ci: restore R dependencies setup in workflow for improved package management

Author: pwwang

.github/workflows/main.yml

@@ -40,39 +40,24 @@ jobs:
           r-version: ${{ matrix.r }}
           Ncpus: '2L'
           use-public-rspm: true
-          # Latest CRAN with latest gsl (2.1-9) causing error:
-          # ! Could not solve package dependencies:
-          # * deps::.: Can't install dependency BorchLab/[email protected]
-          # * BorchLab/[email protected]: Can't install dependency evmix
-          # * evmix: Can't install dependency gsl
-          # * gsl: Needs R >= 4.5.0
-          cran: https://packagemanager.posit.co/cran/2024-10-01
 
       - name: Install libglpk40 for igraph
         run: |
           sudo apt-get update -y && sudo apt-get install -y libglpk40
         shell: bash
 
-      # -- This takes too long to run
-      # - name: Setup R dependencies
-      #   uses: r-lib/actions/setup-r-dependencies@v2
-      #   with:
-      #     cache-version: 2
-      #     extra-packages: |
-      #       any::devtools, any::pkgdown, any::plotthis, any::ComplexHeatmap,
-      #       any::Seurat, any::concaveman, any::gridGraphics, any::ggVennDiagram,
-      #       any::clustree, any::ggwordcloud, any::ggalluvial, any::ggpubr, any::callr,
-      #       any::ggforce, any::ggraph, any::ggridges, any::hexbin, any::igraph,
-      #       any::scattermore, any::ggupset, any::iNEXT, any::metap, any::tidyprompt,
-      #       any::terra, any::GiottoClass, any::GiottoData, any::proxyC, any::metR,
-      #       any::hdf5r
-      - name: Install pak
-        run: |
-          install.packages("pak")
-
-      - name: Install R package dependencies
-        run: |
-          pak::pkg_install(".", dependencies = TRUE, ask = FALSE)
+      - name: Setup R dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 2
+          extra-packages: |
+            any::devtools, any::pkgdown, any::plotthis, any::ComplexHeatmap,
+            any::Seurat, any::concaveman, any::gridGraphics, any::ggVennDiagram,
+            any::clustree, any::ggwordcloud, any::ggalluvial, any::ggpubr, any::callr,
+            any::ggforce, any::ggraph, any::ggridges, any::hexbin, any::igraph,
+            any::scattermore, any::ggupset, any::iNEXT, any::metap, any::tidyprompt,
+            any::terra, any::GiottoClass, any::GiottoData, any::proxyC, any::metR,
+            any::hdf5r
 
       - uses: r-lib/actions/check-r-package@v2
         env: