Try building bioconductor-geoquery #44726
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bgruening
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this pull request
Dec 29, 2023
* a round of fixes and build-skips * add some build failures * correct version for bioconductor-data-packages * add build failure for STdeconvolve * [ci run] trigger bulk run * run_exports on bioconductor-data-packages * [ci run] trigger bulk run * build failure for omnipathr * [ci run] trigger bulk run * Build important packages first * [ci run] trigger bulk run * revert to full build * [ci run] trigger bulk run * build failure files * skip iclusterplus * skip bioconductor-lpsymphony * bump bioconda-repodata-patches build number * [ci run] * build failures * next round of high priority packages * [ci run] trigger bulk run * [ci run] add dependency * [ci run] finish priority packages * re-enable full bulk * [ci run] trigger bulk run * build failures * [ci run] trigger bulk run * next round of high priority packages * [ci run] trigger bulk run * build more high priority packages * [ci run] test local channel fix * [ci run] increase workers * Try building bioconductor-geoquery (#44726) * Delete recipes/bioconductor-geoquery/build_failure.linux-64.yaml * Update meta.yaml * try fixing parsing error * [ci run] try rebuilding bioconductor-coregx (#44727) * try rebuilding bioconductor-coregx * Update meta.yaml * add opencl loading libraries - will this work * [ci run] remove a few build failure files * [ci run] Bioconductor graph (#44733) * remove build failure file * trigger build * Update meta.yaml * add patch back [ci run] * build failures * [ci run] high priority packages * bulk wiki page * [ci run] add missing packges * build failure for bioconductor-sictools * [ci run] missed one * [ci run] full run * Update build.sh * [ci run] fix dexseq * [ci run] next round of high priority packages * [ci run] missing packages * [ci run] high priority package * [ci run] build all bioconductor-bsgenome * [ci run] remove failures associated with bioconductor-bsgenome dependency * full build * use bioconda-common version * build failures: test dev version of utils * escape characters correctly * build failure for bioconductor-pics * use branch * build failure for bioconductor-inspect * try to fix build failure git range * build failure for bioconductor-distinct * use head branch * trigger build failure wf * [ci run] trigger bulk run * build failures fetch depth * build failure for biconductor-benchdamic * build failures * build failures with log * don't run build failures if last commit has ci skip * [ci skip] test build failure wiki * test build failure wiki job * [ci run] reenable record-build-failures * re-add token for build failure updates * build failures add category column * trigger wiki update * fix libsbml version for bioconductor-rsbml * build failure updates * fix bioconductor-glad * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-wppi * [ci skip] add build failure record for recipe recipes/bioconductor-gars * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-metascope * [ci skip] add build failure record for recipe recipes/bioconductor-biggr * [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank * [ci skip] add build failure record for recipe recipes/bioconductor-msbackendrawfilereader * [ci skip] add build failure record for recipe recipes/bioconductor-omicsviewer * [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr * [ci skip] add build failure record for recipe recipes/bioconductor-micsqtl * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-psygenet2r * [ci skip] add build failure record for recipe recipes/bioconductor-gesper * [ci skip] add build failure record for recipe recipes/bioconductor-sctensor * [ci skip] add build failure record for recipe recipes/bioconductor-seqcna * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-inpas * [ci skip] add build failure record for recipe recipes/bioconductor-factr * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-doubletrouble * [ci skip] add build failure record for recipe recipes/bioconductor-phyloprofile * [ci skip] add build failure record for recipe recipes/bioconductor-extrachips * [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank * [ci skip] add build failure record for recipe recipes/bioconductor-ularcirc * [ci skip] add build failure record for recipe recipes/bioconductor-umi4cats * [ci skip] add build failure record for recipe recipes/bioconductor-chipqc * [ci skip] add build failure record for recipe recipes/bioconductor-outsplice * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * [ci skip] add build failure record for recipe recipes/bioconductor-circseqaligntk * [ci skip] add build failure record for recipe recipes/bioconductor-ritan * [ci skip] add build failure record for recipe recipes/bioconductor-guideseq * [ci skip] add build failure record for recipe recipes/bioconductor-vulcan * [ci skip] add build failure record for recipe recipes/bioconductor-singlecelltk * [ci skip] add build failure record for recipe recipes/bioconductor-scfeatures * [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper * [ci skip] add build failure record for recipe recipes/bioconductor-deconvr * [ci skip] add build failure record for recipe recipes/bioconductor-ideal * [ci skip] add build failure record for recipe recipes/bioconductor-esatac * [ci skip] add build failure record for recipe recipes/bioconductor-profileplyr * [ci skip] add build failure record for recipe recipes/bioconductor-inetgrate * [ci skip] add build failure record for recipe recipes/bioconductor-ataccogaps * [ci skip] add build failure record for recipe recipes/bioconductor-lemur * [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign * [ci skip] add build failure record for recipe recipes/bioconductor-regionreport * [ci skip] add build failure record for recipe recipes/bioconductor-motifbreakr * [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-cageminer * [ci skip] add build failure record for recipe recipes/bioconductor-multicrispr * [ci skip] add build failure record for recipe recipes/bioconductor-xde * [ci skip] add build failure record for recipe recipes/bioconductor-affycoretools * [ci skip] add build failure record for recipe recipes/bioconductor-scpipe * Rbowtie2 (#44856) [ci run] fix rbowtie2 builds * [ci run] remove build file * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-biggr * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-guideseq * [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign * [ci skip] remove build failure record for recipe recipes/bioconductor-affycoretools * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh * failure for bioconda-multirnaflow * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-guideseq * [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * bioconductor-lpsymphony fix from master * remove build failures for finished dependencies * restore skip osx-64 * fix bioconductor-rawrr * high priority packages * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci skip] remove build failure record for recipe recipes/bioconductor-proloc * fix bioconductor-chemmineob * [ci run] remove failures for built dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci run] full build * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * remove easy build failures * [ci run] next round of dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-pigengene * [ci skip] add build failure record for recipe recipes/bioconductor-repitools * [ci skip] add build failure record for recipe recipes/bioconductor-xde * [ci skip] add build failure record for recipe recipes/bioconductor-sctensor * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * build failure updates * [ci run] next batch of fixes * [ci skip] add build failure record for recipe recipes/bioconductor-mitoclone2 * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * [ci run] full build * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci run]remove failures for built dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * [ci skip] add build failure record for recipe recipes/bioconductor-gatom * [ci run] set failures to skip * [ci run] reduce resources that are wasted * [ci skip] add build failure record for recipe recipes/bioconductor-pd.barley1 * fix accidental reverts * add GSL to bioconductor-pics * add back fix from master for omnipathr * remove build failure * [ci run] skip root nodes to spread out builds * [ci run] include more root nodes in blacklist * update build failures * [ci run] add more blacklist items and do osx build * [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes * [ci skip] add build failure record for recipe recipes/bioconductor-mumosa * [ci skip] add build failure record for recipe recipes/bioconductor-chromscape * [ci skip] add build failure record for recipe recipes/bioconductor-scmerge * [ci skip] add build failure record for recipe recipes/bioconductor-tadcompare * fix build errors * [ci run] more skipped builds * [ci skip] add build failure record for recipe recipes/bioconductor-cghmcr * [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper * [ci skip] add build failure record for recipe recipes/bioconductor-ccpromise * [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh * [ci skip] add build failure record for recipe recipes/bioconductor-interactivedisplay * [ci run] reduce workers * [ci skip] add build failure record for recipe recipes/bioconductor-cepo * [ci skip] add build failure record for recipe recipes/bioconductor-tbsignatureprofiler * [ci run] manually distribute packages * [ci skip] add build failure record for recipe recipes/bioconductor-cocoa * [ci skip] add build failure record for recipe recipes/bioconductor-condiments * [ci skip] add build failure record for recipe recipes/bioconductor-scclassify * [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf * [ci skip] add build failure record for recipe recipes/bioconductor-gcapc * [ci skip] add build failure record for recipe recipes/bioconductor-cepo * [ci skip] add build failure record for recipe recipes/bioconductor-traviz * remove build failures * remove colon that breaks yaml parsing * remove temporary bioconductor bulk skips * [ci run] remaining packages * [ci skip] add build failure record for recipe recipes/bioconductor-distinct * [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf * [ci skip] add build failure record for recipe recipes/bioconductor-promise * [ci skip] add build failure record for recipe recipes/bioconductor-otubase * [ci skip] add build failure record for recipe recipes/bioconductor-cocoa * [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes * retry http error * [ci run] full bulk build * [ci skip] add build failure record for recipe recipes/bioconductor-deepbluer * [ci skip] remove build failure record for recipe recipes/bioconductor-meb * [ci skip] add build failure record for recipe recipes/bioconductor-distinct * [ci run] categorize failures * add bioconductor-cdi * remove old failure files * update bioconductor-reusedata to 3.18 * remove failures for dependencies that have been built * [ci run] build certain packages * bulk: update bioconductor-ccfindr and bioconductor-rjmcmcnucleosomes with gsl (#44986) * update bioconductor-ccfindr with gsl * update bioconductor-rjmcmcnucleosomes with gsl * [ci run] build updated recipes * [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr * [ci skip] add build failure record for recipe recipes/bioconductor-reusedata * remove temporary changes from workflows * build got bumped in merge * remove temp files --------- Co-authored-by: Ryan Dale <ryan.dale@nih.gov> Co-authored-by: Björn Grüning <bjoern@gruenings.eu> Co-authored-by: Bjoern Gruening <bjoern.gruening@gmail.com> Co-authored-by: BiocondaBot <BiocondaBot@users.noreply.github.com>
erikrikarddaniel
pushed a commit
to erikrikarddaniel/bioconda-recipes
that referenced
this pull request
Jan 10, 2024
* a round of fixes and build-skips * add some build failures * correct version for bioconductor-data-packages * add build failure for STdeconvolve * [ci run] trigger bulk run * run_exports on bioconductor-data-packages * [ci run] trigger bulk run * build failure for omnipathr * [ci run] trigger bulk run * Build important packages first * [ci run] trigger bulk run * revert to full build * [ci run] trigger bulk run * build failure files * skip iclusterplus * skip bioconductor-lpsymphony * bump bioconda-repodata-patches build number * [ci run] * build failures * next round of high priority packages * [ci run] trigger bulk run * [ci run] add dependency * [ci run] finish priority packages * re-enable full bulk * [ci run] trigger bulk run * build failures * [ci run] trigger bulk run * next round of high priority packages * [ci run] trigger bulk run * build more high priority packages * [ci run] test local channel fix * [ci run] increase workers * Try building bioconductor-geoquery (bioconda#44726) * Delete recipes/bioconductor-geoquery/build_failure.linux-64.yaml * Update meta.yaml * try fixing parsing error * [ci run] try rebuilding bioconductor-coregx (bioconda#44727) * try rebuilding bioconductor-coregx * Update meta.yaml * add opencl loading libraries - will this work * [ci run] remove a few build failure files * [ci run] Bioconductor graph (bioconda#44733) * remove build failure file * trigger build * Update meta.yaml * add patch back [ci run] * build failures * [ci run] high priority packages * bulk wiki page * [ci run] add missing packges * build failure for bioconductor-sictools * [ci run] missed one * [ci run] full run * Update build.sh * [ci run] fix dexseq * [ci run] next round of high priority packages * [ci run] missing packages * [ci run] high priority package * [ci run] build all bioconductor-bsgenome * [ci run] remove failures associated with bioconductor-bsgenome dependency * full build * use bioconda-common version * build failures: test dev version of utils * escape characters correctly * build failure for bioconductor-pics * use branch * build failure for bioconductor-inspect * try to fix build failure git range * build failure for bioconductor-distinct * use head branch * trigger build failure wf * [ci run] trigger bulk run * build failures fetch depth * build failure for biconductor-benchdamic * build failures * build failures with log * don't run build failures if last commit has ci skip * [ci skip] test build failure wiki * test build failure wiki job * [ci run] reenable record-build-failures * re-add token for build failure updates * build failures add category column * trigger wiki update * fix libsbml version for bioconductor-rsbml * build failure updates * fix bioconductor-glad * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-wppi * [ci skip] add build failure record for recipe recipes/bioconductor-gars * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-metascope * [ci skip] add build failure record for recipe recipes/bioconductor-biggr * [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank * [ci skip] add build failure record for recipe recipes/bioconductor-msbackendrawfilereader * [ci skip] add build failure record for recipe recipes/bioconductor-omicsviewer * [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr * [ci skip] add build failure record for recipe recipes/bioconductor-micsqtl * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-psygenet2r * [ci skip] add build failure record for recipe recipes/bioconductor-gesper * [ci skip] add build failure record for recipe recipes/bioconductor-sctensor * [ci skip] add build failure record for recipe recipes/bioconductor-seqcna * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-inpas * [ci skip] add build failure record for recipe recipes/bioconductor-factr * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-doubletrouble * [ci skip] add build failure record for recipe recipes/bioconductor-phyloprofile * [ci skip] add build failure record for recipe recipes/bioconductor-extrachips * [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank * [ci skip] add build failure record for recipe recipes/bioconductor-ularcirc * [ci skip] add build failure record for recipe recipes/bioconductor-umi4cats * [ci skip] add build failure record for recipe recipes/bioconductor-chipqc * [ci skip] add build failure record for recipe recipes/bioconductor-outsplice * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * [ci skip] add build failure record for recipe recipes/bioconductor-circseqaligntk * [ci skip] add build failure record for recipe recipes/bioconductor-ritan * [ci skip] add build failure record for recipe recipes/bioconductor-guideseq * [ci skip] add build failure record for recipe recipes/bioconductor-vulcan * [ci skip] add build failure record for recipe recipes/bioconductor-singlecelltk * [ci skip] add build failure record for recipe recipes/bioconductor-scfeatures * [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper * [ci skip] add build failure record for recipe recipes/bioconductor-deconvr * [ci skip] add build failure record for recipe recipes/bioconductor-ideal * [ci skip] add build failure record for recipe recipes/bioconductor-esatac * [ci skip] add build failure record for recipe recipes/bioconductor-profileplyr * [ci skip] add build failure record for recipe recipes/bioconductor-inetgrate * [ci skip] add build failure record for recipe recipes/bioconductor-ataccogaps * [ci skip] add build failure record for recipe recipes/bioconductor-lemur * [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign * [ci skip] add build failure record for recipe recipes/bioconductor-regionreport * [ci skip] add build failure record for recipe recipes/bioconductor-motifbreakr * [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-cageminer * [ci skip] add build failure record for recipe recipes/bioconductor-multicrispr * [ci skip] add build failure record for recipe recipes/bioconductor-xde * [ci skip] add build failure record for recipe recipes/bioconductor-affycoretools * [ci skip] add build failure record for recipe recipes/bioconductor-scpipe * Rbowtie2 (bioconda#44856) [ci run] fix rbowtie2 builds * [ci run] remove build file * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-biggr * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-guideseq * [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign * [ci skip] remove build failure record for recipe recipes/bioconductor-affycoretools * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh * failure for bioconda-multirnaflow * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-guideseq * [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * bioconductor-lpsymphony fix from master * remove build failures for finished dependencies * restore skip osx-64 * fix bioconductor-rawrr * high priority packages * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci skip] remove build failure record for recipe recipes/bioconductor-proloc * fix bioconductor-chemmineob * [ci run] remove failures for built dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci run] full build * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * remove easy build failures * [ci run] next round of dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-pigengene * [ci skip] add build failure record for recipe recipes/bioconductor-repitools * [ci skip] add build failure record for recipe recipes/bioconductor-xde * [ci skip] add build failure record for recipe recipes/bioconductor-sctensor * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * build failure updates * [ci run] next batch of fixes * [ci skip] add build failure record for recipe recipes/bioconductor-mitoclone2 * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * [ci run] full build * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci run]remove failures for built dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * [ci skip] add build failure record for recipe recipes/bioconductor-gatom * [ci run] set failures to skip * [ci run] reduce resources that are wasted * [ci skip] add build failure record for recipe recipes/bioconductor-pd.barley1 * fix accidental reverts * add GSL to bioconductor-pics * add back fix from master for omnipathr * remove build failure * [ci run] skip root nodes to spread out builds * [ci run] include more root nodes in blacklist * update build failures * [ci run] add more blacklist items and do osx build * [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes * [ci skip] add build failure record for recipe recipes/bioconductor-mumosa * [ci skip] add build failure record for recipe recipes/bioconductor-chromscape * [ci skip] add build failure record for recipe recipes/bioconductor-scmerge * [ci skip] add build failure record for recipe recipes/bioconductor-tadcompare * fix build errors * [ci run] more skipped builds * [ci skip] add build failure record for recipe recipes/bioconductor-cghmcr * [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper * [ci skip] add build failure record for recipe recipes/bioconductor-ccpromise * [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh * [ci skip] add build failure record for recipe recipes/bioconductor-interactivedisplay * [ci run] reduce workers * [ci skip] add build failure record for recipe recipes/bioconductor-cepo * [ci skip] add build failure record for recipe recipes/bioconductor-tbsignatureprofiler * [ci run] manually distribute packages * [ci skip] add build failure record for recipe recipes/bioconductor-cocoa * [ci skip] add build failure record for recipe recipes/bioconductor-condiments * [ci skip] add build failure record for recipe recipes/bioconductor-scclassify * [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf * [ci skip] add build failure record for recipe recipes/bioconductor-gcapc * [ci skip] add build failure record for recipe recipes/bioconductor-cepo * [ci skip] add build failure record for recipe recipes/bioconductor-traviz * remove build failures * remove colon that breaks yaml parsing * remove temporary bioconductor bulk skips * [ci run] remaining packages * [ci skip] add build failure record for recipe recipes/bioconductor-distinct * [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf * [ci skip] add build failure record for recipe recipes/bioconductor-promise * [ci skip] add build failure record for recipe recipes/bioconductor-otubase * [ci skip] add build failure record for recipe recipes/bioconductor-cocoa * [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes * retry http error * [ci run] full bulk build * [ci skip] add build failure record for recipe recipes/bioconductor-deepbluer * [ci skip] remove build failure record for recipe recipes/bioconductor-meb * [ci skip] add build failure record for recipe recipes/bioconductor-distinct * [ci run] categorize failures * add bioconductor-cdi * remove old failure files * update bioconductor-reusedata to 3.18 * remove failures for dependencies that have been built * [ci run] build certain packages * bulk: update bioconductor-ccfindr and bioconductor-rjmcmcnucleosomes with gsl (bioconda#44986) * update bioconductor-ccfindr with gsl * update bioconductor-rjmcmcnucleosomes with gsl * [ci run] build updated recipes * [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr * [ci skip] add build failure record for recipe recipes/bioconductor-reusedata * remove temporary changes from workflows * build got bumped in merge * remove temp files --------- Co-authored-by: Ryan Dale <ryan.dale@nih.gov> Co-authored-by: Björn Grüning <bjoern@gruenings.eu> Co-authored-by: Bjoern Gruening <bjoern.gruening@gmail.com> Co-authored-by: BiocondaBot <BiocondaBot@users.noreply.github.com>
apeltzer
added a commit
that referenced
this pull request
Jan 24, 2024
* Updated sativa build, incl. test case * Update meta.yaml with new Sativa release * Linting * Update keggcharter to 1.0.2 (#44992) * Update keggcharter to 1.0.2 * Update meta.yaml Now put all TXTs and TSVs from "resources" folder into "share" folder. --------- Co-authored-by: João Sequeira <maildosequeira@gmail.com> * Update hictk to v0.0.5 (#44988) * Update conanfile.txt.patch * Bump version * Update perl-minion to 10.28 (#44495) * bugfix: strand deprecated and removed in BioPython 1.82 (#44987) - see: chapmanb/bcbb#138 * bugfix: breaking API change between ruamel.yaml 0.17.x and 0.18 (#44989) * Update tsebra to 1.1.2.2 (#45000) * Update sylph to 0.5.1 (#45001) * add r-misha 3.7.0 (history version) (#44981) * add misha version 3.7.0 (history version) * fix hash * fix compiler settings * use template variable to specify name * add run_export to lock version * add r-misha 3.7.1 (history version) (#44984) * add r-misha 3.7.1 (history version) * fix: incorrect commit and hash * Update viguno to 0.2.0 (#44996) * Update viguno to 0.2.0 * run_exports --------- Co-authored-by: Thanh Lee <thanh.le-viet@quadram.ac.uk> * Update annonars to 0.32.0 (#45013) * Fix recognizer (#45012) * Update recognizer to 1.10.0 * Update meta.yaml No more build.sh file * Update meta.yaml Forgot about the other TSV files * Removed build.sh --------- Co-authored-by: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> * Update last to 1522 (#45011) * Update pcaone to 0.4.1 (#45009) * genoflu version 1.02 (#44995) * genoflu version 1.02 * Update meta.yaml * Update meta.yaml * https://spdx.org/licenses/GPL-3.0-or-later.html --------- Co-authored-by: Thanh Lee <thanh.le-viet@quadram.ac.uk> * Update chromhmm to 1.25 (#45016) * Update chromhmm to 1.25 * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Christian Brueffer <christian@brueffer.io> * Update ColabFold to 1.5.5 (#45008) * Update ColabFold to 1.5.4 * Use 1.5.5 instead, 1.5.4 had a bug * OpenMM 8.1 causes issues * Update expam to 1.2.2.4 (#45007) * Update expam to 1.2.2.4 * add run_exports --------- Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> * Update upimapi to 1.13.1 (#45019) Co-authored-by: João Sequeira <maildosequeira@gmail.com> * Update raptor (#44952) multiple binaries and a wrapper scripts depending on available instruction sets. * add AnnoSINE2 recipes (#44980) * add strainscan recipes * add annosine2 recipes * Delete recipes/strainscan/meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Bulk (#45014) * a round of fixes and build-skips * add some build failures * correct version for bioconductor-data-packages * add build failure for STdeconvolve * [ci run] trigger bulk run * run_exports on bioconductor-data-packages * [ci run] trigger bulk run * build failure for omnipathr * [ci run] trigger bulk run * Build important packages first * [ci run] trigger bulk run * revert to full build * [ci run] trigger bulk run * build failure files * skip iclusterplus * skip bioconductor-lpsymphony * bump bioconda-repodata-patches build number * [ci run] * build failures * next round of high priority packages * [ci run] trigger bulk run * [ci run] add dependency * [ci run] finish priority packages * re-enable full bulk * [ci run] trigger bulk run * build failures * [ci run] trigger bulk run * next round of high priority packages * [ci run] trigger bulk run * build more high priority packages * [ci run] test local channel fix * [ci run] increase workers * Try building bioconductor-geoquery (#44726) * Delete recipes/bioconductor-geoquery/build_failure.linux-64.yaml * Update meta.yaml * try fixing parsing error * [ci run] try rebuilding bioconductor-coregx (#44727) * try rebuilding bioconductor-coregx * Update meta.yaml * add opencl loading libraries - will this work * [ci run] remove a few build failure files * [ci run] Bioconductor graph (#44733) * remove build failure file * trigger build * Update meta.yaml * add patch back [ci run] * build failures * [ci run] high priority packages * bulk wiki page * [ci run] add missing packges * build failure for bioconductor-sictools * [ci run] missed one * [ci run] full run * Update build.sh * [ci run] fix dexseq * [ci run] next round of high priority packages * [ci run] missing packages * [ci run] high priority package * [ci run] build all bioconductor-bsgenome * [ci run] remove failures associated with bioconductor-bsgenome dependency * full build * use bioconda-common version * build failures: test dev version of utils * escape characters correctly * build failure for bioconductor-pics * use branch * build failure for bioconductor-inspect * try to fix build failure git range * build failure for bioconductor-distinct * use head branch * trigger build failure wf * [ci run] trigger bulk run * build failures fetch depth * build failure for biconductor-benchdamic * build failures * build failures with log * don't run build failures if last commit has ci skip * [ci skip] test build failure wiki * test build failure wiki job * [ci run] reenable record-build-failures * re-add token for build failure updates * build failures add category column * trigger wiki update * fix libsbml version for bioconductor-rsbml * build failure updates * fix bioconductor-glad * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-wppi * [ci skip] add build failure record for recipe recipes/bioconductor-gars * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-metascope * [ci skip] add build failure record for recipe recipes/bioconductor-biggr * [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank * [ci skip] add build failure record for recipe recipes/bioconductor-msbackendrawfilereader * [ci skip] add build failure record for recipe recipes/bioconductor-omicsviewer * [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr * [ci skip] add build failure record for recipe recipes/bioconductor-micsqtl * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-psygenet2r * [ci skip] add build failure record for recipe recipes/bioconductor-gesper * [ci skip] add build failure record for recipe recipes/bioconductor-sctensor * [ci skip] add build failure record for recipe recipes/bioconductor-seqcna * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-inpas * [ci skip] add build failure record for recipe recipes/bioconductor-factr * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-doubletrouble * [ci skip] add build failure record for recipe recipes/bioconductor-phyloprofile * [ci skip] add build failure record for recipe recipes/bioconductor-extrachips * [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank * [ci skip] add build failure record for recipe recipes/bioconductor-ularcirc * [ci skip] add build failure record for recipe recipes/bioconductor-umi4cats * [ci skip] add build failure record for recipe recipes/bioconductor-chipqc * [ci skip] add build failure record for recipe recipes/bioconductor-outsplice * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * [ci skip] add build failure record for recipe recipes/bioconductor-circseqaligntk * [ci skip] add build failure record for recipe recipes/bioconductor-ritan * [ci skip] add build failure record for recipe recipes/bioconductor-guideseq * [ci skip] add build failure record for recipe recipes/bioconductor-vulcan * [ci skip] add build failure record for recipe recipes/bioconductor-singlecelltk * [ci skip] add build failure record for recipe recipes/bioconductor-scfeatures * [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper * [ci skip] add build failure record for recipe recipes/bioconductor-deconvr * [ci skip] add build failure record for recipe recipes/bioconductor-ideal * [ci skip] add build failure record for recipe recipes/bioconductor-esatac * [ci skip] add build failure record for recipe recipes/bioconductor-profileplyr * [ci skip] add build failure record for recipe recipes/bioconductor-inetgrate * [ci skip] add build failure record for recipe recipes/bioconductor-ataccogaps * [ci skip] add build failure record for recipe recipes/bioconductor-lemur * [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign * [ci skip] add build failure record for recipe recipes/bioconductor-regionreport * [ci skip] add build failure record for recipe recipes/bioconductor-motifbreakr * [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-cageminer * [ci skip] add build failure record for recipe recipes/bioconductor-multicrispr * [ci skip] add build failure record for recipe recipes/bioconductor-xde * [ci skip] add build failure record for recipe recipes/bioconductor-affycoretools * [ci skip] add build failure record for recipe recipes/bioconductor-scpipe * Rbowtie2 (#44856) [ci run] fix rbowtie2 builds * [ci run] remove build file * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-biggr * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-guideseq * [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign * [ci skip] remove build failure record for recipe recipes/bioconductor-affycoretools * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh * failure for bioconda-multirnaflow * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-guideseq * [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * bioconductor-lpsymphony fix from master * remove build failures for finished dependencies * restore skip osx-64 * fix bioconductor-rawrr * high priority packages * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci skip] remove build failure record for recipe recipes/bioconductor-proloc * fix bioconductor-chemmineob * [ci run] remove failures for built dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci run] full build * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * remove easy build failures * [ci run] next round of dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-pigengene * [ci skip] add build failure record for recipe recipes/bioconductor-repitools * [ci skip] add build failure record for recipe recipes/bioconductor-xde * [ci skip] add build failure record for recipe recipes/bioconductor-sctensor * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * build failure updates * [ci run] next batch of fixes * [ci skip] add build failure record for recipe recipes/bioconductor-mitoclone2 * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * [ci run] full build * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci run]remove failures for built dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * [ci skip] add build failure record for recipe recipes/bioconductor-gatom * [ci run] set failures to skip * [ci run] reduce resources that are wasted * [ci skip] add build failure record for recipe recipes/bioconductor-pd.barley1 * fix accidental reverts * add GSL to bioconductor-pics * add back fix from master for omnipathr * remove build failure * [ci run] skip root nodes to spread out builds * [ci run] include more root nodes in blacklist * update build failures * [ci run] add more blacklist items and do osx build * [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes * [ci skip] add build failure record for recipe recipes/bioconductor-mumosa * [ci skip] add build failure record for recipe recipes/bioconductor-chromscape * [ci skip] add build failure record for recipe recipes/bioconductor-scmerge * [ci skip] add build failure record for recipe recipes/bioconductor-tadcompare * fix build errors * [ci run] more skipped builds * [ci skip] add build failure record for recipe recipes/bioconductor-cghmcr * [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper * [ci skip] add build failure record for recipe recipes/bioconductor-ccpromise * [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh * [ci skip] add build failure record for recipe recipes/bioconductor-interactivedisplay * [ci run] reduce workers * [ci skip] add build failure record for recipe recipes/bioconductor-cepo * [ci skip] add build failure record for recipe recipes/bioconductor-tbsignatureprofiler * [ci run] manually distribute packages * [ci skip] add build failure record for recipe recipes/bioconductor-cocoa * [ci skip] add build failure record for recipe recipes/bioconductor-condiments * [ci skip] add build failure record for recipe recipes/bioconductor-scclassify * [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf * [ci skip] add build failure record for recipe recipes/bioconductor-gcapc * [ci skip] add build failure record for recipe recipes/bioconductor-cepo * [ci skip] add build failure record for recipe recipes/bioconductor-traviz * remove build failures * remove colon that breaks yaml parsing * remove temporary bioconductor bulk skips * [ci run] remaining packages * [ci skip] add build failure record for recipe recipes/bioconductor-distinct * [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf * [ci skip] add build failure record for recipe recipes/bioconductor-promise * [ci skip] add build failure record for recipe recipes/bioconductor-otubase * [ci skip] add build failure record for recipe recipes/bioconductor-cocoa * [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes * retry http error * [ci run] full bulk build * [ci skip] add build failure record for recipe recipes/bioconductor-deepbluer * [ci skip] remove build failure record for recipe recipes/bioconductor-meb * [ci skip] add build failure record for recipe recipes/bioconductor-distinct * [ci run] categorize failures * add bioconductor-cdi * remove old failure files * update bioconductor-reusedata to 3.18 * remove failures for dependencies that have been built * [ci run] build certain packages * bulk: update bioconductor-ccfindr and bioconductor-rjmcmcnucleosomes with gsl (#44986) * update bioconductor-ccfindr with gsl * update bioconductor-rjmcmcnucleosomes with gsl * [ci run] build updated recipes * [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr * [ci skip] add build failure record for recipe recipes/bioconductor-reusedata * remove temporary changes from workflows * build got bumped in merge * remove temp files --------- Co-authored-by: Ryan Dale <ryan.dale@nih.gov> Co-authored-by: Björn Grüning <bjoern@gruenings.eu> Co-authored-by: Bjoern Gruening <bjoern.gruening@gmail.com> Co-authored-by: BiocondaBot <BiocondaBot@users.noreply.github.com> * Update deeplc to 2.2.26 (#44238) * Update deeplc to 2.2.23 * Update deeplc to 2.2.24 * add pyopenms * Update deeplc to 2.2.25 * Update deeplc to 2.2.26 * try extended base * revert extended base --------- Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Add recipe for CellBender v0.3.0 (#45024) * Add recipe for CellBender v0.3.0 * add run_exports * Fix nrpys to build on python 3.8+ (#45025) * Update oakvar to 2.9.83 (#45026) * Update foldcomp to 0.0.6 (#45018) * Update foldcomp to 0.0.6 * add run_exports --------- Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> * Update antismash-lite to 7.1.0 (#45027) * Update jcvi to 1.3.9 (#45029) * Update jcvi to 1.3.9 * Update meta.yaml --------- Co-authored-by: Christian Brueffer <christian@brueffer.io> * Update recognizer to 1.10.1 (#45031) Co-authored-by: João Sequeira <maildosequeira@gmail.com> * Update midsv to 0.11.0 (#45028) * Update midsv to 0.11.0 * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Christian Brueffer <christian@brueffer.io> * Update meta.yaml (#45041) Snakemake refactored in newer version. * Rebuild unitig caller for new bifrost version (#45035) * Rebuild unitig caller for new bifrost version * Add run_exports * Fix string interpolation in pinning * Update annosine2 build (#45033) * Update meta.yaml * Update meta.yaml * Update rasusa to 0.8.0 (#45042) * Update rasusa to 0.8.0 * add run_export * bump msrv --------- Co-authored-by: Michael Hall <michael@mbh.sh> * Update annonars to 0.33.0 (#45043) * patch viroconstrictor snakemake requirements to not use version 8.x (#45036) * Add Deepmei version 1.0.0 recipes (#45005) * Update keggcharter to 1.1.0 (#45046) * Update mosca to 2.2.0 (#45054) * Update mosca to 2.2.0 * Update meta.yaml Added run_exports Added pandas as dependency Fixed python version to <3.12 Fixed snakemake version to <8 --------- Co-authored-by: João Sequeira <maildosequeira@gmail.com> * Update fgbio to 2.2.1 (#45050) * Update fgbio-minimal to 2.2.1 (#45051) * Update viralmsa to 1.1.41 (#45047) * Update ndex2 to 3.7.0 (#45049) * Update expam to 1.2.2.5 (#45053) * Update bustools to 0.43.2 (#45055) * Update kb-python to 0.28.1 (#45056) * Update xengsort to 2.0.5 (#44888) * Update xengsort to 2.0.4 * pin python to 3.11 * Update xengsort to 2.0.5 --------- Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> * Update ena-webin-cli to 6.8.0 (#45059) * Update zol to 1.3.17 (#45067) * Update pybiolib to 1.1.1673 (#45057) * Update pybiolib to 1.1.1682 (#45072) * Update adam to 1.0.1 (#45069) * Update adam to 1.0.1 * add pin_subpackage * Update cannoli to 1.0.1 (#45070) * Update cannoli to 1.0.1. * add pin_subpackage * Update keggcharter to 1.1.1 (#45079) * Update galaxy-objectstore to 23.1.4 (#45061) * Update galaxy-files to 23.1.4 (#45062) * Update mashmap to 3.1.3 (#45064) * Update rosella to 0.5.3 (#45075) * Update snakemake-executor-plugin-googlebatch to 0.2.0 (#45039) * Update snakemake-executor-plugin-googlebatch to 0.2.0 * add summary --------- Co-authored-by: mencian <joshua.zhuang@yahoo.com> * Update hifihla to 0.2.3 (#45066) * Update micom to 0.33.1 (#45071) * Update flight-genome to 1.6.3 (#45073) * Update bioframe to 0.6.0 (#45076) * Update metdatamodel to 0.5.5 (#45082) * Update odgi to 0.8.4 (#45077) * Update odgi to 0.8.4 * run_exports --------- Co-authored-by: Thanh Lee <thanh.le-viet@quadram.ac.uk> * Update nanovar to 1.5.1 (#45084) * Update r-ldweaver to 1.4 (#45058) * Update r-ldweaver to 1.4 * drop genbankr dependency * it seems genbankr is still needed --------- Co-authored-by: mencian <joshua.zhuang@yahoo.com> * Update ncbi-datasets-pylib to 16.1.1 (#45090) * Update dbcan to 4.1.0 (#45088) * Update dbcan to 4.1.0 * fix bug * add hatchling and other fixes * edit sha256 --------- Co-authored-by: mencian <joshua.zhuang@yahoo.com> * Update perl-math-bigint to 2.003002 (#45096) * Update nf-test to 0.8.3 (#45098) * Update foldcomp to 0.0.7 (#45097) * Update meta.yaml (#45086) * Update ltr_retriever to 2.9.8 (#45006) * Update ltr_retriever to 2.9.8 * add run_exports * revert channel specifications * remove channels section --------- Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> * prodigal: include upstream patches fixing critical bugs (#45091) * prodigal: freshen up * prodigal: include patches for critical bugs fixed upstream but unreleased The developer has accepted these changes, but no new release has been made in over a year. * Add vcfphasesets (#45092) * Add vcfphasesets. * Change meta.yaml for run exports. * Complexcgr (#45089) * Add complexcgr v0.8.0 * Add complexcgr v0.8.0 * Add complexcgr v0.8.0 * Update ribowaltz to 2.0 (#45065) * Update ribowaltz to 2.0 * add run_exports --------- Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update vcf2variants (#45083) * Update to version 1.0. * Add run_exports. * Extra dependency. * Bump version. * Bump version and test import. * Fix import test. * Add additional requirement. --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update snapatac2 to 2.5.2 (#45078) * Update snapatac2 to 2.5.2 * add typing_extensions to run section --------- Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> * Update breseq to 0.38.2 (#45103) * Update breseq to 0.38.2 * add run_exports --------- Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> * Update mitos to 2.1.6 (#45104) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update harmony-pytorch to 0.1.8 (#45106) * Update harmony-pytorch to 0.1.8 * add run_exports --------- Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> * Update snakemake to 8.1.0 (#45108) * Update ltr_retriever to 2.9.9 (#45107) * Update tn93 to 1.0.13 (#45109) * Update hyphy to 2.5.59 (#45111) * Update pyfaidx to 0.8.0 (#45113) * Depend on gcc; new sha256 * Finally a sativa recipe that puts sativa.py in PATH * Update mitgard to 1.1 (#45101) * Update mitgard to 1.1 * add run_exports --------- Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> * Update bioframe to 0.6.1 (#45120) * Add virusrecom (#45099) * add virusrecom recipes * add virusrecom recipes xx * Update meta.yaml * add python to run section and use SPDX identifier --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * bump mitos1 (#45112) * bump mitos1 * repin blast-legacy .. add tests first * Update pybiolib to 1.1.1685 (#45119) * Update ncbi-datasets-pylib to 16.1.2 (#45124) * Update das_tool to 1.1.7 (#45123) * Update das_tool to 1.1.7 * add run_exports --------- Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> * Update virusrecom to 1.1.3 (#45122) * Update severus to 0.1.2 (#45135) * Update virusrecom (#45130) * add virusrecom recipes * Update meta.yaml * edit recipe-maintainer --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update hybracter to 0.5.0 (#45128) * Update dnaapler to 0.5.1 (#45129) * Update recentrifuge to 1.13.1 (#45132) * Update tissuumaps to 3.2.0.3 (#45137) * mitos: add tests for R packages (#44971) * mitos: add tests for R packages In test with the container I got: Exception: b"Warning message:\npackage \xe2\x80\x98ggplot2\xe2\x80\x99 was built under R version 3.6.3 \nError: package or namespace load failed for \xe2\x80\x98reshape2\xe2\x80\x99 in dyn.load(file, DLLpath = DLLpath, ...):\n unable to load shared object '/usr/local/lib/R/library/stringi/libs/stringi.so':\n libicui18n.so.64: cannot open shared object file: No such file or directory\nIn addition: Warning message:\npackage \xe2\x80\x98reshape2\xe2\x80\x99 was built under R version 3.6.3 \nExecution halted\n" * try to use R directly in tests * try R > 3 * bump and unpin vienna * retry R>3 * another try * try to pin r-stringi * bump * cnt * unpin some more requirements * remove stringi * repin infernal * repin hmmer * repin blast * Revert "repin blast" This reverts commit 6a5717a. * Update kb-python to 0.28.2 (#45138) * Update ena-webin-cli to 6.9.0 (#45139) * Update r-seqmagick to 0.1.7 (#45131) * Update r-seqmagick to 0.1.7 * Update meta.yaml --------- Co-authored-by: Christian Brueffer <christian@brueffer.io> * Update snakefmt to 0.9.0 (#45134) * remove static compilation (#45141) * Update dajin2 to 0.3.6 (#45143) * Update jbrowse2 to 2.10.1 (#45145) * Update ncbi-datasets-pylib to 16.2.0 (#45144) * Add ACI (#45121) * adding aci recipe * fixed entry point typo * fix typo * matplotlib-base * url * revert url * underscore * version --------- Co-authored-by: Thanh Lee <thanh.le-viet@quadram.ac.uk> * Update ngs-chew to 0.9.0 (#45140) * Update vcfpy to 0.13.7 (#45150) * Avoid building on OS X --------- Co-authored-by: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Co-authored-by: João Sequeira <maildosequeira@gmail.com> Co-authored-by: Roberto Rossini <71787608+robomics@users.noreply.github.com> Co-authored-by: DrYak <ivan.topolsky@sib.swiss> Co-authored-by: TPOB <19909103+TTTPOB@users.noreply.github.com> Co-authored-by: Thanh Lee <thanh.le-viet@quadram.ac.uk> Co-authored-by: stuber <tod.p.stuber@usda.gov> Co-authored-by: Christian Brueffer <christian@brueffer.io> Co-authored-by: Milot Mirdita <milot@mirdita.de> Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> Co-authored-by: Enrico Seiler <eseiler@users.noreply.github.com> Co-authored-by: Ray <851836818@qq.com> Co-authored-by: Alicia A. Evans <108547992+aliciaaevans@users.noreply.github.com> Co-authored-by: Ryan Dale <ryan.dale@nih.gov> Co-authored-by: Björn Grüning <bjoern@gruenings.eu> Co-authored-by: Bjoern Gruening <bjoern.gruening@gmail.com> Co-authored-by: BiocondaBot <BiocondaBot@users.noreply.github.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: Carl Mathias Kobel <carl.mathias.kobel@nmbu.no> Co-authored-by: John Lees <lees.john6@gmail.com> Co-authored-by: Michael Hall <michael@mbh.sh> Co-authored-by: Florian Zwagemaker <49153065+florianzwagemaker@users.noreply.github.com> Co-authored-by: Kanglu123 <64641114+Kanglu123@users.noreply.github.com> Co-authored-by: Michael L Heuer <heuermh@acm.org> Co-authored-by: Le (Lena) Huang <lehuang@unc.edu> Co-authored-by: Jens Luebeck <jluebeck@ucsd.edu> Co-authored-by: Afif Elghraoui <aelghraoui@sdsu.edu> Co-authored-by: Mark Santcroos <m.a.santcroos@lumc.nl> Co-authored-by: Koke <49822617+jorgeavilacartes@users.noreply.github.com> Co-authored-by: Zhou ZJ <43747306+ZhijianZhou01@users.noreply.github.com> Co-authored-by: M Bernt <m.bernt@ufz.de> Co-authored-by: boukn <boukn@ncbi.nlm.nih.gov> Co-authored-by: Young <erin.olde@gmail.com> Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
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