Empty #115
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: | |
| 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@v2 | |
| - name: Set up R | |
| uses: grimbough/bioc-actions/setup-bioc@v1 | |
| if: matrix.config.image == null | |
| with: | |
| bioc-version: ${{ matrix.config.bioc }} | |
| - name: Install magick dependencies | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install imagemagick | |
| brew install ffmpeg | |
| - name: Install dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v1 | |
| with: | |
| extra-packages: rcmdcheck, optparse, magick, BiocManager | |
| - name: Install BiocCheck | |
| if: runner.os == 'Linux' | |
| run: BiocManager::install("BiocCheck") | |
| shell: Rscript {0} | |
| - name: Set up pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| if: matrix.config.image == null | |
| - name: Check | |
| uses: r-lib/actions/check-r-package@v2 | |
| - name: BiocCheck | |
| if: runner.os == 'Linux' | |
| run: BiocCheck::BiocCheck(dir('check', 'tar.gz$', 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} | |