Workflow that tests the actions #58
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| on: | |
| workflow_dispatch: | |
| name: Workflow that tests the actions | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| pkg-at-root: | |
| name: Root Pkg - Bioc ${{ matrix.bioc-version }} (${{ matrix.os }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-20.04, ubuntu-22.04, windows-2019, windows-2022, macos-11, macos-12, macos-13, macos-14] | |
| ## Test using both Bioconductor devel and release | |
| bioc-version: [devel, release] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup R and Bioconductor | |
| uses: grimbough/bioc-actions/setup-bioc@v1 | |
| with: | |
| bioc-version: ${{ matrix.bioc-version }} | |
| bioc-mirror: https://ftp.gwdg.de/pub/misc/bioconductor | |
| use-public-rspm: false | |
| - name: Install pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: 1 | |
| - name: Build, Install, Check | |
| id: build-install-check | |
| uses: grimbough/bioc-actions/build-install-check@v1 | |
| with: | |
| package-directory: '.' | |
| ## Turn off the checks that we know will fail | |
| ## Cause the workflow to error if any new errors appear | |
| - name: Run BiocCheck with arguments | |
| uses: grimbough/bioc-actions/run-BiocCheck@v1 | |
| with: | |
| package-directory: '.' | |
| arguments: '--no-check-bioc-views --no-check-vignettes --no-check-bioc-help' | |
| error-on: 'error' | |
| ## upload the Rcheck folder regardless of success of failure | |
| - name: Upload output | |
| uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: ${{ matrix.os }}-bioc-${{ matrix.bioc-version}}-Rcheck | |
| path: | | |
| ${{ steps.build-install-check.outputs.check-dir }} | |
| ## upload source and binary packages | |
| - name: Upload check output | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: ${{ matrix.os }}-bioc-${{ matrix.bioc-version}}-pkgs | |
| path: | | |
| ${{ steps.build-install-check.outputs.source-tarball }} | |
| ${{ steps.build-install-check.outputs.package-binary }} | |
| pkg-in-subfolder: | |
| name: Subfolder Pkg - Bioc ${{ matrix.bioc-version }} (${{ matrix.os }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-22.04] | |
| bioc-version: [release] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| ## We only using Ubuntu and BioC-release here, | |
| ## so lets use the Rstudio package manager | |
| ## to install binary linux packages | |
| - name: Setup R and Bioconductor | |
| uses: grimbough/bioc-actions/setup-bioc@v1 | |
| with: | |
| bioc-version: ${{ matrix.bioc-version }} | |
| bioc-mirror: https://packagemanager.rstudio.com/bioconductor | |
| - name: Install dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: 1 | |
| ## Run the complete build, install, check process like the Bioc Build System | |
| - name: Build, Install, Check | |
| id: build-install-check | |
| uses: grimbough/bioc-actions/build-install-check@v1 | |
| with: | |
| package-directory: 'inst/nestedPKG' | |
| ## Run all tests in BiocCheck, include those we know fail | |
| ## Use the 'error-on' to prevent this failing the workflow | |
| - name: Run BiocCheck without arguments | |
| uses: grimbough/bioc-actions/run-BiocCheck@v1 | |
| with: | |
| package-directory: 'inst/nestedPKG' | |
| error-on: 'never' | |
| ## upload the Rcheck folder if the workflow fails | |
| - name: Upload output | |
| uses: actions/upload-artifact@v4 | |
| if: failure() | |
| with: | |
| name: ${{ matrix.os }}-bioc-${{ matrix.bioc-version}}-sub_folder | |
| path: | | |
| ${{ steps.build-install-check.outputs.check-dir }} | |
| using-bioc-docker: | |
| name: Docker Devel | |
| strategy: | |
| fail-fast: false | |
| runs-on: ubuntu-22.04 | |
| container: bioconductor/bioconductor_docker:devel | |
| steps: | |
| - uses: actions/checkout@v4 | |
| ################################################## | |
| ## no need to install R, BiocManager, or Pandoc ## | |
| ################################################## | |
| ## cache installed packages | |
| - name: Cache install R packages | |
| uses: actions/cache@v3 | |
| with: | |
| path: /usr/local/lib/R/site-library | |
| key: docker-1 | |
| restore-keys: docker- | |
| ## we can use BiocManager will install binary packages in the Docker container | |
| - name: Install dependencies | |
| run: | | |
| BiocManager::install(c('AnnotationHub', 'rtracklayer', 'knitr', 'rmarkdown', 'BiocStyle')) | |
| shell: Rscript {0} | |
| - name: Build, Install, Check | |
| id: build-install-check | |
| uses: grimbough/bioc-actions/build-install-check@v1 | |
| with: | |
| package-directory: '.' | |
| ## Turn off the checks that we know will fail | |
| ## Cause the workflow to error if any new errors appear | |
| - name: Run BiocCheck with arguments | |
| uses: grimbough/bioc-actions/run-BiocCheck@v1 | |
| with: | |
| package-directory: '.' | |
| arguments: '--no-check-bioc-views --no-check-vignettes --no-check-bioc-help' | |
| error-on: 'error' | |
| - name: Upload built package binary | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: docker-binary | |
| path: | | |
| ${{ steps.build-install-check.outputs.package-binary }} |