Fix # 16 #62
Workflow file for this run
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| # For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. | |
| # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - master | |
| pull_request: | |
| branches: | |
| - main | |
| - master | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| container: ${{ matrix.config.image }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }} - ${{ matrix.config.bioc }} - ${{ matrix.config.image }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: ubuntu-latest, r: 'release', image: 'bioconductor/bioconductor_docker:RELEASE_3_13'} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| CRAN: ${{ matrix.config.cran }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v2 | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| if: matrix.config.image == null | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - name: Set up pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| if: matrix.config.image == null | |
| - name: Install remotes | |
| run: | | |
| install.packages('remotes') | |
| shell: Rscript {0} | |
| - name: Set BiocManager version | |
| if: matrix.config.image == null | |
| run: | | |
| install.packages('BiocManager') | |
| BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE) | |
| shell: Rscript {0} | |
| - name: Query dependencies | |
| run: | | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE, repos = c(getOption('repos'), BiocManager::repositories())), 'depends.Rds', version = 2) | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os == 'Linux' && matrix.config.image == null | |
| uses: actions/cache@v1 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-r-${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}- | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| env: | |
| RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
| run: | | |
| Rscript -e "remotes::install_github('r-hub/sysreqs')" | |
| sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") | |
| sudo -s eval "$sysreqs" | |
| sudo apt-get update && sudo apt-get -y install libcurl4-openssl-dev | |
| - name: Install dependencies | |
| run: | | |
| local_deps <- remotes::local_package_deps(dependencies = TRUE) | |
| deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]], Ncpu = 2L) | |
| shell: Rscript {0} | |
| - name: Install remaining dependencies | |
| run: | | |
| ## Pass #2 at installing dependencies | |
| message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****')) | |
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE) | |
| ## For running the checks | |
| message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) | |
| remotes::install_cran("rcmdcheck") | |
| BiocManager::install("BiocCheck") | |
| BiocManager::install("DelayedMatrixStats") | |
| shell: Rscript {0} | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: Check | |
| run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: BiocCheck | |
| run: | | |
| BiocCheck::BiocCheck(".") | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-results | |
| path: check | |
| - name: Test coverage | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/master' && matrix.config.image == 'bioconductor/bioconductor_docker:devel' | |
| run: | | |
| install.packages("covr") | |
| covr::codecov(token = "${{secrets.CODECOV_TOKEN}}") | |
| shell: Rscript {0} | |
| - name: Deploy | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/master' && matrix.config.image == 'bioconductor/bioconductor_docker:devel' | |
| run: | | |
| R CMD INSTALL . | |
| git config --local user.name "$GITHUB_ACTOR" | |
| git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" | |
| Rscript -e "install.packages('pkgdown'); pkgdown::deploy_to_branch(new_process = FALSE)" | |