docs: update pkgdown.yaml

.github/workflows/pkgdown.yaml

@@ -1,5 +1,9 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+# By Stefanie Peschel: Adapted to install Bioconductor packages in advance
+
+name: pkgdown.yaml
+
 on:
   push:
     branches: [main, master]
@@ -9,8 +13,6 @@ on:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown.yaml
-
 permissions: read-all
 
 jobs:
@@ -34,9 +36,14 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: any::pkgdown, any::BiocManager, local::.
           needs: website
 
+      - name: Install Bioconductor dependencies
+        run: |
+          Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")'
+          Rscript -e 'BiocManager::install(c("metagenomeSeq", "Biobase", "phyloseq"))'
+
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}