diff --git a/.github/workflows/render_page.yml b/.github/workflows/render_page.yml index 0d52d08..f8aab8a 100644 --- a/.github/workflows/render_page.yml +++ b/.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 }}