Update github action R and bioc versions (#146) #781
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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: | |
| workflow_dispatch: | |
| push: | |
| branches: [ master, dev ] | |
| pull_request: | |
| schedule: | |
| - cron: "0 6 * * 3" | |
| name: R Build and Checks | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ubuntu-${{ matrix.config.os }} | |
| name: ubuntu-${{ matrix.config.os }} (${{ matrix.config.r }} / ${{ matrix.config.bioc }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| #- {os: 24.04, r: 'devel', bioc: 'devel'} | |
| - {os: 24.04, r: '4.4', bioc: '3.20', pkgdown: "true"} | |
| - {os: 22.04, r: '4.3', bioc: '3.18'} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| CELLHASHR_DEBUG: 1 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install packages | |
| if: runner.os != 'Windows' | |
| # NOTE: switch back to main GMM_demux repo when this is resolved: https://github.com/CHPGenetics/GMM-Demux/pull/8 | |
| # NOTE: switch back to main demuxEM repo when this is resolved: https://github.com/lilab-bcb/demuxEM/pull/16 | |
| # libglpk-dev added due to igraph | |
| # libpoppler-cpp-dev added due to demuxEM | |
| run: | | |
| sudo apt-get update && sudo apt-get install -yq python3 python3-pip libglpk-dev libmagick++-dev libpoppler-cpp-dev | |
| python3 -m pip install --upgrade pip | |
| python3 -m pip install git+https://github.com/bbimber/demuxEM.git | |
| python3 -m pip install git+https://github.com/bbimber/GMM-Demux.git | |
| # The install_github() on remotes is to ensure system_requirements() supports 22.04 | |
| - name: Setup Bioconductor | |
| run: | | |
| install.packages(c('remotes', 'devtools')) | |
| remotes::install_github("r-lib/remotes") | |
| if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager"); | |
| BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE); | |
| cat(append = TRUE, file = "~/.Rprofile", "local({"); | |
| cat(append = TRUE, file = "~/.Rprofile", "repos <- append(getOption('repos'), BiocManager::repositories());"); | |
| cat(append = TRUE, file = "~/.Rprofile", "repos <- repos[!duplicated(names(repos))];"); | |
| cat(append = TRUE, file = "~/.Rprofile", "options(repos = repos);"); | |
| cat(append = TRUE, file = "~/.Rprofile", "});"); | |
| cat(append = TRUE, file = "~/.Rprofile", "Sys.setenv(R_BIOC_VERSION=as.character(BiocManager::version()));"); | |
| cat(append = TRUE, file = "~/.Rprofile", "Sys.setenv(USE_GMMDEMUX_SEED=1);"); | |
| # To avoid pthread_create() error. See: https://github.com/bmbolstad/preprocessCore/issues/1 and https://github.com/bmbolstad/preprocessCore/issues/12 | |
| remotes::install_github("bmbolstad/preprocessCore", dependencies = T, upgrade = "always", force = TRUE, configure.args = "--disable-threading") | |
| shell: Rscript {0} | |
| - name: Query dependencies | |
| run: | | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-${{ matrix.config.bioc }}-1-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-${{ matrix.config.bioc }}-${{ secrets.CACHE_VERSION || 1 }}- | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| run: | | |
| while read -r cmd | |
| do | |
| eval sudo $cmd | |
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "${{ matrix.config.os }}"))') | |
| - name: Install dependencies | |
| run: | | |
| remotes::install_deps(dependencies = TRUE, upgrade = "always") | |
| install.packages("pkgdown") | |
| remotes::install_cran("rcmdcheck") | |
| 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 | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--no-build-vignettes"), error_on = "warning", check_dir = "check") | |
| 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@main | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-bioc${{ matrix.config.bioc }}-results | |
| path: check | |
| - name: Install package | |
| if: github.ref == 'refs/heads/master' && matrix.config.pkgdown == 'true' | |
| run: R CMD INSTALL . | |
| - name: Deploy package | |
| if: github.ref == 'refs/heads/master' && matrix.config.pkgdown == 'true' | |
| run: | | |
| git config --local user.email "actions@github.com" | |
| git config --local user.name "GitHub Actions" | |
| Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, clean = TRUE)' |