fix and simplify R-CMD-check-bioc workflow

Author: hpages

.github/workflows/check-bioc.yml

@@ -35,9 +35,6 @@ name: R-CMD-check-bioc
 ## "/nocache" in the commit message.
 env:
   has_testthat: 'true'
-  run_covr: 'false'
-  run_pkgdown: 'false'
-  has_RUnit: 'false'
   cache-version: 'cache-v1'
   run_docker: 'false'
 
@@ -52,9 +49,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.5', bioc: '3.21', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
-          - { os: macOS-latest, r: '4.5', bioc: '3.21'}
-          - { os: windows-latest, r: '4.5', bioc: '3.21'}
+          - { os: ubuntu-latest, r: '4.5', bioc: '3.22', cont: "bioconductor/bioconductor_docker:RELEASE_3_22", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
+          - { os: macOS-latest, r: '4.5', bioc: '3.22'}
+          - { os: windows-latest, r: '4.5', bioc: '3.22'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -100,46 +97,13 @@ jobs:
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
         shell: Rscript {0}
 
-      - name: Restore R package cache
-        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v3
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
-
-      - name: Cache R packages on Linux
-        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
-        uses: actions/cache@v3
-        with:
-          path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
-
-      # - name: Install Linux system dependencies
-      #   if: runner.os == 'Linux'
-      #   run: |
-      #     sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
-      #     echo $sysreqs
-      #     sudo -s eval "$sysreqs"
-
       - name: Install macOS system dependencies
         if: matrix.config.os == 'macOS-latest'
         run: |
           ## Enable installing XML from source if needed
           brew install libxml2
           echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
 
-          ## Required to install magick as noted at
-          ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
-          brew install imagemagick@6
-
-          ## For textshaping, required by ragg, and required by pkgdown
-          brew install harfbuzz fribidi
-
-          ## For installing usethis's dependency gert
-          brew install libgit2
-
           ## Required for tcltk
           brew install xquartz --cask
 
@@ -186,25 +150,6 @@ jobs:
           remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
         shell: Rscript {0}
 
-      - name: Install BiocGenerics
-        if:  env.has_RUnit == 'true'
-        run: |
-          ## Install BiocGenerics
-          BiocManager::install("BiocGenerics")
-        shell: Rscript {0}
-
-      - name: Install covr
-        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
-        run: |
-          remotes::install_cran("covr")
-        shell: Rscript {0}
-
-      - name: Install pkgdown
-        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
-        run: |
-          remotes::install_github("r-lib/pkgdown")
-        shell: Rscript {0}
-
       - name: Session info
         run: |
           options(width = 100)
@@ -231,108 +176,3 @@ jobs:
         if:  env.has_testthat == 'true'
         run: find . -name testthat.Rout -exec cat '{}' ';'
 
-      - name: Run RUnit tests
-        if:  env.has_RUnit == 'true'
-        run: |
-          BiocGenerics:::testPackage()
-        shell: Rscript {0}
-
-      - name: Run BiocCheck
-        env:
-          DISPLAY: 99.0
-        run: |
-          BiocCheck::BiocCheck(
-              dir('check', 'tar.gz$', full.names = TRUE),
-              `quit-with-status` = TRUE,
-              `no-check-R-ver` = TRUE,
-              `no-check-bioc-help` = TRUE
-          )
-        shell: Rscript {0}
-
-      - name: Test coverage
-        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
-        run: |
-          covr::codecov(coverage = covr::package_coverage(type = "all"))
-        shell: Rscript {0}
-
-      - name: Install package
-        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
-        run: R CMD INSTALL .
-
-      - name: Build pkgdown site
-        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
-        shell: Rscript {0}
-        ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
-        ## at least one locally before this will work. This creates the gh-pages
-        ## branch (erasing anything you haven't version controlled!) and
-        ## makes the git history recognizable by pkgdown.
-
-      - name: Install deploy dependencies
-        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
-        run: |
-          apt-get update && apt-get -y install rsync
-
-      - name: Deploy pkgdown site to GitHub pages 🚀
-        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
-        uses: JamesIves/github-pages-deploy-action@releases/v4
-        with:
-          clean: false
-          branch: gh-pages
-          folder: docs
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@master
-        with:
-          name: ${{ runner.os }}-biocversion-devel-r-devel-results
-          path: check
-
-
-  ## Code adapted from
-  ## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92
-  docker-build-and-push:
-    runs-on: ubuntu-latest
-    needs: build-check
-    steps:
-      - name: Checkout Repository
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
-        uses: actions/checkout@v3
-
-      - name: Register repo name
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
-        id: reg_repo_name
-        run: |
-          echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
-
-      - name: Set up QEMU
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
-        uses: docker/setup-qemu-action@v2
-
-      - name: Set up Docker Buildx
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
-        uses: docker/setup-buildx-action@v2
-
-      - name: Login to Docker Hub
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
-        uses: docker/login-action@v2
-        with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
-      ## Note that DOCKERHUB_TOKEN is really a token for your dockerhub
-      ## account, not your actual dockerhub account password. You can get it
-      ## from https://hub.docker.com/settings/security.
-      ## Check https://github.com/docker/build-push-action/tree/v4.0.0
-      ## for more details.
-      ## Alternatively, try checking
-      ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html.
-
-      - name: Build and Push Docker
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()"
-        uses: docker/build-push-action@v4
-        with:
-          context: .
-          push: true
-          tags: >
-            ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest,
-            ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel