Expanded tests to check for correct handling of gene intersections. #79
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| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| name: R-CMD-check | |
| jobs: | |
| build-check: | |
| runs-on: ubuntu-latest | |
| container: bioconductor/bioconductor_docker:devel | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v4 | |
| - name: Determine the package directory | |
| run: R --no-echo -e "cat(paste0('R_PKG_DIR=', .libPaths()[1], '\n'))" >> $GITHUB_ENV | |
| - name: Restore the package directory | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.R_PKG_DIR }} | |
| key: installed-packages | |
| - name: Install R package dependencies | |
| shell: Rscript {0} | |
| run: | | |
| deets <- read.dcf("DESCRIPTION") | |
| installs <- unlist(strsplit(deets[,c("Imports", "Depends", "Suggests", "LinkingTo")], ",\\s+"), use.names=FALSE) | |
| BiocManager::install(installs) | |
| BiocManager::install("BiocCheck") | |
| - name: Determine the data directories | |
| run: R --no-echo -e "cat(paste0('GYPSUM_DIR=', suppressMessages(gypsum::cacheDirectory()), '\nANNOTATION_HUB_DIR=', suppressMessages(AnnotationHub::getAnnotationHubOption('CACHE')), '\n'))" >> $GITHUB_ENV | |
| - name: Restore the gypsum directory | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.GYPSUM_DIR }} | |
| key: gypsum-cache | |
| - name: Restore the AnnotationHub directory | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.ANNOTATION_HUB_DIR }} | |
| key: AnnotationHub-cache | |
| - name: Run CMD build | |
| run: | | |
| R CMD build . | |
| - name: Run CMD check | |
| run: | | |
| tarball=$(ls | grep "SingleR_.*.tar.gz") | |
| R CMD check --no-manual $tarball | |
| - name: Reveal testthat details | |
| run: find . -name testthat.Rout -exec cat '{}' ';' | |
| - name: Run BiocCheck | |
| run: | | |
| BiocCheck::BiocCheck( | |
| dir('.', 'tar.gz$', full.names = TRUE), | |
| `quit-with-status` = FALSE, | |
| `no-check-R-ver` = TRUE, | |
| `no-check-bioc-help` = TRUE | |
| ) | |
| shell: Rscript {0} |