Be explicit about BiocSyle functions in vignettes #259
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| on: | |
| push: | |
| branches: | |
| - master | |
| - devel | |
| pull_request: | |
| branches: | |
| - master | |
| - devel | |
| name: R-CMD-check | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.bioc-version }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: windows-2022, bioc-version: 'devel', bioc-mirror: 'https://ftp.gwdg.de/pub/misc/bioconductor'} | |
| - { os: macOS-12, bioc-version: 'devel', bioc-mirror: 'https://ftp.gwdg.de/pub/misc/bioconductor'} | |
| - { os: ubuntu-22.04, bioc-version: 'devel', bioc-mirror: 'https://ftp.gwdg.de/pub/misc/bioconductor'} | |
| - { os: ubuntu-22.04, bioc-version: 'release', bioc-mirror: 'https://packagemanager.posit.co/bioconductor'} | |
| steps: | |
| ## R CMD check complains about Windows line endings without this | |
| - name: Configure git | |
| run: | | |
| git config --global core.autocrlf false | |
| - name: Install system libraries | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update && sudo apt-get install libcurl4-openssl-dev | |
| - uses: actions/checkout@v3 | |
| - name: Setup R and Bioconductor | |
| uses: grimbough/bioc-actions/setup-bioc@v1 | |
| with: | |
| bioc-version: ${{ matrix.config.bioc-version }} | |
| bioc-mirror: ${{ matrix.config.bioc-mirror }} | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install dependencies temp | |
| if: runner.os == 'macos' | |
| run: | | |
| BiocManager::install('grimbough/rhdf5filters') | |
| shell: Rscript {0} | |
| - name: Install dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: | | |
| covr | |
| rcmdcheck | |
| - name: Bioc - Build, Install, Check | |
| uses: grimbough/bioc-actions/build-install-check@v1 | |
| - name: Run BiocCheck | |
| uses: grimbough/bioc-actions/run-BiocCheck@v1 | |
| with: | |
| error-on: 'never' | |
| arguments: '--no-check-bioc-help' | |
| - name: Test coverage | |
| if: runner.os == 'Windows' | |
| run: | | |
| covr::codecov() | |
| shell: Rscript {0} |