Fixing workflows

neuroimaginador · Apr 25, 2023 · f96fb5b · f96fb5b
1 parent 5c3a278
commit f96fb5b
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Showing 4 changed files with 17 additions and 11 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -29,7 +29,7 @@ jobs:
           - {os: macOS-latest,   r: 'release', bioc: '3.17'}
           - {os: windows-latest, r: 'release', bioc: '3.17'}
           # - {os: ubuntu-16.04, bioc: '3.13', cont: "bioconductor/bioconductor_docker:devel",   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest", http-user-agent: "R/4.0.0 (ubuntu-16.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-          - {os: ubuntu-20.04,   r: 'release', bioc: '3.17', rspm: "https://packagemanager.rstudio.com/all/__linux__/bionic/latest"}
+          - {os: ubuntu-20.04,   r: 'release', bioc: '3.17', rspm: "https://packagemanager.rstudio.com/all/__linux__/focal/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -44,7 +44,7 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -76,8 +76,10 @@ jobs:
           echo $rversion
 
           ## Save the info for the next job
-          echo "::set-output name=rversion::${rversion}"
-          echo "::set-output name=biocversionnum::${biocversionnum}"
+          echo "rversion=${rversion}" >> $GITHUB_OUTPUT
+          echo "biocversionnum=${biocversionnum}" >> $GITHUB_OUTPUT
+          # echo "::set-output name=rversion::${rversion}"
+          # echo "::set-output name=biocversionnum::${biocversionnum}"
         shell:
           bash {0}
 

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -23,7 +23,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -55,8 +55,10 @@ jobs:
           echo $rversion
 
           ## Save the info for the next job
-          echo "::set-output name=rversion::${rversion}"
-          echo "::set-output name=biocversionnum::${biocversionnum}"
+          echo "rversion=${rversion}" >> $GITHUB_OUTPUT
+          echo "biocversionnum=${biocversionnum}" >> $GITHUB_OUTPUT
+          # echo "::set-output name=rversion::${rversion}"
+          # echo "::set-output name=biocversionnum::${biocversionnum}"
         shell:
           bash {0}
 

diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -39,7 +39,7 @@ jobs:
       - uses: r-lib/actions/pr-fetch@v1
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
       - name: Install dependencies
         run: Rscript -e 'install.packages("styler")'
       - name: Style

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -27,7 +27,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -59,8 +59,10 @@ jobs:
           echo $rversion
 
           ## Save the info for the next job
-          echo "::set-output name=rversion::${rversion}"
-          echo "::set-output name=biocversionnum::${biocversionnum}"
+          echo "rversion=${rversion}" >> $GITHUB_OUTPUT
+          echo "biocversionnum=${biocversionnum}" >> $GITHUB_OUTPUT
+          # echo "::set-output name=rversion::${rversion}"
+          # echo "::set-output name=biocversionnum::${biocversionnum}"
         shell:
           bash {0}