add workflow_dispatch: #4
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| name: R CMD check | |
| on: | |
| push: | |
| branches: | |
| - devel | |
| paths: | |
| - 'DESCRIPTION' | |
| - '**basic_checks.yml' | |
| workflow_dispatch: | |
| pull_request: | |
| branches: | |
| - devel | |
| env: | |
| cache-version: v1 | |
| jobs: | |
| r-build-and-check: | |
| runs-on: ubuntu-latest | |
| container: bioconductor/bioconductor_docker:devel | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: TRUE | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v4 | |
| - name: Query dependencies and update old packages | |
| run: | | |
| BiocManager::install(ask=FALSE) | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' | |
| uses: actions/cache@v4 | |
| with: | |
| path: /usr/local/lib/R/site-library | |
| key: ${{ env.cache-version }}-${{ runner.os }}-r-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r- | |
| - name: Install dependencies | |
| run: | | |
| BiocManager::repositories() | |
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories()) | |
| remotes::install_cran(c("rcmdcheck", "covr")) | |
| shell: Rscript {0} | |
| - name: Run rcmdcheck | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Run BiocCheck | |
| env: | |
| DISPLAY: ':99.0' | |
| run: | | |
| BiocCheck::BiocCheck( | |
| dir('check', 'tar.gz$', full.names = TRUE), | |
| `quit-with-status` = FALSE, | |
| `no-check-R-ver` = TRUE, | |
| `no-check-bioc-help` = TRUE | |
| ) | |
| shell: Rscript {0} |