diff --git a/.github/workflows/dev_check.yaml b/.github/workflows/dev_check.yaml index aeb8403..ff8377f 100644 --- a/.github/workflows/dev_check.yaml +++ b/.github/workflows/dev_check.yaml @@ -10,9 +10,14 @@ jobs: platform: [ubuntu-latest] runs-on: ${{ matrix.platform }} 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 code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: ref: 'devel' @@ -25,42 +30,20 @@ jobs: - name: Cache R packages if: runner.os != 'Windows' - uses: actions/cache@v3 + uses: actions/cache@v4 with: path: /usr/local/lib/R/site-library key: ${{ runner.os }}-r-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-r-1- - - # This lets us augment with additional dependencies - - name: Install system dependencies - if: runner.os == 'Linux' - env: - RHUB_PLATFORM: linux-x86_64-ubuntu-gcc - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - run: | - Rscript -e "remotes::install_github('r-hub/sysreqs')" - sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") - sudo -s eval "$sysreqs" + restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r- - name: Install dependencies - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} run: | - options(repos = c(CRAN = "https://cran.r-project.org")) BiocManager::repositories() remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories()) remotes::install_cran("rcmdcheck") shell: Rscript {0} - - name: Check - env: - _R_CHECK_CRAN_INCOMING_REMOTE_: false - run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check") - shell: Rscript {0} - - name: Build pkgdown - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} run: | PATH=$PATH:$HOME/bin/ Rscript -e 'BiocManager::install(c("knitr", "rmarkdown", "pkgdown")); pkgdown::build_site(".")' # deploy needs rsync? Seems so. @@ -69,7 +52,7 @@ jobs: apt-get update apt-get -y install rsync - name: Deploy 🚀 - uses: JamesIves/github-pages-deploy-action@releases/v4 + uses: JamesIves/github-pages-deploy-action@v4 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} BRANCH: gh-pages # The branch the action should deploy to.