R-CMD-check #933
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| # on: [push, pull_request] | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - develop # This will eventually require a different container | |
| paths: | |
| - 'R/**' | |
| - 'DESCRIPTION' | |
| - 'NAMESPACE' | |
| - 'src/**' | |
| - 'tests/**' | |
| pull_request: | |
| schedule: | |
| # Rerun checks daily, after facilebio/facilebio_base is rebuilt. | |
| # This will catch failures due to changes in functionality of packages | |
| # we depend on. | |
| # facilebio_base builds every day at 1AM pacific and takes about 1 hour | |
| # this runs at same time as facilebio_base_extra | |
| - cron: '0 11 * * *' | |
| workflow_dispatch: | |
| inputs: | |
| dummy: | |
| description: 'A dummy variable to enable manual workflow execution' | |
| required: false | |
| default: 'gitty up' | |
| name: R-CMD-check | |
| env: | |
| has_testthat: 'true' | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| image: ['lianos/sparrow:release', 'lianos/sparrow:devel'] | |
| container: ${{ matrix.image }} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v2 | |
| # with: | |
| # ref: 'main' | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v1 | |
| with: | |
| install-r: false | |
| # I guess I didn't want to install this into the base | |
| # - name: Install dependencies | |
| # run: remotes::install_deps(dependencies = TRUE, upgrade = FALSE) | |
| # shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| DISPLAY: 99.0 | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| rcmdcheck::rcmdcheck( | |
| args = c("--no-manual", "--no-vignettes", "--timings"), | |
| build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"), | |
| error_on = "warning", | |
| check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Reveal testthat details | |
| run: find . -name testthat.Rout -exec cat '{}' ';' | |
| - name: Run BiocCheck | |
| env: | |
| DISPLAY: 99.0 | |
| run: | | |
| BiocCheck::BiocCheck( | |
| dir('check', 'tar.gz$', full.names = TRUE), | |
| `quit-with-status` = TRUE, | |
| `no-check-R-ver` = TRUE, | |
| `no-check-bioc-help` = TRUE, | |
| `no-check-coding-practices` = TRUE) | |
| shell: Rscript {0} | |