Merge pull request #998 from jiajic/mrd_xenium #183
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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: R-CMD-check | |
| on: | |
| push: | |
| branches: | |
| - 'suite' | |
| - 'suite_dev' | |
| permissions: | |
| contents: read | |
| jobs: | |
| R-CMD-check: | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: # matrix of system runners to run workflow on | |
| - {os: macOS-latest, r: 'release'} | |
| - {os: windows-latest, r: 'release'} | |
| # - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} | |
| - {os: ubuntu-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'oldrel-1'} | |
| steps: | |
| - name: Remove vignettes dir | |
| run: rm -rf 'vignettes/' | |
| shell: bash | |
| - name: Checkout repo for workflow access | |
| uses: actions/checkout@v4 | |
| - name: Set up R environment | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| - name: Set up dependencies (general) | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| env: | |
| _R_CHECK_FORCE_SUGGESTS: false | |
| _R_CHECK_RD_XREFS: false | |
| with: | |
| dependencies: '"hard"' # do not use suggested dependencies | |
| install-pandoc: false | |
| extra-packages: | | |
| any::rcmdcheck | |
| any::testthat | |
| any::hdf5r | |
| any::rlang | |
| any::R.utils | |
| any::remotes | |
| any::spdep | |
| any::future.apply | |
| github::drieslab/GiottoData | |
| - name: Test python env install | |
| run: | | |
| if (!GiottoClass::checkGiottoEnvironment()) { | |
| GiottoClass::installGiottoEnvironment() | |
| } | |
| reticulate::py_list_packages(envname = "giotto_env") | |
| shell: Rscript {0} | |
| - name: Run R CMD check | |
| uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| upload-snapshots: true | |
| error-on: '"error"' # workflow errors on error only, can change to include warnings | |
| # show testthat output for ease of access | |
| - name: Show testthat output | |
| if: always() | |
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash |