Updated the BioC check action to the latest release.

We switch to gypsum caching as we're no longer pulling from ExperimentHub. We
also greatly simplify the builds for development by no longer checking on Macs.

.github/workflows/check-bioc.yml

@@ -1,74 +1,33 @@
-on: [push]
+on:
+  push:
+    branches:
+      - master
+  pull_request:
 
 name: R-CMD-check
 
 jobs:
   build-check:
-    runs-on: ${{ matrix.config.os }}
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-    container: ${{ matrix.config.cont }}
-    ## Environment variables unique to this job.
-
-    strategy:
-      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__/focal/latest" }
-          - { os: macOS-latest, r: '4.3', bioc: '3.18'}
-          ## Check https://github.com/r-lib/actions/tree/master/examples
-          ## for examples using the http-user-agent
-    env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
-      NOT_CRAN: true
-      TZ: UTC
-      GITHUB_PAT: ${{ secrets.BEACHMAT_PAT }}
+    runs-on: ubuntu-latest
+    container: bioconductor/bioconductor_docker:devel
 
     steps:
     - name: Checkout Repository
-      uses: actions/checkout@v3
-
-    ## For Macs - none of this is required for the Linux containers.
-    - 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: ${{ matrix.config.http-user-agent }}
-
-    - name: Setup pandoc from r-lib
-      if: runner.os != 'Linux'
-      uses: r-lib/actions/setup-pandoc@v2
-
-    - name: Install BiocManager with the right version
-      if: runner.os != 'Linux'
-      run: |
-        install.packages("BiocManager")
-        BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
-      shell: Rscript {0}
-
-    - name: Install remotes to get beachmat
-      if: runner.os != 'Linux'
-      run: |
-        BiocManager::install("remotes")
-      shell: Rscript {0}
-
-    - 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
+      uses: actions/checkout@v4
 
     - name: Determine the package directory
       run: R --no-echo -e "cat(paste0('R_PKG_DIR=', .libPaths()[1], '\n'))" >> $GITHUB_ENV
 
     - name: Restore the package directory
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ env.R_PKG_DIR }}
-        key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/dependencies.rds') }}
-        restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-
+        key: installed-packages
+
+    - name: Install the very latest assorthead
+      run: |
+        git clone https://github.com/LTLA/assorthead
+        R CMD INSTALL assorthead
 
     - name: Install R package dependencies
       shell: Rscript {0}
@@ -77,24 +36,22 @@ jobs:
         installs <- unlist(strsplit(deets[,c("Imports", "Depends", "Suggests", "LinkingTo")], ",\\s+"), use.names=FALSE)
         BiocManager::install(installs)
         BiocManager::install("BiocCheck")
-        saveRDS(file=".github/dependencies.rds", installs)
+        BiocManager::install("BiocSingular")
 
-    - name: Determine the Hub directories
-      run: R --no-echo -e "cat(paste0('EXPERIMENT_HUB_DIR=', suppressMessages(ExperimentHub::getExperimentHubOption('CACHE')), '\nANNOTATION_HUB_DIR=', suppressMessages(AnnotationHub::getAnnotationHubOption('CACHE')), '\n'))" >> $GITHUB_ENV
+    - name: Determine the data directories
+      run: R --no-echo -e "cat(paste0('GYPSUM_DIR=', suppressMessages(gypsum::cacheDirectory()), '\nANNOTATION_HUB_DIR=', suppressMessages(AnnotationHub::getAnnotationHubOption('CACHE')), '\n'))" >> $GITHUB_ENV
 
-    - name: Restore the ExperimentHub directory
-      uses: actions/cache@v3
+    - name: Restore the gypsum directory
+      uses: actions/cache@v4
       with:
-        path: ${{ env.EXPERIMENT_HUB_DIR }}
-        key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-ExperimentHub-${{ hashFiles('vignettes/*.Rmd') }}
-        restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-ExperimentHub-
+        path: ${{ env.GYPSUM_DIR }}
+        key: gypsum-cache
 
     - name: Restore the AnnotationHub directory
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ env.ANNOTATION_HUB_DIR }}
-        key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-AnnotationHub-${{ hashFiles('vignettes/*.Rmd') }}
-        restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-AnnotationHub-
+        key: AnnotationHub-cache
 
     - name: Run CMD build
       run: |