From 2795fc0aca2c262766bacdaa0ea94c0757aa3214 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Tue, 6 Aug 2024 01:50:31 +0000 Subject: [PATCH] differences for PR #95 --- 03-installing-bioconductor.md | 50 +- config.yaml | 87 -- md5sum.txt | 38 +- renv.lock | 1786 --------------------------------- 4 files changed, 21 insertions(+), 1940 deletions(-) delete mode 100644 config.yaml delete mode 100644 renv.lock diff --git a/03-installing-bioconductor.md b/03-installing-bioconductor.md index 626e2f5..1b20762 100644 --- a/03-installing-bioconductor.md +++ b/03-installing-bioconductor.md @@ -148,54 +148,8 @@ If everything is up-to-date, the function will simply print `TRUE`. BiocManager::valid() ``` -``` warning -Warning: 1 packages out-of-date; 0 packages too new -``` - ``` output - -* sessionInfo() - -R version 4.4.1 (2024-06-14) -Platform: x86_64-pc-linux-gnu -Running under: Ubuntu 22.04.4 LTS -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_2.32.1 - -loaded via a namespace (and not attached): - [1] BiocManager_1.30.23 compiler_4.4.1 fastmap_1.2.0 - [4] cli_3.6.3 htmltools_0.5.8.1 tools_4.4.1 - [7] yaml_2.3.10 rmarkdown_2.27 knitr_1.48 -[10] digest_0.6.36 xfun_0.46 rlang_1.1.4 -[13] renv_1.0.7 evaluate_0.24.0 - -Bioconductor version '3.19' - - * 1 packages out-of-date - * 0 packages too new - -create a valid installation with - - BiocManager::install("withr", update = TRUE, ask = FALSE, force = TRUE) - -more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date +[1] TRUE ``` Conveniently, if any package can be updated, the function generates and displays the command needed to update those packages. @@ -271,7 +225,7 @@ length(BiocManager::available()) ``` ``` output -[1] 24742 +[1] 24752 ``` Specifically, the union of current Bioconductor repositories and other repositories on the search path can be displayed as follows. diff --git a/config.yaml b/config.yaml deleted file mode 100644 index 9135522..0000000 --- a/config.yaml +++ /dev/null @@ -1,87 +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. 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