Update r.yml

Fixing missing dependencies
PiotrTymoszuk · Dec 7, 2023 · 63c9639 · 63c9639
1 parent 531b95d
commit 63c9639
Showing 1 changed file with 9 additions and 3 deletions.
diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml
@@ -23,7 +23,8 @@ jobs:
     strategy:
       matrix:
         r-version: ['4.1.1']
-
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}  
     steps:
       - uses: actions/checkout@v3
       - name: Set up R ${{ matrix.r-version }}
@@ -32,8 +33,13 @@ jobs:
           r-version: ${{ matrix.r-version }}
       - name: Install dependencies
         run: |
-          install.packages(c("remotes", "rcmdcheck"))
-          remotes::install_deps(dependencies = TRUE)
+          install.packages(c("remotes", "rcmdcheck", "BiocManager"))
+          BiocManager::install("limma")
+          remotes::install_github("cran/rcompanion")
+          remotes::install_github("cran/DescTools")
+          remotes::install_github("PiotrTymoszuk/somKernels")
+          remotes::install_github("PiotrTymoszuk/clustTools")
+          remotes::install_deps(dependencies = TRUE)          
         shell: Rscript {0}
       - name: Check
         run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")