adapt to new BIOC versions and use always variables

gagneurlab · Apr 15, 2024 · c87e322 · c87e322
1 parent 72066ed
commit c87e322
Showing 1 changed file with 11 additions and 10 deletions.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -52,10 +52,11 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: ubuntu-latest, r: 'next', bioc: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.2', bioc: '3.16'}
-          - { os: windows-latest, r: '4.2', bioc: '3.16'}
+          # This needs to be updated after each Bioconductor release. Please make sure we have the matching R and Bioc versions in it. 
+          - { os: ubuntu-latest,  r: '4.3',  bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: ubuntu-latest,  r: 'next', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel",        rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest,   r: '4.3',  bioc: '3.18'}
+          - { os: windows-latest, r: '4.3',  bioc: '3.18'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -106,16 +107,16 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ runner.bioc }}-r-${{ runner.r }}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ runner.bioc }}-r-${{ runner.r }}-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
         uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ runner.bioc }}-r-${{ runner.r }}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ runner.bioc }}-r-${{ runner.r }}-
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
@@ -249,7 +250,7 @@ jobs:
           rcmdcheck::rcmdcheck(
               args = c("--no-manual", "--no-vignettes", "--timings"),
               build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
-              error_on = "error",
+              error_on = "warning",
               check_dir = "check"
           )
         shell: Rscript {0}
@@ -313,7 +314,7 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-results
+          name: ${{ runner.os }}-biocversion-${{ runner.bioc }}-r-${{ runner.r }}-results
           path: check
 
         ## Note that DOCKER_PASSWORD is really a token for your dockerhub