Correct the previous fix to #122 #248
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| ## This is a simplified action for building and testing a Bioconductor package | |
| ## based on: | |
| ## * https://github.com/lcolladotor/biocthis/blob/master/actions/check-bioc.yml | |
| ## * https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml | |
| ## * https://github.com/seandavi/BuildABiocWorkshop2020/blob/master/.github/workflows/basic_checks.yaml | |
| name: R-CMD-check-bioc | |
| ## Specify which branches to run on | |
| ## The "devel" branch corresponds to Bioc-devel and "RELEASE_X" branches are | |
| ## Bioconductor releases. See http://bioconductor.org/developers/how-to/git/. | |
| on: | |
| push: | |
| branches: | |
| - devel | |
| - 'RELEASE_*' | |
| - actions | |
| pull_request: | |
| branches: | |
| - devel | |
| - 'RELEASE_*' | |
| - actions | |
| jobs: | |
| get-bioc-release: | |
| # Identify the Bioconductor release from the git branch. Also specifies a | |
| # Bioconductor Docker image to use. | |
| runs-on: ubuntu-latest | |
| outputs: | |
| biocimage: ${{ steps.get-release.outputs.biocimage }} | |
| biocrelease: ${{ steps.get-release.outputs.biocrelease }} | |
| steps: | |
| - id: get-release | |
| name: Get Bioconductor release | |
| run: | | |
| if echo "$GITHUB_REF" | grep -q "RELEASE_"; then | |
| biocrelease="$(basename -- $GITHUB_REF | tr '[:upper:]' '[:lower:]')" | |
| else | |
| biocrelease="devel" | |
| fi | |
| biocimage="bioconductor/bioconductor_docker:${biocrelease}" | |
| echo "Bioc release: ${biocrelease}" | |
| echo "Bioc docker image: {$biocimage}" | |
| ## Store the information | |
| echo "biocimage=${biocimage}" >> $GITHUB_OUTPUT | |
| echo "biocrelease=${biocrelease}" >> $GITHUB_OUTPUT | |
| get-bioc-version: | |
| # Identify the Bioconductor version number and R version to use. This is | |
| # done by checking the versions in the Bioconductor Docker container | |
| # selected by get-bioc-release. | |
| runs-on: ubuntu-latest | |
| needs: get-bioc-release | |
| container: | |
| image: ${{ needs.get-bioc-release.outputs.biocimage }} | |
| outputs: | |
| Rversion: ${{ steps.set-versions.outputs.rversion }} | |
| biocversion: ${{ steps.set-versions.outputs.biocversion }} | |
| steps: | |
| - id: get-versions | |
| name: Get Bioconductor/R versions | |
| run: | | |
| biocconfig <- "https://bioconductor.org/config.yaml" | |
| biocrelease <- "${{ needs.get-bioc-release.outputs.biocrelease }}" | |
| cat("Bioc release RAW:", biocrelease, "\n") | |
| biocrelease <- ifelse( | |
| grepl(biocrelease, "release"), | |
| "release", "devel" | |
| ) | |
| biocmap <- BiocManager:::.version_map_get_online(biocconfig) | |
| biocversion <- subset(biocmap, BiocStatus == biocrelease)[, 'Bioc'] | |
| biocversion_str <- as.character(biocversion) | |
| rversion <- subset(biocmap, BiocStatus == biocrelease)[, 'R'] | |
| rversion_str <- as.character(rversion) | |
| # Use R devel for BioC devel between November and May | |
| if (biocrelease == "devel") { | |
| current_month <- as.numeric(format(Sys.Date(), "%m")) | |
| if (current_month >= 11 || current_month <= 5) { | |
| cat("Setting R version to devel") | |
| rversion <- "devel" | |
| rversion_str <- "devel" | |
| } | |
| } | |
| writeLines(c(biocversion_str, rversion_str), "versions.txt") | |
| cat("GET VERSIONS", "\n") | |
| cat("Bioc release: ", biocrelease, "\n") | |
| cat("Bioc version: ", biocversion_str, "\n") | |
| cat("R version: ", rversion_str, "\n") | |
| shell: Rscript {0} | |
| - id: set-versions | |
| name: Set Bioconductor/R versions | |
| run: | | |
| biocversion=$(head -n 1 versions.txt) | |
| rversion=$(tail -n 1 versions.txt) | |
| echo "SET VERSIONS" | |
| echo "Bioc version: ${biocversion}" | |
| echo "R version: ${rversion}" | |
| ## Store the information | |
| echo "biocversion=${biocversion}" >> $GITHUB_OUTPUT | |
| echo "rversion=${rversion}" >> $GITHUB_OUTPUT | |
| R-CMD-check-docker: | |
| ## Run checks in the Bioconductor Docker container | |
| name: ubuntu-latest (r-biocdocker bioc-${{ needs.get-bioc-version.outputs.biocversion }}) | |
| needs: [get-bioc-release, get-bioc-version] | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ${{ needs.get-bioc-release.outputs.biocimage }} | |
| volumes: | |
| - /home/runner/work/_temp/Library:/usr/local/lib/R/host-site-library | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_BIOC_VERSION: ${{ needs.get-bioc-version.outputs.biocversion }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Install extra linux dependencies | |
| run: sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev devscripts qpdf | |
| - name: Setup R dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: 3 | |
| extra-packages: any::rcmdcheck | |
| needs: check | |
| - name: Show session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: Check R package | |
| uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| upload-snapshots: true | |
| upload-results: true | |
| - name: BiocCheck | |
| run: | | |
| BiocManager::install("BiocCheck") | |
| BiocCheck::BiocCheck( | |
| dir('check', 'tar.gz$', full.names = TRUE), | |
| `no-check-R-ver` = TRUE, | |
| `no-check-bioc-help` = TRUE | |
| ) | |
| shell: Rscript {0} | |
| R-CMD-check: | |
| ## Run checks on other platforms. | |
| name: ${{ matrix.config.os }} (r-${{ needs.get-bioc-version.outputs.rversion }} bioc-${{ needs.get-bioc-version.outputs.biocversion }}) | |
| needs: [get-bioc-release, get-bioc-version] | |
| runs-on: ${{ matrix.config.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| experimental: [true] | |
| config: | |
| - {os: windows-latest} | |
| - {os: macOS-latest} | |
| - {os: ubuntu-20.04, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| R_BIOC_VERSION: ${{ needs.get-bioc-version.outputs.biocversion }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Install Linux system dependencies | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt update | |
| sudo apt-get update | |
| sudo apt-get upgrade libstdc++6 | |
| - name: Setup Pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ needs.get-bioc-version.outputs.rversion }} | |
| use-public-rspm: true | |
| - name: Setup R dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: 3 | |
| extra-packages: any::rcmdcheck | |
| needs: check | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: Check R package | |
| uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| upload-snapshots: true | |
| upload-results: true | |
| test-coverage: | |
| ## Calculate package test coverage. Only runs if R-CMD-check-docker has | |
| ## completed successfully. Uses the Bioconductor Docker image. | |
| if: github.ref == 'refs/heads/devel' | |
| needs: [get-bioc-release, get-bioc-version, R-CMD-check-docker] | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ${{ needs.get-bioc-release.outputs.biocimage }} | |
| volumes: | |
| - /home/runner/work/_temp/Library:/usr/local/lib/R/host-site-library | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_BIOC_VERSION: ${{ needs.get-bioc-version.outputs.biocversion }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Install extra linux dependencies | |
| run: sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev devscripts qpdf | |
| - name: Setup R dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: 3 | |
| extra-packages: any::covr | |
| needs: coverage | |
| - name: Test coverage | |
| run: covr::codecov(quiet = FALSE) | |
| shell: Rscript {0} | |
| pkgdown: | |
| ## Build pkgdown site and push to gh-pages branch. Only runs if on the | |
| ## devel branch and R-CMD-check-docker has completed successfully. Uses | |
| ## the Bioconductor Docker image. | |
| if: github.ref == 'refs/heads/devel' | |
| needs: [get-bioc-release, get-bioc-version, R-CMD-check-docker] | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ${{ needs.get-bioc-release.outputs.biocimage }} | |
| volumes: | |
| - /home/runner/work/_temp/Library:/usr/local/lib/R/host-site-library | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_BIOC_VERSION: ${{ needs.get-bioc-version.outputs.biocversion }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Set git credentials | |
| ## Assign commits to the GitHub Action user. This should happen | |
| ## automatically but doesn't (maybe because of Docker). | |
| - run: | | |
| git config user.name github-actions | |
| git config user.email [email protected] | |
| - name: Install extra linux dependencies | |
| run: sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev devscripts qpdf | |
| - name: Setup R dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: 3 | |
| extra-packages: any::pkgdown, local::. | |
| needs: website | |
| - name: Build pkgdown site | |
| run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | |
| shell: Rscript {0} | |
| - name: Deploy to GitHub pages 🚀 | |
| if: github.event_name != 'pull_request' | |
| uses: JamesIves/[email protected] | |
| with: | |
| clean: false | |
| branch: gh-pages | |
| folder: docs |