Updated bioconductor release in github actions #131
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| on: | |
| push: | |
| branches: | |
| - main | |
| - master | |
| pull_request: | |
| branches: | |
| - main | |
| - master | |
| name: test-coverage | |
| jobs: | |
| test-coverage: | |
| runs-on: macOS-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: macOS-latest, r: 'release', bioc: '3.18'} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@master | |
| - uses: r-lib/actions/setup-r@v2 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-tinytex@v2 | |
| - run: tlmgr --version | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| message(paste('****', Sys.time(), 'installing BiocManager ****')) | |
| remotes::install_cran("BiocManager") | |
| shell: Rscript {0} | |
| ## Find the corresponding R version based on the Bioconductor version | |
| ## to use for the macOS and Windows checks by the next GHA job | |
| - id: findrversion | |
| name: Find Bioc and R versions | |
| run: | | |
| ## Find what branch we are working on | |
| if echo "$GITHUB_REF" | grep -q "master"; then | |
| biocversion="devel" | |
| elif echo "$GITHUB_REF" | grep -q "RELEASE_"; then | |
| biocversion="release" | |
| fi | |
| ## Define the R and Bioconductor version numbers | |
| biocversionnum=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == '${biocversion}')[, 'Bioc']; cat(as.character(res))") | |
| rversion=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == '${biocversion}')[, 'R']; cat(as.character(res))") | |
| ## Print the results | |
| echo $biocversion | |
| echo $biocversionnum | |
| echo $rversion | |
| ## Save the info for the next job | |
| echo "rversion=${rversion}" >> $GITHUB_OUTPUT | |
| echo "biocversionnum=${biocversionnum}" >> $GITHUB_OUTPUT | |
| # echo "::set-output name=rversion::${rversion}" | |
| # echo "::set-output name=biocversionnum::${biocversionnum}" | |
| shell: | |
| bash {0} | |
| - name: Set BiocVersion | |
| run: | | |
| BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, update = FALSE) | |
| shell: Rscript {0} | |
| - name: Install dependencies | |
| run: | | |
| install.packages(c("remotes")) | |
| # remotes::install_deps(dependencies = TRUE) | |
| remotes::install_cran("covr", type = "binary", dependencies = TRUE) | |
| ## remotes::install_deps(dependencies = TRUE) | |
| ## remotes::install_cran("rcmdcheck") | |
| ### Try installing the package dependencies in steps. First the local | |
| ## dependencies, then any remaining dependencies to avoid the | |
| ## issues described at | |
| ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html | |
| ## https://github.com/r-lib/remotes/issues/296 | |
| ## Ideally, all dependencies should get installed in the first pass. | |
| ## Pass #1 at installing dependencies | |
| message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****')) | |
| local_deps <- remotes::local_package_deps(dependencies = TRUE) | |
| deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| # BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]]) | |
| BiocManager::install(local_deps, force = TRUE) | |
| ## Pass #2 at installing dependencies | |
| message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****')) | |
| deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| BiocManager::install(deps$package[deps$diff != 0]) | |
| ## For running the checks | |
| message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) | |
| remotes::install_cran("rcmdcheck") | |
| BiocManager::install("BiocCheck") | |
| shell: Rscript {0} | |
| - name: Test coverage | |
| run: covr::codecov() | |
| shell: Rscript {0} |