Merge pull request #1020 from jiajic/suite_dev #193
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 |