Fix CI (#457)

* install additional libraries for mac os runner

* switch bioc mirror

* switch mirror

* manually fix versions

* try without version map

* try removing workarounds

Author: rcannood

.github/workflows/R-CMD-check-bioc.yaml

@@ -30,7 +30,7 @@ jobs:
         - { os: macOS-latest,   bioc-version: 'devel', bioc-mirror: 'https://bioconductor.posit.co/', cache: 1 }
         - { os: macOS-15-intel, bioc-version: 'devel', bioc-mirror: 'https://bioconductor.posit.co/', cache: 2 }
         - { os: ubuntu-latest,  bioc-version: 'devel', bioc-mirror: 'https://bioconductor.posit.co/', cache: 1 }
-        - { os: ubuntu-latest,  bioc-version: 'release', bioc-mirror: 'https://packagemanager.posit.co/bioconductor', cache: 1 }
+        - { os: ubuntu-latest,  bioc-version: 'release', bioc-mirror: 'https://bioconductor.posit.co/', cache: 1 }
 
     steps:
 
@@ -48,53 +48,21 @@ jobs:
           sudo apt-get update
           sudo apt-get -y install hdf5-tools libsz2 libaec-dev
 
-      ## Workaround: data.table (indirect dep via Seurat) fails to compile
-      ## on macOS ARM because libintl.h is missing.
+      ## Install missing libraries for macOS ARM (macOS-latest)
       - name: Install macOS dependencies
-        if: runner.os == 'macOS'
+        if: matrix.config.os == 'macOS-latest'
         run: |
-          brew install gettext
+          brew install gettext openssl
           mkdir -p ~/.R
-          echo "CPPFLAGS += -I$(brew --prefix gettext)/include" >> ~/.R/Makevars
-          echo "LDFLAGS += -L$(brew --prefix gettext)/lib" >> ~/.R/Makevars
+          echo "CPPFLAGS += -I$(brew --prefix gettext)/include -I$(brew --prefix openssl)/include" >> ~/.R/Makevars
+          echo "LDFLAGS += -L$(brew --prefix gettext)/lib -L$(brew --prefix openssl)/lib" >> ~/.R/Makevars
 
       - name: Setup R and Bioconductor
-        # todo: remove this workaround line once it is working for windows and/or mac os x
-        if: matrix.config.os != 'windows-latest' && matrix.config.os != 'macOS-latest'
-        uses: grimbough/bioc-actions/setup-bioc@v1
+        uses: rcannood/bioc-actions/setup-bioc@remove-version-map
         with:
           bioc-version: ${{ matrix.config.bioc-version }}
           bioc-mirror: ${{ matrix.config.bioc-mirror }}
 
-      ## windows-latest and macOS-latest (ARM) hit a bug in R-devel (commit
-      ## dd03406, 2026-04-09) where BiocManager::install() crashes via
-      ## old.packages(type="both") -> .available.both() -> subscript out of
-      ## bounds. Work around by setting up R manually and calling
-      ## BiocManager::install(update=FALSE) to skip the old.packages() call.
-      - name: Setup R (Windows/macOS-ARM devel)
-        if: matrix.config.os == 'windows-latest' || matrix.config.os == 'macOS-latest'
-        uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: devel
-          rtools-version: 45
-          use-public-rspm: true
-
-      - name: Setup Bioconductor (Windows/macOS-ARM devel)
-        if: matrix.config.os == 'windows-latest' || matrix.config.os == 'macOS-latest'
-        shell: Rscript {0}
-        run: |
-          download.file(
-            'https://bioconductor.org/checkResults/devel/bioc-LATEST/Renviron.bioc',
-            destfile = '~/.Renviron', mode = 'wb')
-          write(
-            'options(BioC_mirror = "${{ matrix.config.bioc-mirror }}")',
-            file = '~/.Rprofile', append = TRUE)
-          install.packages(c("BiocManager", "remotes"), quiet = TRUE)
-          ## update=FALSE avoids calling old.packages(type="both") which
-          ## triggers the R-devel bug in .available.both() (commit dd03406)
-          BiocManager::install(version = "3.23", ask = FALSE, update = FALSE)
-          cat("R_BIOC_VERSION=3.23\n", file = Sys.getenv("GITHUB_ENV"), append = TRUE)
-
       - name: Install pandoc
         uses: r-lib/actions/setup-pandoc@v2