Updated versions of BioC and actions in the CHECK workflow.

Just skip non-Linux builds, it's too much effort. The BBS covers them
anyway and we just need the CI to protect against obvious problems.

Author: LTLA

.github/workflows/check-bioc.yml

@@ -22,6 +22,8 @@
 
 on:
   push:
+    branch:
+      - 'devel'
   pull_request:
 
 name: R-CMD-check-bioc
@@ -52,9 +54,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'devel', bioc: '3.20', cont: "bioconductor/bioconductor_docker:devel-amd64", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: 'devel', bioc: '3.20'}
-          - { os: windows-latest, r: 'devel', bioc: '3.20'}
+          - { os: ubuntu-latest, r: 'devel', bioc: '3.21', cont: "bioconductor/bioconductor_docker:devel" } 
+          #- { os: macOS-latest, r: 'devel', bioc: '3.21'}
+          #- { os: windows-latest, r: 'devel', bioc: '3.21'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -79,7 +81,7 @@ 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@v4
 
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
@@ -102,15 +104,15 @@ jobs:
 
       - name: Restore R package cache
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         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
+        uses: actions/cache@v4
         with:
           path: /home/runner/work/_temp/Library
           key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
@@ -146,6 +148,9 @@ jobs:
           ## Required for terra
           brew install gdal
 
+          ## Required for HDF5
+          brew install openssl
+
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
         run: |