R-CMD-check #349
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| on: | |
| push: | |
| pull_request: | |
| branches: | |
| - devel | |
| schedule: | |
| - cron: '0 9 * * 5' | |
| 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 }} - ${{ matrix.config.pandoc }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: windows-latest, bioc: 'devel'} | |
| - { os: macOS-latest, bioc: 'devel', curlConfigPath: '/usr/bin/'} | |
| - { os: macOS-latest, bioc: 'devel', pandoc: '2.11.4', curlConfigPath: '/usr/bin/'} | |
| # - { os: ubuntu-latest, bioc: 'devel', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"} | |
| - { os: ubuntu-latest, bioc: 'devel'} | |
| - { os: ubuntu-latest, image: 'bioconductor/bioconductor_docker:devel'} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| CRAN: ${{ matrix.config.cran }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| CURL_CONFIG: ${{ matrix.config.curlConfigPath }}curl-config | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v3 | |
| - name: Set up R and install BiocManager | |
| uses: grimbough/bioc-actions/setup-bioc@v1 | |
| if: matrix.config.image == null | |
| with: | |
| bioc-version: ${{ matrix.config.bioc }} | |
| - name: Set up pandoc (default version) | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| if: matrix.config.image == null && matrix.config.pandoc == null | |
| - name: Set up pandoc (specified version) | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| if: matrix.config.image == null && matrix.config.pandoc != null | |
| with: | |
| pandoc-version: ${{ matrix.config.pandoc }} | |
| - name: Set bitmapType | |
| if: runner.os == 'macOS' | |
| run: echo 'options(bitmapType = "cairo")' >> $HOME/.Rprofile | |
| - name: Install remotes and rmarkdown | |
| run: | | |
| install.packages(c('remotes', 'rmarkdown')) | |
| shell: Rscript {0} | |
| - name: Test pandoc configuration | |
| run: | | |
| rmarkdown::pandoc_available() | |
| rmarkdown::pandoc_version() | |
| rmarkdown::pandoc_exec() | |
| rmarkdown::pandoc_citeproc_args() | |
| file.exists(file.path(dirname(rmarkdown::pandoc_exec()), "pandoc-citeproc")) | |
| Sys.which("pandoc") | |
| Sys.which("pandoc-citeproc") | |
| shell: Rscript {0} | |
| - name: Query dependencies | |
| run: | | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE, repos = c(getOption('repos'), BiocManager::repositories())), 'depends.Rds', version = 2) | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' && matrix.config.image == null | |
| uses: actions/cache@v1 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-pandoc-${{ matrix.config.pandoc }}-${{ hashFiles('depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-pandoc-${{ matrix.config.pandoc }}- | |
| - name: Install system dependencies (Linux) | |
| if: runner.os == 'Linux' | |
| env: | |
| RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::rcmdcheck | |
| pak-version: devel | |
| - name: Install system dependencies (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install harfbuzz | |
| brew install fribidi | |
| - name: Install dependencies | |
| run: | | |
| local_deps <- remotes::local_package_deps(dependencies = TRUE) | |
| deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]], Ncpu = 2L) | |
| remotes::install_cran('rcmdcheck', Ncpu = 2L) | |
| shell: Rscript {0} | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: Build, Install, Check | |
| id: build-install-check | |
| uses: grimbough/bioc-actions/build-install-check@v1 | |
| - name: Upload install log if the build/install/check step fails | |
| if: always() && (steps.build-install-check.outcome == 'failure') | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: install-log | |
| path: | | |
| ${{ steps.build-install-check.outputs.install-log }} | |
| - name: Show testthat output (windows) | |
| if: always() && runner.os == 'Windows' | |
| run: | | |
| type ${{ steps.build-install-check.outputs.check-dir }}\tests\testthat.Rout | |
| shell: cmd | |
| - name: Show testthat output (non-windows) | |
| if: always() && runner.os != 'Windows' | |
| run: | | |
| cat ${{ steps.build-install-check.outputs.check-dir }}/tests/testthat.Rout | |
| shell: bash | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-results | |
| path: ${{ steps.build-install-check.outputs.check-dir }} | |
| - name: Run BiocCheck | |
| uses: grimbough/bioc-actions/run-BiocCheck@v1 | |
| with: | |
| arguments: '--no-check-bioc-views --no-check-bioc-help' | |
| error-on: 'error' | |
| - name: Test coverage | |
| if: matrix.config.os == 'macOS-latest' && matrix.config.pandoc == null | |
| run: | | |
| install.packages("covr") | |
| covr::codecov(token = "${{secrets.CODECOV_TOKEN}}") | |
| shell: Rscript {0} | |
| - name: Deploy | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/devel' && matrix.config.os == 'macOS-latest' && matrix.config.pandoc == null | |
| run: | | |
| R CMD INSTALL . | |
| Rscript -e "remotes::install_dev('pkgdown'); pkgdown::deploy_to_branch(new_process = FALSE)" | |