test Makevars c++14

.github/workflows/render_page.yml

@@ -48,19 +48,15 @@ jobs:
 
 #      - name: Install R Dependencies
 #        uses: r-lib/actions/setup-renv@v2
-      - name: Set C++14 flags for renv Makevars
-        run: |
-          # Ensure renv library exists and set the correct Makevars for renv
-          RENV_MAKEVARS_PATH=$(Rscript -e 'cat(renv::paths$library())')/Makevars
-          mkdir -p "$(dirname "$RENV_MAKEVARS_PATH")"
-          echo "CXX=g++-11" >> "$RENV_MAKEVARS_PATH"
-          echo "CXXFLAGS=-std=c++14" >> "$RENV_MAKEVARS_PATH"
 
       - name: installations
         run: |
+          echo "CXX=g++-11" >> $(Rscript -e 'cat(renv::paths$library())')/Makevars && \
+          echo "CXXFLAGS=-std=c++14" >> $(Rscript -e 'cat(renv::paths$library())')/Makevars && \
           R -e 'install.packages(c("devtools","BiocManager", "tidyverse", "RColorBrewer", "pheatmap", "ggrepel", "cowplot"))' 
+          R -e 'BiocManager::install("fgsea")
           R -e 'devtools::install_github("stephenturner/annotables")'
-          R -e 'BiocManager::install(c("DESeq2", "clusterProfiler", "fgsea", "DOSE", "org.Hs.eg.db", "pathview", "DEGreport", "tximport", "AnnotationHub", "ensembldb","apeglm","ggnewscale"))'
+          R -e 'BiocManager::install(c("DESeq2", "clusterProfiler", "DOSE", "org.Hs.eg.db", "pathview", "DEGreport", "tximport", "AnnotationHub", "ensembldb","apeglm","ggnewscale"))'
           R -e 'install.packages(c("rmarkdown", "markdown", "knitr"))' 
         env:
           GITHUB_PAT: ${{ secrets.TOKEN }}