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adding Bioconductor dependency for github.io
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‎.github/workflows/check-bioc.yml‎

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## Read more about GitHub actions the features of this GitHub Actions workflow
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## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action
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##
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## For more details, check the biocthis developer notes vignette at
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## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html
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##
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## You can add this workflow to other packages using:
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## > biocthis::use_bioc_github_action()
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##
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## Using GitHub Actions exposes you to many details about how R packages are
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## compiled and installed in several operating system.s
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### If you need help, please follow the steps listed at
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## https://github.com/r-lib/actions#where-to-find-help
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##
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## If you found an issue specific to biocthis's GHA workflow, please report it
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## with the information that will make it easier for others to help you.
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## Thank you!
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## Acronyms:
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## * GHA: GitHub Action
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## * OS: operating system
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on:
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push:
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pull_request:
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name: R-CMD-check-bioc
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## These environment variables control whether to run GHA code later on that is
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## specific to testthat, covr, and pkgdown.
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##
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## If you need to clear the cache of packages, update the number inside
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## cache-version as discussed at https://github.com/r-lib/actions/issues/86.
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## Note that you can always run a GHA test without the cache by using the word
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## "/nocache" in the commit message.
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env:
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has_testthat: 'false'
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run_covr: 'false'
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run_pkgdown: 'false'
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has_RUnit: 'false'
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cache-version: 'cache-v1'
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run_docker: 'false'
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bioc_version: 'bioc-release'
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## Valid options are:
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## "bioc-release"
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## "bioc-devel"
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## or a specific number like "3.20"
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jobs:
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bioc-config:
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runs-on: ubuntu-latest
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outputs:
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matrix: ${{ steps.set-bioc-matrix.outputs.matrix }}
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steps:
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## Adapted from
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## https://runs-on.com/github-actions/the-matrix-strategy/#dynamic-matrix-generation
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- id: set-bioc-matrix
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run: |
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bioc=$(curl -L https://bioconductor.org/config.yaml)
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if [[ "$bioc_version" == "bioc-release" ]]; then
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echo "Finding the latest BioC release version and the corresponding R version"
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biocversion=$(echo "$bioc" | grep "release_version: " | grep -Eo "[0-9]{1}\.[0-9]{2}")
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rversion=$(echo "$bioc" | grep "r_version_associated_with_release: " | grep -Eo "[0-9]{1}\.[0-9]{1}")
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biocmajor=$(echo "$biocversion" | cut -c 1-1)
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biocminor=$(echo "$biocversion" | cut -c 3-4)
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bioccont=$(echo "bioconductor/bioconductor_docker:RELEASE_${biocmajor}_${biocminor}")
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elif [[ "$bioc_version" == "bioc-devel" ]]; then
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echo "Finding the latest BioC devel version and the corresponding R version"
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biocversion=$(echo "$bioc" | grep "devel_version: " | grep -Eo "[0-9]{1}\.[0-9]{2}")
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rversion_release=$(echo "$bioc" | grep "r_version_associated_with_release: " | grep -Eo "[0-9]{1}\.[0-9]{1}")
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rversion_devel=$(echo "$bioc" | grep "r_version_associated_with_devel: " | grep -Eo "[0-9]{1}\.[0-9]{1}")
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if [[ "$rversion_release" == "$rversion_devel" ]]; then
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rversion=$(echo "$rversion_devel")
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else
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rversion="devel"
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fi
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bioccont="bioconductor/bioconductor_docker:devel"
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else
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echo "Finding the the R version for bioc version ${bioc_version}"
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biocversion=$(echo "$bioc_version")
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rversion=$(echo "$bioc" | sed -En "/r_ver_for_bioc_ver/,/release_dates/p" | grep "$bioc_version\":" | grep -Eo ": \"[0-9]{1}\.[0-9]{1}" | grep -Eo "[0-9]{1}\.[0-9]{1}")
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biocmajor=$(echo "$biocversion" | cut -c 1-1)
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biocminor=$(echo "$biocversion" | cut -c 3-4)
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bioccont=$(echo "bioconductor/bioconductor_docker:RELEASE_${biocmajor}_${biocminor}")
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fi
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echo "Found these settings:"
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echo "Bioconductor version: $biocversion, R version: $rversion, Bioconductor docker name: $bioccont"
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echo "matrix={ \"config\": [{\"os\" : \"ubuntu-latest\", \"r\" : \"${rversion}\", \"bioc\" : \"${biocversion}\", \"cont\" : \"${bioccont}\"} , {\"os\" : \"macOS-latest\", \"r\" : \"${rversion}\", \"bioc\" : \"${biocversion}\"} , {\"os\" : \"windows-latest\", \"r\" : \"${rversion}\", \"bioc\" : \"${biocversion}\" }] }" >> "$GITHUB_OUTPUT"
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## If an OS is failing and you don't want to test it, manually remove it from the 'matrix' JSON entries above
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build-check:
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needs: bioc-config
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strategy:
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fail-fast: false
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matrix: ${{fromJson(needs.bioc-config.outputs.matrix)}}
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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container: ${{ matrix.config.cont }}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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NOT_CRAN: true
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TZ: UTC
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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## Most of these steps are the same as the ones in
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## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
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## If they update their steps, we will also need to update ours.
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- name: Checkout Repository
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uses: actions/checkout@v3
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## R is already included in the Bioconductor docker images
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- name: Setup R from r-lib
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if: runner.os != 'Linux'
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uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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## pandoc is already included in the Bioconductor docker images
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- name: Setup pandoc from r-lib
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if: runner.os != 'Linux'
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uses: r-lib/actions/setup-pandoc@v2
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## Create the path that will be used for caching packages on Linux
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- name: Create R_LIBS_USER on Linux
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if: runner.os == 'Linux'
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run: |
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R_LIBS_USER=/__w/_temp/Library
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echo "R_LIBS_USER=$R_LIBS_USER" >> "$GITHUB_ENV"
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mkdir -p $R_LIBS_USER
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## Use cached R packages
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- name: Restore R package cache
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if: "!contains(github.event.head_commit.message, '/nocache')"
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uses: actions/cache@v4
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ matrix.config.os }}-${{ matrix.config.r }}-${{ matrix.config.bioc }}-${{ inputs.cache-version }}
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restore-keys: ${{ matrix.config.os }}-${{ matrix.config.r }}-${{ matrix.config.bioc }}--${{ inputs.cache-version }}
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## remotes is needed for isntalling the Linux system dependencies
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## as well as other R packages later on.
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- name: Install remotes
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run: |
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message(paste('****', Sys.time(), 'installing remotes ****'))
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install.packages('remotes')
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shell: Rscript {0}
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## This will work again once https://github.com/r-lib/remotes/commit/0e4e23051041d9f1b15a5ab796defec31af6190d
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## makes it to the CRAN version of remotes
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# - name: Install Linux system dependencies
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# if: runner.os == 'Linux'
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# run: |
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# sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "24.04")), collapse = " "))')
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# echo $sysreqs
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# sudo -s eval "$sysreqs"
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- name: Install macOS system dependencies
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if: matrix.config.os == 'macOS-latest'
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run: |
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## Enable installing XML from source if needed
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brew install libxml2
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echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
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## Required to install magick as noted at
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## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
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brew install imagemagick@6
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## For textshaping, required by ragg, and required by pkgdown
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brew install harfbuzz fribidi
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## For installing usethis's dependency gert
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brew install libgit2
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## Required for tcltk
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brew install xquartz --cask
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- name: Install Windows system dependencies
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if: runner.os == 'Windows'
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run: |
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## Edit below if you have any Windows system dependencies
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shell: Rscript {0}
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- name: Install BiocManager
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run: |
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message(paste('****', Sys.time(), 'installing BiocManager ****'))
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remotes::install_cran("BiocManager")
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shell: Rscript {0}
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- name: Set BiocVersion
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run: |
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BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
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shell: Rscript {0}
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- name: Install dependencies pass 1
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run: |
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## Try installing the package dependencies in steps. First the local
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## dependencies, then any remaining dependencies to avoid the
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## issues described at
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## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
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## https://github.com/r-lib/remotes/issues/296
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## Ideally, all dependencies should get installed in the first pass.
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## For running the checks
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message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
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install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories())
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## Pass #1 at installing dependencies
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message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
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remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
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continue-on-error: true
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shell: Rscript {0}
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- name: Install dependencies pass 2
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run: |
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## Pass #2 at installing dependencies
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message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
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remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
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shell: Rscript {0}
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- name: Install BiocGenerics
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if: env.has_RUnit == 'true'
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run: |
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## Install BiocGenerics
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BiocManager::install("BiocGenerics")
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shell: Rscript {0}
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- name: Install covr
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if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
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run: |
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remotes::install_cran("covr")
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shell: Rscript {0}
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- name: Install pkgdown
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if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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run: |
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remotes::install_cran("pkgdown")
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shell: Rscript {0}
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- name: Session info
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run: |
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options(width = 100)
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pkgs <- installed.packages()[, "Package"]
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sessioninfo::session_info(pkgs, include_base = TRUE)
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shell: Rscript {0}
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- name: Run CMD check
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env:
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_R_CHECK_CRAN_INCOMING_: false
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DISPLAY: 99.0
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run: |
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options(crayon.enabled = TRUE)
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rcmdcheck::rcmdcheck(
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args = c("--no-manual", "--no-vignettes", "--timings"),
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build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
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error_on = "warning",
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check_dir = "check"
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)
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shell: Rscript {0}
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## Might need an to add this to the if: && runner.os == 'Linux'
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- name: Reveal testthat details
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if: env.has_testthat == 'true'
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run: find . -name testthat.Rout -exec cat '{}' ';'
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- name: Run RUnit tests
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if: env.has_RUnit == 'true'
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run: |
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BiocGenerics:::testPackage()
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shell: Rscript {0}
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- name: Run BiocCheck
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env:
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DISPLAY: 99.0
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run: |
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BiocCheck::BiocCheck(
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dir('check', 'tar.gz$', full.names = TRUE),
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`quit-with-status` = TRUE,
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`no-check-R-ver` = TRUE,
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`no-check-bioc-help` = TRUE
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)
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shell: Rscript {0}
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- name: Test coverage
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if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
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run: |
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covr::codecov(coverage = covr::package_coverage(type = "all"))
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shell: Rscript {0}
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- name: Install package
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if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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run: R CMD INSTALL .
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- name: Build pkgdown site
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if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
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shell: Rscript {0}
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## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
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## at least one locally before this will work. This creates the gh-pages
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## branch (erasing anything you haven't version controlled!) and
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## makes the git history recognizable by pkgdown.
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- name: Install deploy dependencies
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if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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run: |
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apt-get update && apt-get -y install rsync
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- name: Deploy pkgdown site to GitHub pages 🚀
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if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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uses: JamesIves/github-pages-deploy-action@releases/v4
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with:
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clean: false
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branch: gh-pages
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folder: docs
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- name: Upload check results
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if: failure()
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uses: actions/upload-artifact@master
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with:
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name: ${{ runner.os }}-${{ matrix.config.r }}-${{ matrix.config.bioc }}-results
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path: check
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## Code adapted from
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## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92
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docker-build-and-push:
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runs-on: ubuntu-latest
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needs: build-check
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steps:
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- name: Checkout Repository
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if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
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uses: actions/checkout@v3
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- name: Register repo name
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if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
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id: reg_repo_name
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run: |
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echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
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- name: Set up QEMU
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if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
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uses: docker/setup-qemu-action@v2
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- name: Set up Docker Buildx
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if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
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uses: docker/setup-buildx-action@v2
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- name: Login to Docker Hub
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if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
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uses: docker/login-action@v2
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with:
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username: ${{ secrets.DOCKERHUB_USERNAME }}
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password: ${{ secrets.DOCKERHUB_TOKEN }}
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## Note that DOCKERHUB_TOKEN is really a token for your dockerhub
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## account, not your actual dockerhub account password. You can get it
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## from https://hub.docker.com/settings/security.
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## Check https://github.com/docker/build-push-action/tree/v4.0.0
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## for more details.
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## Alternatively, try checking
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## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html.
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- name: Build and Push Docker
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if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()"
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uses: docker/build-push-action@v4
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with:
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context: .
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push: true
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tags: >
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${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest,
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${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel

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