version bump #288
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| on: | |
| push: | |
| branches: | |
| - devel | |
| pull_request: | |
| branches: | |
| - 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', Ncpus: 4} | |
| - { os: macOS-14, bioc-version: 'devel', bioc-mirror: 'https://ftp.gwdg.de/pub/misc/bioconductor', Ncpus: 3} | |
| - { os: macOS-12, bioc-version: 'devel', bioc-mirror: 'https://ftp.gwdg.de/pub/misc/bioconductor', Ncpus: 3} | |
| - { os: ubuntu-22.04, bioc-version: 'devel', bioc-mirror: 'https://ftp.gwdg.de/pub/misc/bioconductor', Ncpus: 4} | |
| - { os: ubuntu-22.04, bioc-version: 'release', bioc-mirror: 'https://packagemanager.posit.co/bioconductor', Ncpus: 4} | |
| 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@v4 | |
| - 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: temp rhdf5filters install | |
| if: matrix.config.os == 'macOS-14' | |
| run: | | |
| sudo R -e 'source("https://mac.R-project.org/bin/install.R")' -e 'install.libs("openssl")' | |
| - name: temp rhdf5filters install | |
| if: matrix.config.os == 'macOS-14' | |
| run: | | |
| install.packages("remotes") | |
| 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} |