From 9bb234a4298529a17553c6c64e1ac21dd80f5da0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alba=20Refoyo=20Mart=C3=ADnez?=
 <44649699+albarema@users.noreply.github.com>
Date: Fri, 20 Dec 2024 13:12:44 +0100
Subject: [PATCH] test Makevars c++14

---
 .github/workflows/render_page.yml | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

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 }}