Update README.md #403
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: windows-latest, r: 'release'} | |
| - {os: macOS-latest, r: 'devel', http-user-agent: 'release'} | |
| - {os: macOS-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} | |
| - {os: ubuntu-latest, r: 'release'} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| - name: Install libraries for Linux | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get install libcurl4-openssl-dev | |
| - name: Install bioconductor packages | |
| run: | | |
| install.packages("BiocManager") | |
| BiocManager::install(c('DESeq2', 'limma', 'SummarizedExperiment', 'sva')) | |
| shell: Rscript {0} | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| pak-version: devel | |
| extra-packages: any::rcmdcheck, any::XML | |
| needs: check | |
| # See https://github.com/r-lib/actions/issues/559 for the XML issue | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| args: 'c("--no-manual", "--as-cran", "--run-donttest")' | |
| error-on: '"error"' | |
| check-dir: '"check"' |