ requirements: build: - {{ compiler('c') }} # [not win] - {{ compiler('cxx') }} # [not win] - host: - r-base 4.* - bioconductor-genomicranges + - bioconductor-genbankr - r-matrix - r-matrixextra - r-rcolorbrewer @@ -37,7 +37,6 @@ requirements: - r-data.table - r-dplyr - r-fitdistrplus - - bioconductor-genbankr - r-ggnewscale - r-ggplot2 - r-ggraph @@ -47,12 +46,12 @@ requirements: - r-igraph - r-phytools - r-plyr - - r-stringi + - r-stringi - openjdk - run: - r-base 4.* - bioconductor-genomicranges + - bioconductor-genbankr - r-matrix - r-matrixextra - r-rcolorbrewer @@ -63,7 +62,6 @@ requirements: - r-data.table - r-dplyr - r-fitdistrplus - - bioconductor-genbankr - r-ggnewscale - r-ggplot2 - r-ggraph @@ -73,7 +71,7 @@ requirements: - r-igraph - r-phytools - r-plyr - - r-stringi + - r-stringi - openjdk test: @@ -86,5 +84,4 @@ about: license: GPL-3.0-or-later summary: Perform genomewide epistasis analysis by evaluating the LD structure in bacteria. license_family: GPL3 - license_file: - - LICENSE + license_file: LICENSE From 55a7cdc3a4a0a8b5c7e0cc3d5412ce9eabb56df5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 16:00:03 -0500 Subject: [PATCH 072/121] Update ncbi-datasets-pylib to 16.1.1 (#45090) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 2712a35e55419..8e24d691bd6a8 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.0.0" %} -{% set sha256 = "499f5664b768ae4c6e2e5ab2965e0b6e150de2f81c667ba89eb5f29a2e67ce1d" %} +{% set version = "16.1.1" %} +{% set sha256 = "cddfde551d1a5948d0f3b87660968887a0e22d31db2f2810384393192c112eaf" %} package: name: {{ name|lower }} From 34d6cc9b3f325c3f62c2ea251c3003c5a714da48 Mon Sep 17 00:00:00 2001 From: "Le (Lena) Huang" Date: Fri, 5 Jan 2024 18:10:15 -0500 Subject: [PATCH 073/121] Update dbcan to 4.1.0 (#45088) * Update dbcan to 4.1.0 * fix bug * add hatchling and other fixes * edit sha256 --------- Co-authored-by: mencian --- recipes/dbcan/meta.yaml | 45 +++++++++++++++++++++++++++++------------ 1 file changed, 32 insertions(+), 13 deletions(-) diff --git a/recipes/dbcan/meta.yaml b/recipes/dbcan/meta.yaml index e9856eac10155..b4c30e8cb658f 100644 --- a/recipes/dbcan/meta.yaml +++ b/recipes/dbcan/meta.yaml @@ -1,29 +1,38 @@ {% set name = "dbcan" %} -{% set version = "4.0.0" %} +{% set version = "4.1.0" %} package: name: "{{ name|lower }}" version: {{ version }} source: + # the sha256 sum is generated by doing + # wget -0- [URL] | shasum -a 256 url: https://github.com/linnabrown/run_dbcan/releases/download/{{ version }}/dbcan-{{ version }}.tar.gz - sha256: c90e99168fa3414696575b8f5a6c2862173151d1f0d7246ebd5713704b597435 + sha256: cb0907eb10eb916bcf676c58f54e67a67dd4ed559152e5547bb44d071f063b8f + build: number: 0 - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python + entry_points: + - run_dbcan = dbcan.cli.run_dbcan:cli_main + - cgc_standard2json = dbcan.cli.cgc_process_json:main + - syntenic_plot = dbcan.cli.syntenic_plot:main + - dbcan_utils = dbcan.utils.utils:main + - dbcan_plot = dbcan.utils.plots:main + - dbcan_asmfree = dbcan.utils.diamond_unassembly:main + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: host: - - natsort - pip - - python - - setuptools - - setuptools_scm_git_archive - + - python >=3.6 + - hatchling run: - natsort - - python + - python >=3.6 - diamond - hmmer - prodigal @@ -32,18 +41,28 @@ requirements: - numpy >1.19 - biopython - pandas + - session-info test: imports: - dbcan + commands: + - run_dbcan --help about: - home: http://bcb.unl.edu/dbCAN2/ + home: https://bcb.unl.edu/dbCAN2/ dev_url: https://github.com/linnabrown/run_dbcan - license: GPLv3 + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE - summary: Standalone version of dbCAN annotation tool for automated CAZyme annotation + summary: "Standalone version of dbCAN annotation tool for automated CAZyme annotation" + doc_url: https://dbcan.readthedocs.io/en/latest/ extra: recipe-maintainers: - - Le Huang + - linnabrown + identifiers: + - doi:10.1093/nar/gkx894 + - doi:10.1093/nar/gky418 + - doi:10.1093/nar/gkad328 + - biotools:dbcan2 From 19d675086c0f4bc8ee657395bff422a8b259f040 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Jan 2024 07:17:10 -0500 Subject: [PATCH 074/121] Update perl-math-bigint to 2.003002 (#45096) --- recipes/perl-math-bigint/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/perl-math-bigint/meta.yaml b/recipes/perl-math-bigint/meta.yaml index ac043f49bd2c9..f72bad5acfaaf 100644 --- a/recipes/perl-math-bigint/meta.yaml +++ b/recipes/perl-math-bigint/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-math-bigint" %} -{% set version = "2.003001" %} -{% set sha256 = "9e14c5b0b7eecd1dca6d7c1eca680befccf212f7e6683f0b874348375a0333fc" %} +{% set version = "2.003002" %} +{% set sha256 = "5ac1fd255cca29d7cf5cb9283e6bb8177cdb07c5bb97502a58084b1c6eace35c" %} package: name: {{ name }} From 3b83e97a865fd696e32b68e33f22aaf6108f1286 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Jan 2024 12:38:27 -0500 Subject: [PATCH 075/121] Update nf-test to 0.8.3 (#45098) --- recipes/nf-test/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nf-test/meta.yaml b/recipes/nf-test/meta.yaml index 1ad10e7398e1e..21bcaf9fe3c08 100644 --- a/recipes/nf-test/meta.yaml +++ b/recipes/nf-test/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.2" %} +{% set version = "0.8.3" %} package: @@ -13,7 +13,7 @@ build: source: url: https://github.com/askimed/nf-test/releases/download/v{{version}}/nf-test-{{version}}.tar.gz - sha256: 5d640cea4339da4de50ce3687e9a61bd10488f2cac342eb1f11743414c6a27cd + sha256: af48883e8d0cd2d65b0846b3f60a476a5ec28a3799ba9374e0cb307a2a2d634d requirements: host: From ec103fbf6eae463017ca64cc835ff8215d3acd06 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Jan 2024 12:38:41 -0500 Subject: [PATCH 076/121] Update foldcomp to 0.0.7 (#45097) --- recipes/foldcomp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/foldcomp/meta.yaml b/recipes/foldcomp/meta.yaml index f645e6e9482ca..96977ef6197a7 100644 --- a/recipes/foldcomp/meta.yaml +++ b/recipes/foldcomp/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.0.6" %} -{% set sha256 = "7f77fded798ea711f816220e4ca20fe4a9fed9917b9b2d3f7eba22ad5e1aa7f5" %} +{% set version = "0.0.7" %} +{% set sha256 = "34cf6df7bb48f6bdd5c94337ddb1e1f16eafead841da8afed62dac1b5b8a9467" %} package: name: foldcomp From 5bceb9a7d8636f108488072c8de899ef4c8f80c9 Mon Sep 17 00:00:00 2001 From: Jens Luebeck Date: Sun, 7 Jan 2024 09:40:47 -0800 Subject: [PATCH 077/121] Update meta.yaml (#45086) --- recipes/ampliconsuite/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/ampliconsuite/meta.yaml b/recipes/ampliconsuite/meta.yaml index 84c00115d5bdf..24da7d68a4da9 100644 --- a/recipes/ampliconsuite/meta.yaml +++ b/recipes/ampliconsuite/meta.yaml @@ -1,7 +1,7 @@ {% set name="ampliconsuite" %} -{% set AS_version="1.2.0" %} +{% set AS_version="1.2.1" %} {% set AA_version="1.3.r7" %} -{% set AC_version="1.1.0" %} +{% set AC_version="1.1.1" %} package: name: {{ name }} @@ -11,12 +11,12 @@ source: # the sha256 sum is generated by doing # $ wget -O- [URL] | shasum -a 256 - url: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/archive/v{{ AS_version }}.tar.gz - sha256: 749aa74579aa19d400078fc045d1f1d943159b2ebdcd43a449ee7d5ab2d8ca6d + sha256: 79515b2c1a57a8ea22905737f3c02047a4319d7ab91554dff1a058ead653c720 - url: https://github.com/AmpliconSuite/AmpliconArchitect/archive/v{{ AA_version }}.tar.gz sha256: be65a0293da9ced3f6f744657db475c16dd4dcaf9f037e17ee1a19f4ceaa7430 folder: ampliconarchitectlib - url: https://github.com/AmpliconSuite/AmpliconClassifier/archive/v{{ AC_version }}.tar.gz - sha256: e656b557fd8e1c598dd8df9b29e25d4208cb0e1c66e97235c27104751654b7f6 + sha256: 040400d2eb0b4c847245666a481de927eb0c9a368088c1e97f117e7a228c8c5d build: noarch: python From 308daed0c4c7497d1e99b43d38d7431319462596 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Jan 2024 12:41:34 -0500 Subject: [PATCH 078/121] Update ltr_retriever to 2.9.8 (#45006) * Update ltr_retriever to 2.9.8 * add run_exports * revert channel specifications * remove channels section --------- Co-authored-by: joshuazhuang7 --- recipes/ltr_retriever/meta.yaml | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/recipes/ltr_retriever/meta.yaml b/recipes/ltr_retriever/meta.yaml index 64ee4402ab215..0945912461b47 100644 --- a/recipes/ltr_retriever/meta.yaml +++ b/recipes/ltr_retriever/meta.yaml @@ -1,6 +1,6 @@ {% set name = "LTR_retriever" %} -{% set version = "2.9.5" %} -{% set sha256 = "f50812e6342a1d427a69e11e7ccbf21d7d72acf52c373fbd4ffdbe8a96dd62b7" %} +{% set version = "2.9.8" %} +{% set sha256 = "c5723c69c8897e717f03a7a0690a8f9b4a6c56991d947eddb224066ddf2d1448" %} package: name: "{{ name|lower }}" @@ -13,21 +13,17 @@ source: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('ltr_retriever', max_pin="x") }} -channels: - - bioconda - - anaconda - - conda-forge - - defaults - requirements: run: - perl-text-soundex - perl - cd-hit - repeatmasker <4.1.5 - - rmblast <2.11 - - libstdcxx-ng <13 + - rmblast + - libstdcxx-ng - tesorter test: @@ -36,8 +32,13 @@ test: about: home: https://github.com/oushujun/LTR_retriever - license: GPLv3 - license_family: GPL + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: Sensitive and accurate identification of LTR retrotransposons dev_url: https://github.com/oushujun/LTR_retriever + +extra: + identifiers: + - doi:10.1104/pp.17.01310 + - biotools:ltr_retriever From 54e0e627275e500c41bc10f6e1fc03e8fe42b472 Mon Sep 17 00:00:00 2001 From: Afif Elghraoui Date: Sun, 7 Jan 2024 09:42:55 -0800 Subject: [PATCH 079/121] prodigal: include upstream patches fixing critical bugs (#45091) * prodigal: freshen up * prodigal: include patches for critical bugs fixed upstream but unreleased The developer has accepted these changes, but no new release has been made in over a year. --- recipes/prodigal/meta.yaml | 11 +++++- recipes/prodigal/score_nodes.patch | 32 ++++++++++++++++++ recipes/prodigal/sd_motif_A.patch | 32 ++++++++++++++++++ recipes/prodigal/sd_motif_B.patch | 54 ++++++++++++++++++++++++++++++ 4 files changed, 128 insertions(+), 1 deletion(-) create mode 100644 recipes/prodigal/score_nodes.patch create mode 100644 recipes/prodigal/sd_motif_A.patch create mode 100644 recipes/prodigal/sd_motif_B.patch diff --git a/recipes/prodigal/meta.yaml b/recipes/prodigal/meta.yaml index f8c5bcbcff963..abb4fd87c74b2 100644 --- a/recipes/prodigal/meta.yaml +++ b/recipes/prodigal/meta.yaml @@ -5,9 +5,17 @@ package: source: url: https://github.com/hyattpd/Prodigal/archive/v2.6.3.zip sha256: 4f73f64ea09be8421e08afabdc641db7775632210f5ef896f5fab4604c9dfcd9 + patches: + # accepted PR https://github.com/hyattpd/Prodigal/pull/88 + - score_nodes.patch + # accepted PR https://github.com/hyattpd/Prodigal/pull/100 + - sd_motif_A.patch + - sd_motif_B.patch build: - number: 6 + number: 7 + run_exports: + - {{ pin_subpackage('prodigal', max_pin=None) }} requirements: build: @@ -22,5 +30,6 @@ test: about: home: http://prodigal.ornl.gov/ + dev_url: https://github.com/hyattpd/Prodigal license: GPL v3 summary: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program diff --git a/recipes/prodigal/score_nodes.patch b/recipes/prodigal/score_nodes.patch new file mode 100644 index 0000000000000..890a7ef773286 --- /dev/null +++ b/recipes/prodigal/score_nodes.patch @@ -0,0 +1,32 @@ +From b34b63b17f712aedb371a70eccf6660c3e524808 Mon Sep 17 00:00:00 2001 +From: Martin Larralde +Date: Sun, 12 Sep 2021 14:30:12 +0200 +Subject: [PATCH] Fix typo in `score_nodes` function of `node.c` +URL: https://github.com/hyattpd/Prodigal/pull/88 + +--- + node.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/node.c b/node.c +index 5f7ccc4..7438dfb 100644 +--- a/node.c ++++ b/node.c +@@ -487,7 +487,7 @@ void score_nodes(unsigned char *seq, unsigned char *rseq, int slen, + /* genes are also penalized. */ + /**************************************************************/ + if(is_meta == 1 && slen < 3000 && edge_gene == 0 && +- (nod[i].cscore < 5.0 || abs(nod[i].ndx-nod[i].stop_val < 120))) { ++ (nod[i].cscore < 5.0 || abs(nod[i].ndx-nod[i].stop_val) < 120)) { + nod[i].cscore -= META_PEN*dmax(0, (3000-slen)/2700.0); + } + +@@ -515,7 +515,7 @@ void score_nodes(unsigned char *seq, unsigned char *rseq, int slen, + else nod[i].sscore -= 0.5; + } + else if(nod[i].cscore < 5.0 && is_meta == 1 && abs(nod[i].ndx- +- nod[i].stop_val < 120) && nod[i].sscore < 0.0) ++ nod[i].stop_val) < 120 && nod[i].sscore < 0.0) + nod[i].sscore -= tinf->st_wt; + } + } diff --git a/recipes/prodigal/sd_motif_A.patch b/recipes/prodigal/sd_motif_A.patch new file mode 100644 index 0000000000000..972921686fcc4 --- /dev/null +++ b/recipes/prodigal/sd_motif_A.patch @@ -0,0 +1,32 @@ +From 7b8614dced6b431d872b6e8c8d5d62566caa0214 Mon Sep 17 00:00:00 2001 +From: Martin Larralde +Date: Fri, 27 Jan 2023 17:54:59 +0100 +Subject: [PATCH] Fix buffer initialization in SD motif detection code +URL: https://github.com/hyattpd/Prodigal/pull/100 + +--- + sequence.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/sequence.c b/sequence.c +index d5c8436..b2be997 100644 +--- a/sequence.c ++++ b/sequence.c +@@ -663,7 +663,7 @@ int shine_dalgarno_exact(unsigned char *seq, int pos, int start, double *rwt) { + double match[6], cur_ctr, dis_flag; + + limit = imin(6, start-4-pos); +- for(i = limit; i < 6; i++) match[i] = -10.0; ++ for(i = 0; i < 6; i++) match[i] = -10.0; + + /* Compare the 6-base region to AGGAGG */ + for(i = 0; i < limit; i++) { +@@ -739,7 +739,7 @@ int shine_dalgarno_mm(unsigned char *seq, int pos, int start, double *rwt) { + double match[6], cur_ctr, dis_flag; + + limit = imin(6, start-4-pos); +- for(i = limit; i < 6; i++) match[i] = -10.0; ++ for(i = 0; i < 6; i++) match[i] = -10.0; + + /* Compare the 6-base region to AGGAGG */ + for(i = 0; i < limit; i++) { diff --git a/recipes/prodigal/sd_motif_B.patch b/recipes/prodigal/sd_motif_B.patch new file mode 100644 index 0000000000000..91d2e519519aa --- /dev/null +++ b/recipes/prodigal/sd_motif_B.patch @@ -0,0 +1,54 @@ +From 7cb28c92f50e910d3cc14fc92bf6b9c197c8c6bf Mon Sep 17 00:00:00 2001 +From: Martin Larralde +Date: Fri, 27 Jan 2023 20:52:51 +0100 +Subject: [PATCH] Slightly refactor comparison code in `shine_dalgarno` + functions +URL: https://github.com/hyattpd/Prodigal/pull/100 + +--- + sequence.c | 25 +++++++++++++------------ + 1 file changed, 13 insertions(+), 12 deletions(-) + +diff --git a/sequence.c b/sequence.c +index b2be997..515c8b1 100644 +--- a/sequence.c ++++ b/sequence.c +@@ -667,10 +667,10 @@ int shine_dalgarno_exact(unsigned char *seq, int pos, int start, double *rwt) { + + /* Compare the 6-base region to AGGAGG */ + for(i = 0; i < limit; i++) { +- if(pos+i < 0) continue; +- if(i%3 == 0 && is_a(seq, pos+i) == 1) match[i] = 2.0; +- else if(i%3 != 0 && is_g(seq, pos+i) == 1) match[i] = 3.0; +- else match[i] = -10.0; ++ if(pos + i >= 0) { ++ if(i%3 == 0 && is_a(seq, pos+i) == 1) match[i] = 2.0; ++ else if(i%3 != 0 && is_g(seq, pos+i) == 1) match[i] = 3.0; ++ } + } + + /* Find the maximally scoring motif */ +@@ -743,14 +743,15 @@ int shine_dalgarno_mm(unsigned char *seq, int pos, int start, double *rwt) { + + /* Compare the 6-base region to AGGAGG */ + for(i = 0; i < limit; i++) { +- if(pos+i < 0) continue; +- if(i % 3 == 0) { +- if(is_a(seq, pos+i) == 1) match[i] = 2.0; +- else match[i] = -3.0; +- } +- else { +- if(is_g(seq, pos+i) == 1) match[i] = 3.0; +- else match[i] = -2.0; ++ if(pos+i >= 0) { ++ if(i % 3 == 0) { ++ if(is_a(seq, pos+i) == 1) match[i] = 2.0; ++ else match[i] = -3.0; ++ } ++ else { ++ if(is_g(seq, pos+i) == 1) match[i] = 3.0; ++ else match[i] = -2.0; ++ } + } + } + From 9411ddeff3f82bc66b4af39140d470b1925c9ead Mon Sep 17 00:00:00 2001 From: Mark Santcroos Date: Sun, 7 Jan 2024 18:53:57 +0100 Subject: [PATCH 080/121] Add vcfphasesets (#45092) * Add vcfphasesets. * Change meta.yaml for run exports. --- recipes/vcfphasesets/meta.yaml | 40 ++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 recipes/vcfphasesets/meta.yaml diff --git a/recipes/vcfphasesets/meta.yaml b/recipes/vcfphasesets/meta.yaml new file mode 100644 index 0000000000000..a7e53659eb6f4 --- /dev/null +++ b/recipes/vcfphasesets/meta.yaml @@ -0,0 +1,40 @@ +{% set name = "vcfphasesets" %} +{% set version = "0.3" %} + +package: + name: '{{ name|lower }}' + version: '{{ version }}' + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 2a6b8fc061d42bb4fa0d2c717978f90137a55a956928b535d6ea55c2dbd1be81 + +build: + number: 0 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + noarch: python + run_exports: + - {{ pin_subpackage('vcfphasesets', max_pin="x") }} + + +requirements: + host: + - python >=3.7 + - pip + run: + - python >=3.7 + - pysam + +test: + imports: + - vcfphasesets + +about: + home: https://github.com/LUMC/vcfphasesets + license: MIT + license_family: MIT + summary: Get variants as phase sets from a VCF file using pysam. + +extra: + recipe-maintainers: + - marksantcroos From 25ac72759255abd4bd598f82f838d4d91f766384 Mon Sep 17 00:00:00 2001 From: Koke <49822617+jorgeavilacartes@users.noreply.github.com> Date: Sun, 7 Jan 2024 19:05:05 +0100 Subject: [PATCH 081/121] Complexcgr (#45089) * Add complexcgr v0.8.0 * Add complexcgr v0.8.0 * Add complexcgr v0.8.0 --- recipes/complexcgr/meta.yaml | 49 ++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 recipes/complexcgr/meta.yaml diff --git a/recipes/complexcgr/meta.yaml b/recipes/complexcgr/meta.yaml new file mode 100644 index 0000000000000..0dd7c0b71a5f1 --- /dev/null +++ b/recipes/complexcgr/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "complexcgr" %} +{% set version = "0.8.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/complexcgr-{{ version }}.tar.gz + sha256: 800085b4f2187a0acc4c2cb09d4c8459d9192f6d91a502101393e012978960dd + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + build: + run_exports: + - {{ pin_subpackage('complexcgr', max_pin="x.x") }} + +requirements: + host: + - python >=3.9,<4.0 + - poetry-core >=1.0.0 + - pip + run: + - python >=3.9.0,<4.0.0 + - tqdm >=4.61.2,<5.0.0 + - matplotlib-base >=3.4.2,<4.0.0 + - pillow >=10.0.0,<11.0.0 + - numpy >=1.22.3,<2.0.0 + - biopython >=1.79.0,<2.0.0 + +test: + imports: + - complexcgr + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/AlgoLab/complexCGR + summary: Encoders and Image representation of DNA/RNA sequences based on the Chaos Game Representation of DNA + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - jorgeavilacartes From f3ac82001f45cfffce2ad224e5897f6680ffa396 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Jan 2024 13:20:19 -0500 Subject: [PATCH 082/121] Update ribowaltz to 2.0 (#45065) * Update ribowaltz to 2.0 * add run_exports --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/ribowaltz/meta.yaml | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/recipes/ribowaltz/meta.yaml b/recipes/ribowaltz/meta.yaml index 1d3b50dd02917..1725593a487e9 100755 --- a/recipes/ribowaltz/meta.yaml +++ b/recipes/ribowaltz/meta.yaml @@ -1,21 +1,23 @@ {% set name = "riboWaltz" %} -{% set version = "1.2.0" %} -{% set sha256 = "1a915eccd23fd122eca470320b8f17762687350fdeb642aef01fb7990e98938b" %} +{% set version = "2.0" %} +{% set sha256 = "55f2f4e44709f1b41f788351b64cce4615194062775f5e0dc714320e01d6f65c" %} package: - name: {{ name|lower }} - version: {{ version }} + name: {{ name|lower }} + version: {{ version }} source: - url: https://github.com/LabTranslationalArchitectomics/{{ name }}/archive/v{{ version }}.tar.gz - sha256: {{ sha256 }} + url: https://github.com/LabTranslationalArchitectomics/{{ name }}/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} build: - number: 1 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('ribowaltz', max_pin="x") }} requirements: host: @@ -47,5 +49,6 @@ test: about: home: https://github.com/LabTranslationalArchitectomics/riboWaltz license: MIT + license_family: MIT license_file: LICENSE summary: Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. From 46538a2c01da939cf76530298f2dc46276f1f30d Mon Sep 17 00:00:00 2001 From: Mark Santcroos Date: Sun, 7 Jan 2024 20:24:58 +0100 Subject: [PATCH 083/121] Update vcf2variants (#45083) * Update to version 1.0. * Add run_exports. * Extra dependency. * Bump version. * Bump version and test import. * Fix import test. * Add additional requirement. --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/vcf2variants/meta.yaml | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/recipes/vcf2variants/meta.yaml b/recipes/vcf2variants/meta.yaml index 06461f2201e7e..ce21048d701da 100644 --- a/recipes/vcf2variants/meta.yaml +++ b/recipes/vcf2variants/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vcf2variants" %} -{% set version = "0.3" %} +{% set version = "1.2" %} package: name: '{{ name|lower }}' @@ -7,12 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 8780f3cf331e76dde7add454dbf346b38a69eb0b398b8b751f07413824f1b9a4 + sha256: 7830202ec67de08e7b223649365eed4a4a66d1339c985123d21c65cca7283728 build: number: 0 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv noarch: python + run_exports: + - {{ pin_subpackage('vcf2variants', max_pin="x") }} requirements: host: @@ -20,11 +22,15 @@ requirements: - pip run: - python >=3.6 - - cyvcf2 + - natsort + - pysam + - vcfphasesets test: commands: - vcf2variants -h + imports: + - vcf2variants about: home: https://github.com/varda/varda2_preprocessing From caff19a0dda546de5356bbaca64cb1cb5f209fc4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Jan 2024 18:16:37 -0500 Subject: [PATCH 084/121] Update snapatac2 to 2.5.2 (#45078) * Update snapatac2 to 2.5.2 * add typing_extensions to run section --------- Co-authored-by: joshuazhuang7 --- recipes/snapatac2/meta.yaml | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/recipes/snapatac2/meta.yaml b/recipes/snapatac2/meta.yaml index 52674eddb1726..725e76a0f899f 100644 --- a/recipes/snapatac2/meta.yaml +++ b/recipes/snapatac2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "snapatac2" %} -{% set version = "2.5.1" %} -{% set sha256 = "c60fff185fb502d03518b440b63e24b794f8c6f9592df06cd94d85e156721fa6" %} +{% set version = "2.5.2" %} +{% set sha256 = "7d851340005b72881311ab712a435c2ac3864155be305ff24ccdcd7972c3d2c7" %} package: name: {{ name }} @@ -12,10 +12,9 @@ source: build: number: 0 - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . -vvv --no-build-isolation --no-deps run_exports: - - {{ pin_subpackage('snapatac2', max_pin="x.x.x") }} - + - {{ pin_subpackage('snapatac2', max_pin="x") }} requirements: build: @@ -23,12 +22,10 @@ requirements: - cmake - rust - {{ compiler('c') }} - host: - python - pip - setuptools-rust - run: - python - anndata @@ -45,6 +42,7 @@ requirements: - packaging - rustworkx - pooch + - typing_extensions test: imports: @@ -52,9 +50,12 @@ test: about: home: https://github.com/kaizhang/SnapATAC2 - summary: Python/Rust package for single-cell epigenomics analysis + summary: "Python/Rust package for single-cell epigenomics analysis" license: MIT + license_family: MIT license_file: LICENSE + doc_url: https://kzhang.org/SnapATAC2/ + dev_url: https://github.com/kaizhang/SnapATAC2 extra: identifiers: From 996eb5e6c41772d82a5d21cc4f7b06129d211c84 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Jan 2024 19:30:08 -0500 Subject: [PATCH 085/121] Update breseq to 0.38.2 (#45103) * Update breseq to 0.38.2 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/breseq/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/breseq/meta.yaml b/recipes/breseq/meta.yaml index ee573da392da4..2b9c00862c815 100644 --- a/recipes/breseq/meta.yaml +++ b/recipes/breseq/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.38.1" %} +{% set version = "0.38.2" %} package: name: breseq @@ -6,10 +6,12 @@ package: source: url: https://github.com/barricklab/breseq/releases/download/v{{ version }}/breseq-{{ version }}-Source.tar.gz - sha256: "92af34f7248f7c8cf65951e1b86ffc0d6f7446dbe9d3323aa43c577ea1ff48b3" + sha256: "d451670b9e7e3c87b76d3107efe7f1a9a94904011a32e5d407f4cce7ee3b2892" build: - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('breseq', max_pin="x.x") }} requirements: build: @@ -31,8 +33,9 @@ test: about: home: https://github.com/barricklab/breseq - license: GPL-3.0 + license: GPL-2.0-or-later license_family: GPL license_file: COPYING summary: A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data. + doc_url: "https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/" From 54c6341e61b2214fd7f527cadf54243a644c3212 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Jan 2024 19:30:24 -0500 Subject: [PATCH 086/121] Update mitos to 2.1.6 (#45104) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/mitos/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mitos/meta.yaml b/recipes/mitos/meta.yaml index ee2cddc84aeb1..eec1dc7b5f508 100644 --- a/recipes/mitos/meta.yaml +++ b/recipes/mitos/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mitos" %} -{% set version = "2.1.5" %} +{% set version = "2.1.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: c82a48eeaf63f7733c3439047154c1869842ba0106e95bb4ab556131d161b428 + sha256: 66d6ca1138bdda459d4ed6271a946ff86ea6298dcf7e3bb6f63c283213f77284 build: number: 0 From 045ad7258594f9daca96b3fc179f50ad5a99d49e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Jan 2024 19:30:53 -0500 Subject: [PATCH 087/121] Update harmony-pytorch to 0.1.8 (#45106) * Update harmony-pytorch to 0.1.8 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/harmony-pytorch/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/harmony-pytorch/meta.yaml b/recipes/harmony-pytorch/meta.yaml index e29cb986fdae9..ac40e479722ae 100644 --- a/recipes/harmony-pytorch/meta.yaml +++ b/recipes/harmony-pytorch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "harmony-pytorch" %} -{% set version = "0.1.7" %} +{% set version = "0.1.8" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "90b6d6d7a9ae0a20584840828cff415d503be5449a7328b0c76fc45ed3f8c4df" + sha256: "1b097906d49c6ed9dde6cf234f7d987fb49a3b649b8a1323d99e6ea71b5b7df2" build: - number: 1 + number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('harmony-pytorch', max_pin="x.x") }} requirements: host: @@ -35,7 +37,8 @@ test: about: home: "https://github.com/lilab-bcb/harmony-pytorch" - license: BSD + license: BSD-3-Clause + license_family: BSD license_file: LICENSE summary: "This is a Pytorch implementation of Harmony algorithm on single-cell sequencing data integration." From db701557985e59042d20c09335564b2a1aebf6ae Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 06:45:25 -0500 Subject: [PATCH 088/121] Update snakemake to 8.1.0 (#45108) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 66d8213406374..ec9cb7290f522 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.0.1" %} +{% set version = "8.1.0" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 72f1158a345e8c53f73a14b3480bdfd6c1605f7c1c4a8a46f96fac489133ab80 + sha256: 3aeb95197ced3f50d89eabaa95ad93414db64bda7683283bdec6690810d598e9 build: number: 0 From 037b36ec16fe9d7721c55f5a8bf431b32c992866 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 10:14:12 -0500 Subject: [PATCH 089/121] Update ltr_retriever to 2.9.9 (#45107) --- recipes/ltr_retriever/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ltr_retriever/meta.yaml b/recipes/ltr_retriever/meta.yaml index 0945912461b47..fab51c19ad426 100644 --- a/recipes/ltr_retriever/meta.yaml +++ b/recipes/ltr_retriever/meta.yaml @@ -1,6 +1,6 @@ {% set name = "LTR_retriever" %} -{% set version = "2.9.8" %} -{% set sha256 = "c5723c69c8897e717f03a7a0690a8f9b4a6c56991d947eddb224066ddf2d1448" %} +{% set version = "2.9.9" %} +{% set sha256 = "ef7d59349c0cbb3c819a102e68488b85cb116c099a4512d72d8a70293f13c7c8" %} package: name: "{{ name|lower }}" From a7f0ce1df654cd10b29d16ee033c7725a7882e33 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 10:16:40 -0500 Subject: [PATCH 090/121] Update tn93 to 1.0.13 (#45109) --- recipes/tn93/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tn93/meta.yaml b/recipes/tn93/meta.yaml index dd24eb3675cba..37df7d1f5e9e2 100644 --- a/recipes/tn93/meta.yaml +++ b/recipes/tn93/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.12" %} +{% set version = "1.0.13" %} package: name: tn93 @@ -6,7 +6,7 @@ package: source: url: https://github.com/veg/tn93/archive/v{{ version }}.tar.gz - sha256: d60281b1b4375bff585bcfae57be6938606500a656682249da3e10ce222b889d + sha256: 58f26807cd762cfc5cb6f088b57dfb26c69e8dd8e59a3e3db42a51ddea03bb3c build: number: 0 From 577b95f5dcd10161e163a50ca9476799a70c1eac Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 11:41:42 -0500 Subject: [PATCH 091/121] Update hyphy to 2.5.59 (#45111) --- recipes/hyphy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hyphy/meta.yaml b/recipes/hyphy/meta.yaml index 66f4c7839bcdf..7e05e89fcba7a 100644 --- a/recipes/hyphy/meta.yaml +++ b/recipes/hyphy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.5.58" %} -{% set sha256 = "f448d4a95bdb356eb6b1384b0c507a79f152511ad76bb67170ab5b8eb2798231" %} +{% set version = "2.5.59" %} +{% set sha256 = "18d7fc1569ca9fa5cbd7df0517ccb3e03de118fb42ab339073dbf3a7d82c8546" %} package: name: hyphy From c3b5108db4d27cccc69c6e97412354bbb74adfb9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 12:46:59 -0500 Subject: [PATCH 092/121] Update pyfaidx to 0.8.0 (#45113) --- recipes/pyfaidx/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pyfaidx/meta.yaml b/recipes/pyfaidx/meta.yaml index d39bacf8ec44f..9209e777f8e00 100644 --- a/recipes/pyfaidx/meta.yaml +++ b/recipes/pyfaidx/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "0.7.2.2" %} +{% set version = "0.8.0" %} package: name: pyfaidx version: {{ version }} source: - url: https://files.pythonhosted.org/packages/19/ec/929a2ab2247105210ccc6ea61ab1af0bd9316eb6b3412123cfbd88a0bc60/pyfaidx-0.7.2.2.tar.gz - sha256: 3b7693c052c82691000fe4a92475db82ffc3b5a721a12b10dfbc87119c4b4d30 + url: https://files.pythonhosted.org/packages/ef/95/aa7e6d1c1b68e64234d5ed985a761edbbce124baea17c2056935626958d2/pyfaidx-0.8.0.tar.gz + sha256: 1eed70f4eafb4ba9c4cf7022cd748947b8ebe0f4c86cb56f42f587ab7f2da027 build: number: 0 From 7f65759410092b5d3f10a80532fe3a093e0c8081 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Mon, 8 Jan 2024 20:57:01 +0100 Subject: [PATCH 093/121] Depend on gcc; new sha256 --- recipes/sativa/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/sativa/meta.yaml b/recipes/sativa/meta.yaml index 45f3caa97d650..8b08a26cc1c86 100644 --- a/recipes/sativa/meta.yaml +++ b/recipes/sativa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sativa" %} -{% set version = "0.9.2" %} +{% set version = "0.9.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/amkozlov/sativa/archive/refs/tags/v{{ version }}.zip - sha256: e1ba4a89937dad23115575c0f6d185527ad1bb062b3fdd313a151492c21a6e2b + sha256: 0d0ae82f0f9608f51301ecadc367f85653fe9954855d9ebbbef8f889eef586b8 build: number: 0 @@ -17,7 +17,7 @@ build: requirements: build: - make - - {{ compiler('c') }} + - gcc >=4.7.0 - python >=3.0.0 host: - python >=3.0.0 From 9ca64d5d2d12a52e57eb2fd69e85ae35ce2b42b0 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Wed, 10 Jan 2024 09:59:23 +0100 Subject: [PATCH 094/121] Finally a sativa recipe that puts sativa.py in PATH --- recipes/sativa/build.sh | 15 +++++++++------ recipes/sativa/meta.yaml | 4 ++-- 2 files changed, 11 insertions(+), 8 deletions(-) diff --git a/recipes/sativa/build.sh b/recipes/sativa/build.sh index b983fcee56e33..9f821444e5974 100644 --- a/recipes/sativa/build.sh +++ b/recipes/sativa/build.sh @@ -1,8 +1,11 @@ #!/bin/bash -mkdir ${PREFIX}/sativa/ -mv * ${PREFIX}/sativa/ -cd ${PREFIX}/sativa -./install.sh -cd ${PREFIX}/bin -ln -s ${PREFIX}/sativa/sativa.py . +export USE_AVX=yes +export USE_AVX2=yes + +make -C raxml + +cp -r raxml ${PREFIX}/bin +cp -r epac ${PREFIX}/bin +cp *.py ${PREFIX}/bin +cp sativa.cfg ${PREFIX}/bin diff --git a/recipes/sativa/meta.yaml b/recipes/sativa/meta.yaml index 8b08a26cc1c86..26b62174f5b84 100644 --- a/recipes/sativa/meta.yaml +++ b/recipes/sativa/meta.yaml @@ -17,7 +17,7 @@ build: requirements: build: - make - - gcc >=4.7.0 + - {{ compiler('c') }} - python >=3.0.0 host: - python >=3.0.0 @@ -29,7 +29,7 @@ test: - sequences.alnfna - taxonomy.tsv commands: - - $PREFIX/sativa/sativa.py -s sequences.alnfna -t taxonomy.tsv -x bac -debug + - sativa.py -s sequences.alnfna -t taxonomy.tsv -x bac -debug about: home: https://github.com/amkozlov/sativa From d185e0bc6231150ee5f765f0d39c6fbaa001ea60 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 16:29:03 -0500 Subject: [PATCH 095/121] Update mitgard to 1.1 (#45101) * Update mitgard to 1.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/mitgard/meta.yaml | 32 ++++++++++++++++++-------------- 1 file changed, 18 insertions(+), 14 deletions(-) diff --git a/recipes/mitgard/meta.yaml b/recipes/mitgard/meta.yaml index 2f83790b1ea71..7c3341012ee75 100644 --- a/recipes/mitgard/meta.yaml +++ b/recipes/mitgard/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0" %} +{% set version = "1.1" %} package: name: mitgard @@ -6,32 +6,36 @@ package: source: url: https://github.com/pedronachtigall/MITGARD/archive/refs/tags/v{{ version }}.tar.gz - sha256: 97bf3299242c573e744ded016f70f7e0d3a07c3f4b62ce88d084b9a2c3a9dabd + sha256: f00bf3d7795e6d320416cb1fb856d8dee936d95055f77b19ac74e1d42e88ed5f build: noarch: generic - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('mitgard', max_pin="x") }} requirements: - host: - - python>=3.6 - run: - - samtools=1.9 - - bowtie2=2.3 - - minimap2=2.17 - - trinity=2.8.5 - - spades=3.13.1 - - python>=3.6 - - biopython=1.69 + - samtools + - bowtie2 + - minimap2 + - trinity =2.8.5 + - spades =3.13.1 + - python >=3.6 + - biopython + - hifiasm + - canu + - blast test: commands: - "MITGARD.py -h" + - "MITGARD-LR.py -h" about: home: https://github.com/pedronachtigall/MITGARD - license: GPLv3 + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE.txt summary: "Mitochondrial Genome Assembly from RNA-seq Data." doc_url: https://github.com/pedronachtigall/MITGARD From 29ac2c2c8484f20acb734e85e44d66484469014c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 19:00:37 -0500 Subject: [PATCH 096/121] Update bioframe to 0.6.1 (#45120) --- recipes/bioframe/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioframe/meta.yaml b/recipes/bioframe/meta.yaml index 0cd0bbd8b9c45..81590d40e0556 100644 --- a/recipes/bioframe/meta.yaml +++ b/recipes/bioframe/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bioframe" %} -{% set version = "0.6.0" %} +{% set version = "0.6.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 7998f6aa072ab9655354b64c511a093c9f1a181f2d994f0e884b9c48c4d0c313 + sha256: 63aec69ac37aebcdc8298ed41154a875ba99652cc7ef081dd1458bc90537f73b build: noarch: python From 316692ba8c0c45542edc1d1374d296fc8ce36891 Mon Sep 17 00:00:00 2001 From: Zhou ZJ <43747306+ZhijianZhou01@users.noreply.github.com> Date: Tue, 9 Jan 2024 08:01:01 +0800 Subject: [PATCH 097/121] Add virusrecom (#45099) * add virusrecom recipes * add virusrecom recipes xx * Update meta.yaml * add python to run section and use SPDX identifier --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/virusrecom/build.sh | 4 +++ recipes/virusrecom/meta.yaml | 47 ++++++++++++++++++++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 recipes/virusrecom/build.sh create mode 100644 recipes/virusrecom/meta.yaml diff --git a/recipes/virusrecom/build.sh b/recipes/virusrecom/build.sh new file mode 100644 index 0000000000000..c65b9bb44d4b1 --- /dev/null +++ b/recipes/virusrecom/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +# build +$PYTHON setup.py install --single-version-externally-managed --record=record.txt \ No newline at end of file diff --git a/recipes/virusrecom/meta.yaml b/recipes/virusrecom/meta.yaml new file mode 100644 index 0000000000000..7c76abee9b068 --- /dev/null +++ b/recipes/virusrecom/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "virusrecom" %} +{% set version = "1.1.2.2" %} + +package: + name: "{{ name }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: d06eb57299eb38b3fbf2341af3ede2265a400962c2d147d84d19993ed496d024 + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage('virusrecom', max_pin="x") }} + + +requirements: + host: + - python >=3.5,<3.8 + - pip + - setuptools + + run: + - matplotlib-base + - numpy >=1.19.3 + - pandas >=1.1.5 + - scipy >=1.5.4 + - psutil >=5.9.1 + - python >=3.5,<3.8 + - openpyxl >=3.0.5 + +test: + commands: + - virusrecom --help + +about: + home: "https://github.com/ZhijianZhou01/virusrecom" + license: "LGPL-2.1-or-later" + license_family: "LGPL" + license_file: LICENSE + summary: "An information-theory-based method for recombination detection of viral lineages." + +extra: + identifiers: + - doi:10.1093/bib/bbac513 From c69f9e783606acb7a48fd823704b4141062c321b Mon Sep 17 00:00:00 2001 From: M Bernt Date: Tue, 9 Jan 2024 01:01:24 +0100 Subject: [PATCH 098/121] bump mitos1 (#45112) * bump mitos1 * repin blast-legacy .. add tests first --- recipes/mitos/mitos1/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/mitos/mitos1/meta.yaml b/recipes/mitos/mitos1/meta.yaml index 9ce262fca6fec..c1a015275ecc6 100644 --- a/recipes/mitos/mitos1/meta.yaml +++ b/recipes/mitos/mitos1/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mitos" %} -{% set version = "1.1.3" %} +{% set version = "1.1.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 0e750ada0f69626407e81bd953c83717a917c6b96f49d0f154bbe740a4b5fe12 + sha256: 4f541044977dd3b33628ff780f6435094f1d633a031a88b5bda80342efa05bae build: number: 0 @@ -25,8 +25,7 @@ requirements: - python >=3 - blast-legacy =2.2 - infernal =1.0 - - viennarna <2 - - r-base >=4 + - viennarna - r-ggplot2 - r-reshape2 - openjdk >8 @@ -61,6 +60,8 @@ test: - mitos.webserver commands: - runmitos.py -h + - 'R -e "library(''reshape2'')"' + - 'R -e "library(''ggplot2'')"' about: home: http://mitos.bioinf.uni-leipzig.de From 25a47d31a64c7f4012885068df8cdb69624e168d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 19:28:19 -0500 Subject: [PATCH 099/121] Update pybiolib to 1.1.1685 (#45119) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 135ea9c49e89f..d7727d223aa67 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1682" %} +{% set version = "1.1.1685" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 3bb0789aea5e55cf7fc33f41e898e6d3abb05adbafd870ba6be1c761e762c105 + sha256: 44921a3ec42de028d164b048374691906edeaa59b8fb7b9366e82dabee1aba8c build: noarch: python From f2cad9eb9016034c649d343e347712bc1a897bb2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 21:18:23 -0500 Subject: [PATCH 100/121] Update ncbi-datasets-pylib to 16.1.2 (#45124) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 8e24d691bd6a8..42d3681568ee5 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.1.1" %} -{% set sha256 = "cddfde551d1a5948d0f3b87660968887a0e22d31db2f2810384393192c112eaf" %} +{% set version = "16.1.2" %} +{% set sha256 = "4bee7893737320c5b63887b513ad92712db3c2a3eb306b3ba26ac5590088cba7" %} package: name: {{ name|lower }} From c1f99b2ebcf2ad6afa23a3d2bbeb5e392ebc5f67 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 21:18:32 -0500 Subject: [PATCH 101/121] Update das_tool to 1.1.7 (#45123) * Update das_tool to 1.1.7 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/das_tool/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/das_tool/meta.yaml b/recipes/das_tool/meta.yaml index 2fdb95251dd2e..6aab0c2d4911b 100644 --- a/recipes/das_tool/meta.yaml +++ b/recipes/das_tool/meta.yaml @@ -1,6 +1,6 @@ {% set name = "DAS_Tool" %} -{% set version = "1.1.6" %} -{% set sha256 = "a4c02f6789e7f6ca61e0b563261d5f17f12e1b931157a4ae0f413ffdea6eacfb" %} +{% set version = "1.1.7" %} +{% set sha256 = "3633b69242209ceee9cd523e3458adbe89da9c52ecd8724afef2e2099923c56c" %} package: name: {{ name|lower }} @@ -16,6 +16,8 @@ build: rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('das_tool', max_pin="x") }} requirements: host: @@ -30,7 +32,6 @@ requirements: - prodigal >=2.6.3 - blast >=2.7.1 - diamond >=0.9.14 - run: - codeutils # [osx] - unzip From 2183ad006a46e95b4177d6b843444aededababca Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 21:18:44 -0500 Subject: [PATCH 102/121] Update virusrecom to 1.1.3 (#45122) --- recipes/virusrecom/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/virusrecom/meta.yaml b/recipes/virusrecom/meta.yaml index 7c76abee9b068..84f3000fefdb9 100644 --- a/recipes/virusrecom/meta.yaml +++ b/recipes/virusrecom/meta.yaml @@ -1,5 +1,5 @@ {% set name = "virusrecom" %} -{% set version = "1.1.2.2" %} +{% set version = "1.1.3" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: d06eb57299eb38b3fbf2341af3ede2265a400962c2d147d84d19993ed496d024 + sha256: 1950537ea6f2cf83dcfc44dd31b5c524a8e5b6988ca284c1ed291a2234d692c7 build: number: 0 From d28aa80bb4f6509b43833af1fa3428f48dcab988 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 10:20:35 -0500 Subject: [PATCH 103/121] Update severus to 0.1.2 (#45135) --- recipes/severus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/severus/meta.yaml b/recipes/severus/meta.yaml index 51de9dbeecbb8..6fbcfbe6a28f5 100644 --- a/recipes/severus/meta.yaml +++ b/recipes/severus/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: severus @@ -6,7 +6,7 @@ package: source: url: https://github.com/KolmogorovLab/Severus/archive/refs/tags/{{ version }}.tar.gz - sha256: aa9cf7bfc78234b770e5b67a38e6ee98ee94c1e45e11d61429d8e02df8793570 + sha256: 6fd60f673aea6e6ff930a207311be3c533a944c8875e9a677235b99dc18e5135 build: number: 0 From 23dbe7366556e29a85f71d1fdfb7488be96eca36 Mon Sep 17 00:00:00 2001 From: Zhou ZJ <43747306+ZhijianZhou01@users.noreply.github.com> Date: Tue, 9 Jan 2024 23:42:25 +0800 Subject: [PATCH 104/121] Update virusrecom (#45130) * add virusrecom recipes * Update meta.yaml * edit recipe-maintainer --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/virusrecom/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/virusrecom/meta.yaml b/recipes/virusrecom/meta.yaml index 84f3000fefdb9..bafd8ea722121 100644 --- a/recipes/virusrecom/meta.yaml +++ b/recipes/virusrecom/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 1950537ea6f2cf83dcfc44dd31b5c524a8e5b6988ca284c1ed291a2234d692c7 build: - number: 0 + number: 1 noarch: python run_exports: - {{ pin_subpackage('virusrecom', max_pin="x") }} @@ -18,7 +18,7 @@ build: requirements: host: - - python >=3.5,<3.8 + - python >=3.5,!=3.8 - pip - setuptools @@ -28,7 +28,7 @@ requirements: - pandas >=1.1.5 - scipy >=1.5.4 - psutil >=5.9.1 - - python >=3.5,<3.8 + - python >=3.5,!=3.8 - openpyxl >=3.0.5 test: @@ -45,3 +45,5 @@ about: extra: identifiers: - doi:10.1093/bib/bbac513 + recipe-maintainers: + - ZhijianZhou01 From 67ca4d31fd08fb4041a811da726e90043f079c78 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 10:42:41 -0500 Subject: [PATCH 105/121] Update hybracter to 0.5.0 (#45128) --- recipes/hybracter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml index 4fd336ec8d85d..8e85a27f1af6e 100644 --- a/recipes/hybracter/meta.yaml +++ b/recipes/hybracter/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybracter" %} -{% set version = "0.4.1" %} +{% set version = "0.5.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz - sha256: 934eb7cc5024a4aac40e6f239a371cd2f1c987361d0c423f27cb24cc65b39217 + sha256: 6bdc2376e0000556622b957e765f27014972784700f306943b345956739d4592 build: number: 0 From c0d42065038ed0b5e7d19bccc8f756883675ed71 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 10:42:49 -0500 Subject: [PATCH 106/121] Update dnaapler to 0.5.1 (#45129) --- recipes/dnaapler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dnaapler/meta.yaml b/recipes/dnaapler/meta.yaml index e483b65cb9b96..5737d45fcec6a 100644 --- a/recipes/dnaapler/meta.yaml +++ b/recipes/dnaapler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dnaapler" %} -{% set version = "0.5.0" %} +{% set version = "0.5.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 19bc7c140b9047be5a094ad65c71f042b438cc1bb1a9c03a2c11ea8b54c3d506 + sha256: 9bc6289ebefaa2e9725709cae2dbfa2723ad0d4e7f073f781a23e9b799bac8a8 build: number: 0 From 72567a45ccb818bd2fc39270750909ece78f7b5d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 10:43:01 -0500 Subject: [PATCH 107/121] Update recentrifuge to 1.13.1 (#45132) --- recipes/recentrifuge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/recentrifuge/meta.yaml b/recipes/recentrifuge/meta.yaml index 76f4032164e44..2490ce7708084 100644 --- a/recipes/recentrifuge/meta.yaml +++ b/recipes/recentrifuge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "recentrifuge" %} -{% set version = "1.13.0" %} +{% set version = "1.13.1" %} package: name: {{ name }} @@ -14,7 +14,7 @@ build: source: url: https://github.com/khyox/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 6b7c4d80ad53115bca363d72352ee4d9074aa3385ed2556840ce4e3f24855e17 + sha256: a8c3826302c7a39fe0735176b49fc635964b83d5cc110fc3139c83783c27984d requirements: host: From 07ed883ad583ac7c36543b2ab48c135bff86022d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 10:44:18 -0500 Subject: [PATCH 108/121] Update tissuumaps to 3.2.0.3 (#45137) --- recipes/tissuumaps/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml index a8cc66ef61471..8555dcfae9eba 100644 --- a/recipes/tissuumaps/meta.yaml +++ b/recipes/tissuumaps/meta.yaml @@ -4,7 +4,7 @@ # - add pyqt6 (or possibly pyqt>=6) dependency # Until then, only the "tissuumaps_server" script is available, not "tissuumaps" -{% set version = "3.2.0.2" %} +{% set version = "3.2.0.3" %} package: name: tissuumaps @@ -12,7 +12,7 @@ package: source: url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz - sha256: d47443e5cda7c1f8dd63879feeb799a1874638026d15c7ce1f190004d87fd384 + sha256: 372a92e7aa8fb5f6149bac1133aae6d04653c87ba3048af9ed95da84a64f2592 build: number: 0 From 85f54be8996f76bd37d5df515708d8e2f8a813a9 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Tue, 9 Jan 2024 16:45:08 +0100 Subject: [PATCH 109/121] mitos: add tests for R packages (#44971) * mitos: add tests for R packages In test with the container I got: Exception: b"Warning message:\npackage \xe2\x80\x98ggplot2\xe2\x80\x99 was built under R version 3.6.3 \nError: package or namespace load failed for \xe2\x80\x98reshape2\xe2\x80\x99 in dyn.load(file, DLLpath = DLLpath, ...):\n unable to load shared object '/usr/local/lib/R/library/stringi/libs/stringi.so':\n libicui18n.so.64: cannot open shared object file: No such file or directory\nIn addition: Warning message:\npackage \xe2\x80\x98reshape2\xe2\x80\x99 was built under R version 3.6.3 \nExecution halted\n" * try to use R directly in tests * try R > 3 * bump and unpin vienna * retry R>3 * another try * try to pin r-stringi * bump * cnt * unpin some more requirements * remove stringi * repin infernal * repin hmmer * repin blast * Revert "repin blast" This reverts commit 6a5717a86f8231c1ced5ca58e21f97f01c264e2f. --- recipes/mitos/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/mitos/meta.yaml b/recipes/mitos/meta.yaml index eec1dc7b5f508..7523ada0fc540 100644 --- a/recipes/mitos/meta.yaml +++ b/recipes/mitos/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 66d6ca1138bdda459d4ed6271a946ff86ea6298dcf7e3bb6f63c283213f77284 build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " noarch: python run_exports: @@ -23,11 +23,11 @@ requirements: run: - biopython <1.82 - python >=3 - - blast =2.9 + - blast >=2.9 - hmmer =3.2 - infernal =1.1 - - viennarna <2 - - r-base >=3 + - viennarna + - r-base - r-ggplot2 - r-reshape2 - openjdk >8 @@ -61,6 +61,8 @@ test: - mitos.webserver commands: - runmitos.py -h + - 'R -e "library(''reshape2'')"' + - 'R -e "library(''ggplot2'')"' about: home: http://mitos.bioinf.uni-leipzig.de From 5aa4846581086b65a89174bfd0a29bc139e9468c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 11:47:42 -0500 Subject: [PATCH 110/121] Update kb-python to 0.28.2 (#45138) --- recipes/kb-python/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/kb-python/meta.yaml b/recipes/kb-python/meta.yaml index 9838dbed1aff6..23a0ad79fcaaa 100644 --- a/recipes/kb-python/meta.yaml +++ b/recipes/kb-python/meta.yaml @@ -1,5 +1,5 @@ {% set name = "kb-python" %} -{% set version = "0.28.1" %} +{% set version = "0.28.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/pachterlab/kb_python/archive/v{{ version }}.tar.gz - sha256: a45f396046f544326089c0c25deabcca254989eebab040b12e07114e6d87a09d + sha256: e8c910865fd5196b1b3163e18a565ef96c8518b2cf34f87f288dfdc85b339078 patches: config.py.patch build: From b83481ec0d183d6ef336933c973158289c4b5f77 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 11:47:49 -0500 Subject: [PATCH 111/121] Update ena-webin-cli to 6.9.0 (#45139) --- recipes/ena-webin-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ena-webin-cli/meta.yaml b/recipes/ena-webin-cli/meta.yaml index 582fa0f98d569..98bc27a785056 100644 --- a/recipes/ena-webin-cli/meta.yaml +++ b/recipes/ena-webin-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "6.8.0" %} -{% set sha256 = "08d39ed646f00d2e682ea83849c04e0665106af9f7ae25ca04c07bdd086c91ef" %} +{% set version = "6.9.0" %} +{% set sha256 = "13218491e3d0dce8b28360606e23ffd54bd491452449c996e7f05944bf352217" %} package: name: ena-webin-cli From dd284745ee878fa8384aa9d661439b7db8d9638d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 11:49:50 -0500 Subject: [PATCH 112/121] Update r-seqmagick to 0.1.7 (#45131) * Update r-seqmagick to 0.1.7 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/r-seqmagick/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/r-seqmagick/meta.yaml b/recipes/r-seqmagick/meta.yaml index dd1ab5449d137..72e09c9aa4e16 100644 --- a/recipes/r-seqmagick/meta.yaml +++ b/recipes/r-seqmagick/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.1.6' %} +{% set version = '0.1.7' %} package: name: r-seqmagick @@ -8,24 +8,28 @@ source: url: - {{ cran_mirror }}/src/contrib/seqmagick_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/seqmagick/seqmagick_{{ version }}.tar.gz - sha256: 4f872c7b3f39e5b21a5820478102e0b39ecf5d7e2a12dfba263568ab250ab1f5 + sha256: 95cf80c9c0a266e07cf7b124de105818c58f8f843f70ab25e0877a910211b8e5 build: - number: 1 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-seqmagick', max_pin="x.x") }} requirements: host: - r-base - bioconductor-biostrings - r-magrittr + - r-yulab.utils >0.1.1 run: - r-base - bioconductor-biostrings - r-magrittr + - r-yulab.utils >0.1.1 test: commands: From 7444bc26218c52af9f981292d4b3d0b02cc3f1dd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 12:17:47 -0500 Subject: [PATCH 113/121] Update snakefmt to 0.9.0 (#45134) --- recipes/snakefmt/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakefmt/meta.yaml b/recipes/snakefmt/meta.yaml index 49a1189437a9a..9ef41f71bddc2 100644 --- a/recipes/snakefmt/meta.yaml +++ b/recipes/snakefmt/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.5" %} +{% set version = "0.9.0" %} package: name: snakefmt @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakefmt/snakefmt-{{ version }}.tar.gz - sha256: 5aa5182dbbbeb84d477dd0f5a9eeeba41bac1f185cfd4897a0b005d4af59ba71 + sha256: 54c78050edead20cea5f87a6c9674ee1b5e4e38faac2852b45d0650faf9cb319 build: number: 0 From ce2596346fb033c9631cc21c18be94dd793ddc55 Mon Sep 17 00:00:00 2001 From: boukn Date: Tue, 9 Jan 2024 15:37:26 -0500 Subject: [PATCH 114/121] remove static compilation (#45141) --- recipes/ncbi-fcs-gx/meta.yaml | 2 +- recipes/ncbi-fcs-gx/no_static.patch | 19 ++++++++----------- 2 files changed, 9 insertions(+), 12 deletions(-) diff --git a/recipes/ncbi-fcs-gx/meta.yaml b/recipes/ncbi-fcs-gx/meta.yaml index 2ed106374b726..e1f67d2619dea 100644 --- a/recipes/ncbi-fcs-gx/meta.yaml +++ b/recipes/ncbi-fcs-gx/meta.yaml @@ -26,7 +26,7 @@ requirements: - grep >=3.4 build: - number: 2 + number: 3 skip: True # [not linux or not x86_64] run_exports: - {{ pin_compatible('ncbi-fcs-gx', max_pin="0.5") }} diff --git a/recipes/ncbi-fcs-gx/no_static.patch b/recipes/ncbi-fcs-gx/no_static.patch index 3d09172fa9770..8d8e22f22579e 100644 --- a/recipes/ncbi-fcs-gx/no_static.patch +++ b/recipes/ncbi-fcs-gx/no_static.patch @@ -1,13 +1,10 @@ -diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt -index b2d24ff..007a3ac 100644 ---- a/src/CMakeLists.txt -+++ b/src/CMakeLists.txt -@@ -32,7 +32,7 @@ include_directories(${PROJECT_SOURCE_DIR}/include/) +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -5,6 +5,6 @@ + set(gx_VERSION_MINOR 0) - set_source_files_properties(main.cpp PROPERTIES COMPILE_FLAGS "-DGIT_REVISION=`../../build-support/git_describe.sh`") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS} -O0 -ggdb3 -DDEBUG") +-set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS} -static -O2 -DNDEBUG") # TODO: investigate whether can/should enable -march=x86-64-v4 ++set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS} -O2 -DNDEBUG") # TODO: investigate whether can/should enable -march=x86-64-v4 --link_libraries("-flto -pthread -Wl,--format=binary -Wl,../../LICENSE -Wl,--format=default") # see show-license command in main.cpp -+link_libraries("-flto -Wl,--whole-archive -lrt -lpthread -Wl,--no-whole-archive -Wl,--format=binary -Wl,../../LICENSE -Wl,--format=default") # see show-license command in main.cpp - - #add_compile_options(-fsanitize=address) - #add_link_options(-fsanitize=address) + add_subdirectory(src) From ae6cf40b86f9915702f4d7f9ff67b9edb219cbea Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 21:56:33 -0500 Subject: [PATCH 115/121] Update dajin2 to 0.3.6 (#45143) --- recipes/dajin2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dajin2/meta.yaml b/recipes/dajin2/meta.yaml index ec633abd38945..eca8b4b9afad9 100644 --- a/recipes/dajin2/meta.yaml +++ b/recipes/dajin2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "DAJIN2" %} -{% set version = "0.3.5" %} +{% set version = "0.3.6" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/DAJIN2-{{ version }}.zip - sha256: f6a6c20eda88b3b1a86ccde2e3ac1a63d934c503eda0f44604f4d83ca77441d5 + sha256: cf9e686f78041682589c8e90bcac8eb2ad6473987c96bd574faf36e0b461613c build: entry_points: From 001af1ddebc06810d7eedc21a65ba50d2ae56105 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 21:56:46 -0500 Subject: [PATCH 116/121] Update jbrowse2 to 2.10.1 (#45145) --- recipes/jbrowse2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml index 05698606f2fc5..48774c686d68b 100644 --- a/recipes/jbrowse2/meta.yaml +++ b/recipes/jbrowse2/meta.yaml @@ -1,12 +1,12 @@ # When updating, check the @jbrowse/cli version in build.sh too -{% set version = "2.10.0" %} +{% set version = "2.10.1" %} package: name: jbrowse2 version: {{ version }} source: - sha256: c1dcb2c3e4edd544dcdd566d9f96ca51f93587c444ad6d16d5deff7d3e271862 + sha256: 9495e73d98e4eb287c8a48d8d4a61f2523755a4582681ce4e8e09b9e0fbef291 url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip build: From bcbcbb705d3166667084fa96684ffaca36d9079c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 21:56:56 -0500 Subject: [PATCH 117/121] Update ncbi-datasets-pylib to 16.2.0 (#45144) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 42d3681568ee5..6327205797c4f 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.1.2" %} -{% set sha256 = "4bee7893737320c5b63887b513ad92712db3c2a3eb306b3ba26ac5590088cba7" %} +{% set version = "16.2.0" %} +{% set sha256 = "2be4cc1b4bf42dabf0c9a4eabfa2db66bc4eb740b844f87b371da861bc995891" %} package: name: {{ name|lower }} From 9564341918709fee79a6a0c0f9fdacf22685a9be Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 9 Jan 2024 19:58:31 -0700 Subject: [PATCH 118/121] Add ACI (#45121) * adding aci recipe * fixed entry point typo * fix typo * matplotlib-base * url * revert url * underscore * version --------- Co-authored-by: Thanh Lee --- recipes/aci/meta.yaml | 49 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 recipes/aci/meta.yaml diff --git a/recipes/aci/meta.yaml b/recipes/aci/meta.yaml new file mode 100644 index 0000000000000..92a18bd603fcd --- /dev/null +++ b/recipes/aci/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "aci" %} +{% set repo = "amplicon_coverage_inspector" %} +{% set version = "1.2.20231229" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ repo[0] }}/{{ repo }}/{{ repo }}-{{ version }}.tar.gz + sha256: f54b1829a8eb1972751fce0b5d6a7d48a62d9cc80935a609302779a9966f104d + +build: + number: 0 + noarch: python + entry_points: + - aci=aci.aci:main + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('aci', max_pin='x') }} + +requirements: + host: + - python >=3.7,<4.0 + - pip + run: + - python >=3.7,<4.0 + - matplotlib-base >=3.8.2 + - numpy >=1.26.2 + - pandas >=2.1.4 + - pysam >=0.22.0 + +test: + imports: + - aci + commands: + - aci --help + +about: + home: https://github.com/erinyoung/ACI + license: MIT + license_family: MIT + license_file: LICENSE + summary: Visualizes coverage for amplicons + doc_url: https://github.com/erinyoung/ACI/blob/main/README.md + +extra: + recipe-maintainers: + - erinyoung From df10d838cb46a2890b671f9c741fa844e2635618 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Jan 2024 03:26:52 -0500 Subject: [PATCH 119/121] Update ngs-chew to 0.9.0 (#45140) --- recipes/ngs-chew/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/ngs-chew/meta.yaml b/recipes/ngs-chew/meta.yaml index bf1055c64d5b6..70a556610a8a9 100644 --- a/recipes/ngs-chew/meta.yaml +++ b/recipes/ngs-chew/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.8.1" %} -{% set sha256 = "28b27061a6f418ef8dd805ce3135d4f8210521bab8c65a44b5c61092f2a999e8" %} +{% set version = "0.9.2" %} +{% set sha256 = "5220182a9b2e6d2c2adf8ca6053c5a8ebf917942c6486eeee19aa2ccc6bea561" %} package: name: ngs-chew @@ -14,15 +14,18 @@ build: noarch: python entry_points: - ngs-chew = chew.cli:cli - script: python -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + run_exports: + - {{ pin_subpackage('ngs-chew', max_pin="x.x") }} requirements: host: - - python >=3.7 + - python >=3.8 - pip run: - - python >=3.7 + - python >=3.8 - attrs + - cattrs - click - logzero - numpy From f2ae4225a444fa9436b11eba128071265287754b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Jan 2024 03:27:39 -0500 Subject: [PATCH 120/121] Update vcfpy to 0.13.7 (#45150) --- recipes/vcfpy/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/vcfpy/meta.yaml b/recipes/vcfpy/meta.yaml index fff3b36cc93c2..a16833b549124 100644 --- a/recipes/vcfpy/meta.yaml +++ b/recipes/vcfpy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.13.6" %} -{% set sha256 = "778afe1dfec387206ddac754186e0777c326e0c300496b7631ade532532ce0bb" %} +{% set version = "0.13.8" %} +{% set sha256 = "e7d00965105e7ca9567299f073ad60c6bbfc78d685d25ba33353988af9b33160" %} package: name: vcfpy @@ -10,16 +10,18 @@ source: sha256: {{ sha256 }} build: - script: python -m pip install --no-deps --ignore-installed . noarch: python number: 0 + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + run_exports: + - {{ pin_subpackage('vcfpy', max_pin="x.x") }} requirements: host: - - python >=3 + - python >=3.8 - pip run: - - python >=3 + - python >=3.8 - pysam >=0.10.0 test: From bf351daa9c04055e8a5b874472416cb3fe8e4d02 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Wed, 10 Jan 2024 15:20:18 +0100 Subject: [PATCH 121/121] Avoid building on OS X --- recipes/sativa/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/sativa/meta.yaml b/recipes/sativa/meta.yaml index 26b62174f5b84..7fa6e1aee16b4 100644 --- a/recipes/sativa/meta.yaml +++ b/recipes/sativa/meta.yaml @@ -11,6 +11,7 @@ source: build: number: 0 + skip: true # [osx] run_exports: - {{ pin_subpackage('sativa', max_pin="x.x") }}