R-CMD-check #803
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| on: | |
| push: | |
| branches-ignore: | |
| - updateREADME | |
| pull_request: | |
| branches: | |
| - master | |
| schedule: | |
| - cron: '0 8 * * 4' | |
| name: R-CMD-check | |
| jobs: | |
| ## pre-job to determine if a job has been run for the same SHA (e.g. on a different branch) | |
| gatekeeper: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| should_skip: ${{ steps.skip_check.outputs.should_skip }} | |
| steps: | |
| - id: skip_check | |
| uses: fkirc/skip-duplicate-actions@master | |
| with: | |
| github_token: ${{ github.token }} | |
| versions: | |
| needs: gatekeeper | |
| if: (github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (github.event_name != 'schedule' && (needs.gatekeeper.outputs.should_skip == 'false') && !contains(github.event.head_commit.message, 'worksave') && !contains(github.event.head_commit.message, 'skip-ci')) | |
| runs-on: ubuntu-latest | |
| outputs: | |
| r: ${{ steps.setup.outputs.r }} | |
| bioc: ${{ steps.setup.outputs.bioc }} | |
| dockerise: ${{ steps.setup.outputs.dockerise }} | |
| docker_tag: ${{ steps.setup.outputs.docker_tag }} | |
| steps: | |
| - uses: rlespinasse/github-slug-action@v3.x | |
| - uses: r-lib/actions/setup-r@v2 | |
| - name: Get R/Bioc versions | |
| id: setup | |
| run: | | |
| BRANCH_NAME="${{ env.GITHUB_REF_SLUG }}" | |
| ## R and Bioc versions | |
| Rscript -e "install.packages('BiocManager', Ncpus=2)" | |
| r_devel=$(Rscript -e "vm=BiocManager:::.version_map(); cat(as.character(vm[vm\$BiocStatus == 'devel',]\$R))") | |
| r_release=$(Rscript -e "vm=BiocManager:::.version_map(); cat(as.character(vm[vm\$BiocStatus == 'release',]\$R))") | |
| if [[ $BRANCH_NAME =~ "release_" ]] | |
| then | |
| bioc="latest" | |
| r="$r_release" | |
| else | |
| bioc="devel" | |
| r="$r_devel" | |
| fi | |
| echo "r=$r" >> $GITHUB_OUTPUT | |
| echo "bioc=$bioc" >> $GITHUB_OUTPUT | |
| ## Docker | |
| # Only Dockerise for 'master' or 'RELEASE_*' branches | |
| dockerise='false' | |
| [[ github.event_name != 'schedule' && ($BRANCH_NAME == "master" || $BRANCH_NAME =~ "release_") ]] && dockerise='true' | |
| echo "dockerise=$dockerise" >> $GITHUB_OUTPUT | |
| # Docker tag is 'github' for master and the branch name for release branches | |
| docker_tag="github" | |
| [[ $BRANCH_NAME =~ "release_" ]] && docker_tag=$BRANCH_NAME | |
| echo "docker_tag=$docker_tag" >> $GITHUB_OUTPUT | |
| R-CMD-check: | |
| needs: [gatekeeper, versions] | |
| ## run scheduled jobs only on main repo - do not run a duplicate job for merges etc. Do not run if commit messages include any of 'worksave' or 'skip-ci' | |
| if: (github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (github.event_name != 'schedule' && (needs.gatekeeper.outputs.should_skip == 'false') && !contains(github.event.head_commit.message, 'worksave') && !contains(github.event.head_commit.message, 'skip-ci')) | |
| runs-on: ${{ matrix.config.os }} | |
| container: ${{ matrix.config.image }} | |
| name: ${{ matrix.config.os }} (r_${{ matrix.config.r }} - bioc_${{ matrix.config.bioc }} - image_${{ matrix.config.image }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| # - { os: windows-latest, r: '${{ needs.versions.outputs.r }}', bioc: '${{ needs.versions.outputs.bioc }}'} | |
| # - { os: macOS-latest, r: '${{ needs.versions.outputs.r }}', bioc: '${{ needs.versions.outputs.bioc }}'} | |
| - { os: ubuntu-latest, r: '${{ needs.versions.outputs.r }}', bioc: '${{ needs.versions.outputs.bioc }}', image: 'bioconductor/bioconductor_docker:${{ needs.versions.outputs.bioc }}'} | |
| 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: ${{ matrix.config.r }} | |
| - name: Create slug/short variables | |
| uses: rlespinasse/github-slug-action@v3.x | |
| - name: Install remotes 🔭 | |
| run: | | |
| install.packages('remotes', Ncpus=2) | |
| shell: Rscript {0} | |
| - name: Set BiocManager version 📆 | |
| if: matrix.config.image == null | |
| run: | | |
| install.packages('BiocManager', Ncpus=2) | |
| BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, Ncpus=2) | |
| 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 != 'Windows' && 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: | | |
| options(repos = c(CRAN = "https://cran.r-project.org")) | |
| remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories(), Ncpus=2) | |
| remotes::install_cran("rcmdcheck", Ncpus=2) | |
| remotes::install_cran("covr", Ncpus=2) | |
| 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 ✅ | |
| if: (!contains(github.event.head_commit.message, 'skip-check')) | |
| run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Check --as-cran ✅ ✅ | |
| if: github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics' | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--ignore-vignettes", "--run-dontrun"), error_on = "never", check_dir = "check/asCRAN", build_args = c("--no-build-vignettes")) | |
| shell: Rscript {0} | |
| # - name: BiocCheck 🧬 ✅ | |
| # if: github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics' | |
| # run: | | |
| # BiocManager::install("BiocCheck", Ncpus=2) | |
| # BiocCheck::BiocCheck(".") | |
| # shell: Rscript {0} | |
| - name: Upload check results ⬆️ | |
| if: failure() | |
| uses: actions/upload-artifact@master | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| path: check | |
| - name: Show testthat output 📖 | |
| if: always() | |
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Push to DockerHub 📦 | |
| if: needs.versions.outputs.dockerise == 'true' && !contains(github.event.head_commit.message, 'skip-docker') | |
| uses: docker/build-push-action@v1 | |
| with: | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| repository: mixomicsteam/mixomics | |
| tags: ${{ needs.versions.outputs.docker_tag }} | |
| build_args: BIOC_VERSION=${{ needs.versions.outputs.bioc }} | |
| - name: Test coverage 🔍 | |
| # if: (matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release') | |
| # the commands between 'set +e' and 'set -e' are run without throwing any error | |
| run: | | |
| set +e | |
| Rscript -e "covr::codecov(type = c('tests', 'examples'))" | |
| set -e | |
| - name: Notify Slack 📣 | |
| uses: 8398a7/action-slack@v3 | |
| with: | |
| status: ${{ job.status }} | |
| fields: repo,message,commit,author,action,eventName,ref,workflow,job,took # selectable (default: repo,message) | |
| env: | |
| SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }} # set in rep's setting >> secrets |