Merge pull request #217 from satijalab/basic_ci #4
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| name: Integration Checks | |
| # because `main` is a protected branch this workflow is triggered when a PR | |
| # is opened/updated and again when it is merged | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| check-package: | |
| # system dependencies for cannot be automatically resolved by | |
| # `r-lib/actions/setup-r@v2` for macos or windows - to avoid having to | |
| # maintain separate logic to infer and install system of those operating | |
| # systems we'll only run integration checks with the ubuntu | |
| runs-on: ubuntu-latest | |
| # run integration checks with R-release, R-devel, and R-oldrelease | |
| strategy: | |
| matrix: | |
| r-version: ['release', 'devel', 'oldrel'] | |
| steps: | |
| # pull the latest changes from the repository down to the runner | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| # install R and any system dependencies | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| # install the R version specified by the current strategy | |
| r-version: ${{ matrix.r-version }} | |
| # specify additional repositories to pull dependencies not | |
| # available on CRAN (i.e. `BPCells`) | |
| extra-repositories: ${{ 'https://bnprks.r-universe.dev' }} | |
| # install R dependencies | |
| - name: Install Dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: | |
| any::rcmdcheck | |
| any::pkgdown | |
| # installed packages are cached by default - force an upgrade to the | |
| # latest version of all dependencies | |
| upgrade: 'TRUE' | |
| # run CRAN checks - fails if any ERRORs or WARNINGs are raised in which | |
| # case the `rcmdcheck` output will be uploaded as an artifact | |
| - name: Run Checks | |
| uses: r-lib/actions/check-r-package@v2 | |
| env: | |
| # suppress NOTEs that are accepted by CRAN | |
| # see: https://www.rdocumentation.org/packages/rcmdcheck/versions/1.4.0/topics/rcmdcheck | |
| _R_CHECK_PKG_SIZES_: false | |
| _R_CHECK_RD_XREFS_: false | |
| _R_CHECK_CRAN_INCOMING_NOTE_GNU_MAKE_: false | |
| _R_CHECK_PACKAGE_DATASETS_SUPPRESS_NOTES_: true | |
| continue-on-error: true | |
| # build pkgdown site | |
| - name: Build Website | |
| run: | | |
| pkgdown::build_site_github_pages( | |
| new_process = FALSE, | |
| install = FALSE | |
| ) | |
| shell: Rscript {0} |