test new staging workflow.

.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.