test remotes fgsea

.github/workflows/render_page.yml

@@ -38,11 +38,6 @@ jobs:
       - name: Install R and setup-renv
         uses: r-lib/actions/setup-r@v2
 
-      - name: Set up renv
-        uses: r-lib/actions/setup-renv@v2
-        with:
-          profile: 'ci' # Use the 'ci' profile
-
 #      - name: Check renv paths
 #        run: |
 #          Rscript -e 'cat("Project Library:", renv::paths$library(), "\n")'
@@ -53,23 +48,16 @@ jobs:
 
 #      - name: Install R Dependencies
 #        uses: r-lib/actions/setup-renv@v2
-
-      - name: Extra packages
+          
+      - name: installations
         run: |
-          R -e 'install.packages(c("devtools", "rmarkdown", "markdown", "knitr"))' 
+          R -e 'install.packages(c("devtools", "remotes", "BiocManager", "tidyverse", "RColorBrewer", "pheatmap", "ggrepel", "cowplot"))' 
           R -e 'devtools::install_github("stephenturner/annotables")'
+          R -e 'remotes::install_github("ctlab/fgsea")'
+          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 }}
-
-#      - name: installations
-#        run: |
-#          R -e 'install.packages(c("devtools"))' 
-#          R -e 'install.packages(c("devtools", "BiocManager", "tidyverse", "RColorBrewer", "pheatmap", "ggrepel", "cowplot"))' 
-#          R -e 'devtools::install_github("stephenturner/annotables")'
-#          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 }}
 
       - name: Pull Notebooks folder content
         if: runner.os == 'Linux'