diff --git a/03-installing-bioconductor.md b/03-installing-bioconductor.md index 074fc9bf..38834e3d 100644 --- a/03-installing-bioconductor.md +++ b/03-installing-bioconductor.md @@ -159,8 +159,56 @@ If everything is up-to-date, the function will simply print `TRUE`. BiocManager::valid() ``` +```{.warning} +Warning: 2 packages out-of-date; 1 packages too new +``` + ```{.output} -[1] TRUE + +* sessionInfo() + +R version 4.3.1 (2023-06-16) +Platform: x86_64-pc-linux-gnu (64-bit) +Running under: Ubuntu 22.04.3 LTS + +Matrix products: default +BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 +LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 + +locale: + [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 + [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 + [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C +[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C + +time zone: UTC +tzcode source: system (glibc) + +attached base packages: +[1] stats graphics grDevices utils datasets methods base + +other attached packages: +[1] BiocStyle_2.28.1 + +loaded via a namespace (and not attached): + [1] BiocManager_1.30.22 compiler_4.3.1 fastmap_1.1.1 + [4] cli_3.6.1 htmltools_0.5.7 tools_4.3.1 + [7] yaml_2.3.7 rmarkdown_2.25 knitr_1.45 +[10] digest_0.6.33 xfun_0.41 rlang_1.1.2 +[13] renv_1.0.3 evaluate_0.23 + +Bioconductor version '3.17' + + * 2 packages out-of-date + * 1 packages too new + +create a valid installation with + + BiocManager::install(c( + "lifecycle", "matrixStats", "SparseArray" + ), update = TRUE, ask = FALSE, force = TRUE) + +more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date ``` Conveniently, if any package can be updated, the function generates and displays the command needed to update those packages. @@ -236,7 +284,7 @@ length(BiocManager::available()) ``` ```{.output} -[1] 23382 +[1] 23524 ``` Specifically, the current Bioconductor and CRAN repositories can be displayed as follows. diff --git a/config.yaml b/config.yaml deleted file mode 100644 index c55fe3b4..00000000 --- a/config.yaml +++ /dev/null @@ -1,85 +0,0 @@ -#------------------------------------------------------------ -# Values for this lesson. -#------------------------------------------------------------ - -# Which carpentry is this (swc, dc, lc, or cp)? -# swc: Software Carpentry -# dc: Data Carpentry -# lc: Library Carpentry -# cp: Carpentries (to use for instructor training for instance) -# incubator: The Carpentries Incubator -carpentry: 'incubator' - -# Overall title for pages. -title: 'The Bioconductor project' - -# Date the lesson was created (YYYY-MM-DD, this is empty by default) -created: '2020-09-14' - -# Comma-separated list of keywords for the lesson -keywords: 'software, data, lesson, The Carpentries' - -# Life cycle stage of the lesson -# possible values: pre-alpha, alpha, beta, stable -life_cycle: 'pre-alpha' - -# License of the lesson -license: 'CC-BY 4.0' - -# Link to the source repository for this lesson -source: 'https://github.com/carpentries-incubator/bioc-project' - -# Default branch of your lesson -branch: 'main' - -# Who to contact if there are any issues -contact: 'team@carpentries.org' - -# Navigation ------------------------------------------------ -# -# Use the following menu items to specify the order of -# individual pages in each dropdown section. Leave blank to -# include all pages in the folder. -# -# Example ------------- -# -# episodes: -# - introduction.md -# - first-steps.md -# -# learners: -# - setup.md -# -# instructors: -# - instructor-notes.md -# -# profiles: -# - one-learner.md -# - another-learner.md - -# Order of episodes in your lesson -episodes: -- 01-setup.Rmd -- 02-introduction-to-bioconductor.Rmd -- 03-installing-bioconductor.Rmd -- 04-getting-help.Rmd -- 05-s4.Rmd -- 06-biological-sequences.Rmd -- 07-genomic-ranges.Rmd - -# Information for Learners -learners: - -# Information for Instructors -instructors: - -# Learner Profiles -profiles: - -# Customisation --------------------------------------------- -# -# This space below is where custom yaml items (e.g. pinning -# sandpaper and varnish versions) should live - - -url: 'https://carpentries-incubator.github.io/bioc-project' diff --git a/md5sum.txt b/md5sum.txt index da00bfe0..c61cf8c9 100644 --- a/md5sum.txt +++ b/md5sum.txt @@ -1,18 +1,18 @@ "file" "checksum" "built" "date" -"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2023-09-06" -"LICENSE.md" "afaf427b4223952624dcb6d8ded53ec0" "site/built/LICENSE.md" "2023-09-06" -"config.yaml" "136b895030e91653fc32afb614ad6812" "site/built/config.yaml" "2023-09-06" -"index.md" "6cf23d25cc71edcff0cdd1f6d60039da" "site/built/index.md" "2023-09-06" -"episodes/01-setup.Rmd" "052eaf8fb2a945b10aafd94e1b906abc" "site/built/01-setup.md" "2023-09-06" -"episodes/02-introduction-to-bioconductor.Rmd" "95db83520fedb68fb63fc660fb583ff5" "site/built/02-introduction-to-bioconductor.md" "2023-09-06" -"episodes/03-installing-bioconductor.Rmd" "5d19f8467009662b729aa4150258c832" "site/built/03-installing-bioconductor.md" "2023-09-06" -"episodes/04-getting-help.Rmd" "d6145a8228a881508820e4b95b99b61b" "site/built/04-getting-help.md" "2023-09-06" -"episodes/05-s4.Rmd" "e97eed7893703ad409eb937d95e357b1" "site/built/05-s4.md" "2023-09-06" -"episodes/06-biological-sequences.Rmd" "b43619a42edd5275aa6896fc6ab484ab" "site/built/06-biological-sequences.md" "2023-09-06" -"episodes/07-genomic-ranges.Rmd" "1678d11e207781b420e36810e603000b" "site/built/07-genomic-ranges.md" "2023-09-06" -"instructors/instructor-notes.md" "a848c3b904c16f0840e7ec385de58d7d" "site/built/instructor-notes.md" "2023-09-06" -"learners/discuss.md" "90557a59d285aa7ce2a8adfc5799b1a8" "site/built/discuss.md" "2023-09-06" -"learners/reference.md" "c0ac274d8350e94fbaef3e28b458c7f4" "site/built/reference.md" "2023-09-06" -"learners/setup.md" "bc1698a1f013e3dc5b0651375ce60d4d" "site/built/setup.md" "2023-09-06" -"profiles/learner-profiles.md" "60b93493cf1da06dfd63255d73854461" "site/built/learner-profiles.md" "2023-09-06" -"renv/profiles/lesson-requirements/renv.lock" "502539c2e1b4bf9dc71473db1a75a2f7" "site/built/renv.lock" "2023-09-06" +"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2023-11-07" +"LICENSE.md" "afaf427b4223952624dcb6d8ded53ec0" "site/built/LICENSE.md" "2023-11-07" +"config.yaml" "136b895030e91653fc32afb614ad6812" "site/built/config.yaml" "2023-11-07" +"index.md" "6cf23d25cc71edcff0cdd1f6d60039da" "site/built/index.md" "2023-11-07" +"episodes/01-setup.Rmd" "052eaf8fb2a945b10aafd94e1b906abc" "site/built/01-setup.md" "2023-11-07" +"episodes/02-introduction-to-bioconductor.Rmd" "95db83520fedb68fb63fc660fb583ff5" "site/built/02-introduction-to-bioconductor.md" "2023-11-07" +"episodes/03-installing-bioconductor.Rmd" "5d19f8467009662b729aa4150258c832" "site/built/03-installing-bioconductor.md" "2023-11-07" +"episodes/04-getting-help.Rmd" "d6145a8228a881508820e4b95b99b61b" "site/built/04-getting-help.md" "2023-11-07" +"episodes/05-s4.Rmd" "e97eed7893703ad409eb937d95e357b1" "site/built/05-s4.md" "2023-11-07" +"episodes/06-biological-sequences.Rmd" "b43619a42edd5275aa6896fc6ab484ab" "site/built/06-biological-sequences.md" "2023-11-07" +"episodes/07-genomic-ranges.Rmd" "1678d11e207781b420e36810e603000b" "site/built/07-genomic-ranges.md" "2023-11-07" +"instructors/instructor-notes.md" "a848c3b904c16f0840e7ec385de58d7d" "site/built/instructor-notes.md" "2023-11-07" +"learners/discuss.md" "90557a59d285aa7ce2a8adfc5799b1a8" "site/built/discuss.md" "2023-11-07" +"learners/reference.md" "c0ac274d8350e94fbaef3e28b458c7f4" "site/built/reference.md" "2023-11-07" +"learners/setup.md" "bc1698a1f013e3dc5b0651375ce60d4d" "site/built/setup.md" "2023-11-07" +"profiles/learner-profiles.md" "60b93493cf1da06dfd63255d73854461" "site/built/learner-profiles.md" "2023-11-07" +"renv/profiles/lesson-requirements/renv.lock" "0f922ff3a44cb2d66b68fcfdf4da594f" "site/built/renv.lock" "2023-11-07" diff --git a/renv.lock b/renv.lock deleted file mode 100644 index fb2837c1..00000000 --- a/renv.lock +++ /dev/null @@ -1,1165 +0,0 @@ -{ - 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