Merge branch 'master' of git.bioconductor.org:packages/SingleR #47
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| on: [push] | |
| name: R-CMD-check | |
| jobs: | |
| build-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| container: ${{ matrix.config.cont }} | |
| ## Environment variables unique to this job. | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } | |
| - { os: macOS-latest, r: '4.3', bioc: '3.18'} | |
| ## Check https://github.com/r-lib/actions/tree/master/examples | |
| ## for examples using the http-user-agent | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| NOT_CRAN: true | |
| TZ: UTC | |
| GITHUB_PAT: ${{ secrets.BEACHMAT_PAT }} | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v3 | |
| ## For Macs - none of this is required for the Linux containers. | |
| - name: Setup R from r-lib | |
| if: runner.os != 'Linux' | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| - name: Setup pandoc from r-lib | |
| if: runner.os != 'Linux' | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install BiocManager with the right version | |
| if: runner.os != 'Linux' | |
| run: | | |
| install.packages("BiocManager") | |
| BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE) | |
| shell: Rscript {0} | |
| - name: Install remotes to get beachmat | |
| if: runner.os != 'Linux' | |
| run: | | |
| BiocManager::install("remotes") | |
| shell: Rscript {0} | |
| - name: Install macOS system dependencies | |
| if: matrix.config.os == 'macOS-latest' | |
| run: | | |
| ## Enable installing XML from source if needed | |
| brew install libxml2 | |
| echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV | |
| - 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@v3 | |
| with: | |
| path: ${{ env.R_PKG_DIR }} | |
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/dependencies.rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_${{ matrix.config.bioc }}-r-${{ matrix.config.r }}- | |
| - 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") | |
| saveRDS(file=".github/dependencies.rds", installs) | |
| - name: Determine the Hub directories | |
| run: R --no-echo -e "cat(paste0('EXPERIMENT_HUB_DIR=', suppressMessages(ExperimentHub::getExperimentHubOption('CACHE')), '\nANNOTATION_HUB_DIR=', suppressMessages(AnnotationHub::getAnnotationHubOption('CACHE')), '\n'))" >> $GITHUB_ENV | |
| - name: Restore the ExperimentHub directory | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.EXPERIMENT_HUB_DIR }} | |
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-ExperimentHub-${{ hashFiles('vignettes/*.Rmd') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-ExperimentHub- | |
| - name: Restore the AnnotationHub directory | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.ANNOTATION_HUB_DIR }} | |
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-AnnotationHub-${{ hashFiles('vignettes/*.Rmd') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-AnnotationHub- | |
| - 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} |