use lower case matrix var #22
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| name: Release R CMD check and build site | ||
| on: | ||
| push: | ||
| branches: | ||
| - RELEASE_3_19 | ||
| workflow_dispatch: | ||
| env: | ||
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest | ||
| BIOC_VERSION: RELEASE_3_19 | ||
| jobs: | ||
| checkRelease: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
|
Check failure on line 19 in .github/workflows/build_site.yml
|
||
| bioc_version: [RELEASE_3_19] # Define versions as matrix variables | ||
| container: bioconductor/bioconductor_docker:${{ matrix.bioc_version }} | ||
| steps: | ||
| - name: Checkout Repository | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| ref: ${{ env.BIOC_VERSION }} | ||
| - name: Query dependencies | ||
| run: | | ||
| BiocManager::install("remotes") | ||
| 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: ${{ runner.os }}-r-${{ env.BIOC_VERSION }}-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ runner.os }}-r-${{ env.BIOC_VERSION }}- | ||
| - name: Install Dependencies | ||
| run: | | ||
| remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories()) | ||
| BiocManager::install(c("rcmdcheck", "pkgdown", "covr"), ask = FALSE, update = TRUE) | ||
| shell: Rscript {0} | ||
| - name: System dependencies | ||
| run: | | ||
| pip install ghp-import | ||
| - 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, | ||
| clean = FALSE, | ||
| install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") | ||
| ) | ||
| shell: Rscript {0} | ||
| - name: Build pkgdown | ||
| run: | | ||
| PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site()' | ||
| - name: Install deploy dependencies | ||
| run: | | ||
| apt-get update | ||
| apt-get -y install rsync | ||
| - name: Deploy 🚀 | ||
| uses: JamesIves/github-pages-deploy-action@v4 | ||
| with: | ||
| TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| BRANCH: gh-pages # The branch the action should deploy to. | ||
| FOLDER: docs # The folder the action should deploy. | ||
