version bump 2.19.2 #59
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| name: Devel R CMD check and Docker | |
| on: | |
| push: | |
| paths: | |
| - 'DESCRIPTION' | |
| - '**.yml' | |
| branches: | |
| - devel | |
| jobs: | |
| check: | |
| runs-on: ubuntu-22.04 | |
| container: bioconductor/bioconductor_docker:devel | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v3 | |
| - name: Query dependencies | |
| run: | | |
| BiocManager::install(c("covr", "BiocCheck")) | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' | |
| uses: actions/cache@v3 | |
| with: | |
| path: /usr/local/lib/R/site-library | |
| key: ${{ runner.os }}-r-1-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-r-1- | |
| - name: Install Dependencies | |
| run: | | |
| remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| BiocManager::install(ask = FALSE, update = TRUE) | |
| shell: Rscript {0} | |
| - name: Check Package | |
| id: rcmdcheck | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Test coverage | |
| run: covr::codecov(quiet = FALSE) | |
| shell: Rscript {0} | |
| - name: Run BiocCheck | |
| id: bioccheck | |
| run: | | |
| BiocCheck::BiocCheck( | |
| dir('check', 'tar.gz$', full.names = TRUE), | |
| `quit-with-status` = TRUE, `no-check-bioc-help` = TRUE | |
| ) | |
| shell: Rscript {0} | |
| dock: | |
| runs-on: ubuntu-22.04 | |
| needs: check | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v3 | |
| - name: Register repo name | |
| id: reg_repo_name | |
| run: | | |
| echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV | |
| - name: Login to Docker Hub | |
| uses: docker/login-action@v2 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Build and Push Docker | |
| if: ${{ success() }} | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| file: ./inst/docker/pkg/Dockerfile | |
| push: true | |
| tags: > | |
| ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest, | |
| ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel |