22 #124
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| on: | |
| push: | |
| pull_request: | |
| branches: | |
| - master | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| container: ${{ matrix.config.image }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.bioc }} - ${{ matrix.config.image }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: windows-latest, bioc: 'release'} | |
| - { os: windows-latest, bioc: 'devel'} | |
| - { os: macOS-latest, bioc: 'release'} | |
| - { os: macOS-latest, bioc: 'devel'} | |
| - { os: ubuntu-latest, bioc: 'release'} | |
| - { os: ubuntu-latest, bioc: 'devel'} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| CRAN: ${{ matrix.config.cran }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v3 | |
| - name: Set up R | |
| uses: grimbough/bioc-actions/setup-bioc@v1 | |
| if: matrix.config.image == null | |
| with: | |
| bioc-version: ${{ matrix.config.bioc }} | |
| - name: Install magick dependencies | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install imagemagick | |
| brew install ffmpeg | |
| - name: Install dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: rcmdcheck, optparse, magick, BiocManager, devtools | |
| - name: Install BiocCheck | |
| if: runner.os == 'Linux' | |
| run: BiocManager::install("BiocCheck") | |
| shell: Rscript {0} | |
| - name: Set up pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| if: matrix.config.image == null | |
| - name: basilisk utils | |
| if: matrix.config.os == 'windows-latest' && matrix.config.bioc == 'devel' | |
| run: | | |
| devtools::install_github("alanocallaghan/basilisk.utils") | |
| shell: Rscript {0} | |
| - name: Debug | |
| if: matrix.config.os == 'windows-latest' && matrix.config.bioc == 'devel' | |
| run: | | |
| devtools::load_all() | |
| m <- matrix(rnorm(2000), ncol=20) | |
| out <- fitsne(m, random_state = 42L) | |
| shell: Rscript {0} | |
| - name: Check | |
| uses: r-lib/actions/check-r-package@v2 | |
| - name: BiocCheck | |
| if: runner.os == 'Linux' | |
| run: BiocCheck::BiocCheck(dir('check', 'tar.gz$', full.names = TRUE), `quit-with-status` = TRUE) | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@v1 | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-results | |
| path: check | |
| - name: Test coverage | |
| if: matrix.config.os == 'macOS-latest' && matrix.config.r == 'release' | |
| run: | | |
| install.packages("covr") | |
| covr::codecov(token = "${{secrets.CODECOV_TOKEN}}") | |
| shell: Rscript {0} |