R-CMD-check-bioc #873
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| # Based on | |
| # - https://lcolladotor.github.io/biocthis/reference/use_bioc_github_action | |
| # - https://github.com/tidyverse/ggplot2/blob/master/.github/workflows/R-CMD-check.yaml | |
| # - https://github.com/r-lib/actions/tree/master/examples | |
| # - https://github.com/maxheld83/ghactions | |
| # - https://github.com/seandavi/BiocActions | |
| on: | |
| push: | |
| branches-ignore: | |
| - gh-pages | |
| pull_request: | |
| branches-ignore: | |
| - gh-pages | |
| schedule: | |
| - cron: "0 7 * * 1,3,5" # Run every Monday/Wednesday/Friday at 07:00 UTC | |
| name: R-CMD-check-bioc | |
| # Increment to clear the cache or include "/nocache" in commit message | |
| env: | |
| cache-version: v5 | |
| jobs: | |
| R-CMD-check-r-lib: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (bioc-${{ matrix.config.biocversion }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| # - {os: windows-latest, biocversion: "release"} | |
| # - {os: windows-latest, biocversion: "devel"} | |
| - {os: macOS-latest, biocversion: "release"} | |
| # - {os: macOS-latest, biocversion: "devel"} | |
| - {os: ubuntu-latest, biocversion: "release"} | |
| # - {os: ubuntu-latest, biocversion: "devel"} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| TZ: UTC | |
| NOT_CRAN: true | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| BIOCVERSION: ${{ matrix.config.biocversion }} | |
| steps: | |
| # https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml | |
| - uses: actions/checkout@v3 | |
| - name: Find R version to run | |
| run: | | |
| # Define R version to use | |
| config="https://bioconductor.org/config.yaml" | |
| rversion=$(curl ${config} | \ | |
| grep r_version_associated_with_${BIOCVERSION} | \ | |
| grep -o "[0-9]*\.[0-9]*\.[0-9]*") | |
| echo "Using R ${rversion}..." | |
| echo "rversion=${rversion}" >> $GITHUB_ENV | |
| shell: | |
| bash {0} | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ env.rversion }} | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: | | |
| any::rcmdcheck | |
| any::BiocCheck | |
| needs: check | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| args: 'c("--no-build-vignettes", "--no-manual", "--timings")' | |
| build_args: 'c("--no-manual", "--no-resave-data")' | |
| error-on: '"warning"' | |
| check-dir: '"check"' | |
| - name: R CMD BiocCheck | |
| run: | | |
| # Continue even if BiocCheck finds an error | |
| BiocCheck::BiocCheck(dir('check', 'tar.gz$', full.names = TRUE), `no-check-R-ver` = TRUE, `no-check-bioc-help` = TRUE) | |
| # For more options: http://bioconductor.org/packages/release/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html | |
| shell: Rscript {0} | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@master | |
| with: | |
| name: ${{ runner.os }}-bioc-${{ matrix.config.biocversion }}-r-${{ env.rversion }}-results | |
| path: check | |
| - name: Test coverage | |
| if: runner.os == 'macOS' && matrix.config.biocversion == 'release' | |
| run: | | |
| install.packages("remotes") | |
| remotes::install_cran("covr") | |
| covr::codecov() | |
| shell: Rscript {0} |