From: François Michonneau <francois.michonneau@gmail.com>
Date: Fri, 8 Jan 2021 16:18:15 +0000 (+0100)
Subject: GitHub Actions: cache required R packages (#534)
X-Git-Url: https://git.arvados.org/rnaseq-cwl-training.git/commitdiff_plain/2cd3c9c1a2499ac7b7c3b9a80995eb643b917960

GitHub Actions: cache required R packages (#534)
---

diff --git a/.github/workflows/template.yml b/.github/workflows/template.yml
index 7e86e02..84015e4 100644
--- a/.github/workflows/template.yml
+++ b/.github/workflows/template.yml
@@ -96,7 +96,7 @@ jobs:
       - name: Install needed packages
         if: steps.check-rmd.outputs.count != 0
         run: |
-          install.packages(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'))
+          install.packages(setdiff(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'), rownames(installed.packages())))
         shell: Rscript {0}
 
       - name: Query dependencies
diff --git a/.github/workflows/website.yml b/.github/workflows/website.yml
index b67e07e..59e3235 100644
--- a/.github/workflows/website.yml
+++ b/.github/workflows/website.yml
@@ -51,10 +51,18 @@ jobs:
         with:
           r-version: 'release'
 
+      - name: Cache R packages
+        if: steps.check-rmd.outputs.count != 0
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
       - name: Install needed packages
         if: steps.check-rmd.outputs.count != 0
         run: |
-          install.packages(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'))
+          install.packages(setdiff(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'), rownames(installed.packages()))
         shell: Rscript {0}
 
       - name: Query dependencies
@@ -67,13 +75,6 @@ jobs:
           writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
 
-      - name: Cache R packages
-        if: steps.check-rmd.outputs.count != 0
-        uses: actions/cache@v1
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
 
       - name: Install system dependencies for R packages
         if: steps.check-rmd.outputs.count != 0