Revert "Update check-bioc.yml"

stemangiola · stemangiola · commit 4710a0e81608 · 2023-08-29T10:15:13.000+10:00
This reverts commit 5aeac41.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -39,7 +39,6 @@ env:
   run_pkgdown: 'true'
   has_RUnit: 'false'
   cache-version: 'cache-v1'
-  run_docker: 'false'
 
 jobs:
   build-check:
@@ -52,11 +51,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
-          - { os: macOS-latest, r: '4.3', bioc: '3.18'}
-          - { os: windows-latest, r: '4.3', bioc: '3.18'}
-          ## Check https://github.com/r-lib/actions/tree/master/examples
-          ## for examples using the http-user-agent
+          - { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: '4.2', bioc: '3.16'}
+          - { os: windows-latest, r: '4.2', bioc: '3.16'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -79,15 +76,14 @@ jobs:
       ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
       ## If they update their steps, we will also need to update ours.
       - name: Checkout Repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v2
 
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
         if: runner.os != 'Linux'
         uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
 
       ## pandoc is already included in the Bioconductor docker images
       - name: Setup pandoc from r-lib
@@ -100,28 +96,28 @@ jobs:
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
         shell: Rscript {0}
 
-      - name: Restore R package cache
+      - name: Cache R packages
         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-4.3-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.3-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
 
       - 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-4.3-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.3-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
 
-      # - 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 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'
@@ -139,9 +135,10 @@ jobs:
 
           ## For installing usethis's dependency gert
           brew install libgit2
-
-          ## Required for tcltk
-          brew install xquartz --cask
+          
+          ## To fix x11/cairo error with tidyHeatmap/Complexheatmap here https://github.com/stemangiola/tidybulk/runs/1388237421?check_suite_focus=true#step:14:2134
+          ## Suggested here https://stackoverflow.com/questions/63648591/how-to-install-x11-before-testing-with-github-actions-for-macos
+          brew install --cask xquartz 
 
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
@@ -157,7 +154,7 @@ jobs:
 
       - name: Set BiocVersion
         run: |
-          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
+          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
         shell: Rscript {0}
 
       - name: Install dependencies pass 1
@@ -169,21 +166,22 @@ jobs:
           ## https://github.com/r-lib/remotes/issues/296
           ## Ideally, all dependencies should get installed in the first pass.
 
-          ## For running the checks
-          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
-          install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories())
-
           ## Pass #1 at installing dependencies
           message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
-          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
         continue-on-error: true
         shell: Rscript {0}
 
       - name: Install dependencies pass 2
         run: |
           ## Pass #2 at installing dependencies
           message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
-          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
+          
+          ## For running the checks
+          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
+          remotes::install_cran("rcmdcheck")
+          BiocManager::install("BiocCheck")
         shell: Rscript {0}
 
       - name: Install BiocGenerics
@@ -194,15 +192,15 @@ jobs:
         shell: Rscript {0}
 
       - name: Install covr
-        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/master' && 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'
+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
-          remotes::install_github("r-lib/pkgdown")
+          remotes::install_cran("pkgdown")
         shell: Rscript {0}
 
       - name: Session info
@@ -215,12 +213,10 @@ jobs:
       - name: Run CMD check
         env:
           _R_CHECK_CRAN_INCOMING_: false
-          DISPLAY: 99.0
         run: |
-          options(crayon.enabled = TRUE)
           rcmdcheck::rcmdcheck(
-              args = c("--no-manual", "--no-vignettes", "--timings"),
-              build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
+              args = c("--no-build-vignettes", "--no-manual", "--timings"),
+              build_args = c("--no-manual", "--no-resave-data"),
               error_on = "warning",
               check_dir = "check"
           )
@@ -238,101 +234,45 @@ jobs:
         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
+              `no-check-bioc-help` = TRUE,
+              `no-check-library-calls` = TRUE,
+              `no-check-coding-practices` = TRUE
           )
         shell: Rscript {0}
 
       - name: Test coverage
-        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
         run: |
           covr::codecov()
         shell: Rscript {0}
 
       - name: Install package
-        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/master' && 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}
+      - name: Deploy package
+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: |
+          ## Temporary workaround for https://github.com/actions/checkout/issues/766
+          git config --global --add safe.directory "$GITHUB_WORKSPACE"
+          
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
+        shell: bash {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
+        uses: actions/upload-artifact@v3
         with:
-          name: ${{ runner.os }}-biocversion-devel-r-4.3-results
+          name: ${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-results
           path: check
-
-
-  ## Code adapted from
-  ## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92
-  docker-build-and-push:
-    runs-on: ubuntu-latest
-    needs: build-check
-    steps:
-      - name: Checkout Repository
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
-        uses: actions/checkout@v3
-
-      - name: Register repo name
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
-        id: reg_repo_name
-        run: |
-          echo CONT_IMG_NAME=$(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
