Merge pull request #18 from fmicompbio/test-actions

Use the bioc-action to set up R/BiocManager

Author: csoneson

.github/workflows/check-bioc.yml

@@ -44,17 +44,17 @@ env:
 jobs:
   build-check:
     runs-on: ${{ matrix.config.os }}
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    name: ${{ matrix.config.os }} (${{ matrix.config.bioc }})
     container: ${{ matrix.config.cont }}
     ## Environment variables unique to this job.
 
     strategy:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'devel', bioc: '3.17', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: 'devel', bioc: '3.17'}
-          - { os: windows-latest, r: 'devel', bioc: '3.17'}
+          - { os: ubuntu-latest, bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, bioc: 'devel'}
+          - { os: windows-latest, bioc: 'devel'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -82,12 +82,11 @@ jobs:
         uses: actions/checkout@v3
 
       ## R is already included in the Bioconductor docker images
-      - name: Setup R from r-lib
+      - name: Set up R and install BiocManager
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-r@v2
+        uses: grimbough/bioc-actions/setup-bioc@v1
         with:
-          r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
+          bioc-version: ${{ matrix.config.bioc }}
 
       ## pandoc is already included in the Bioconductor docker images
       - name: Setup pandoc from r-lib
@@ -105,16 +104,16 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-
 
       - 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-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
@@ -155,11 +154,6 @@ jobs:
           remotes::install_cran("BiocManager")
         shell: Rscript {0}
 
-      - name: Set BiocVersion
-        run: |
-          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
-        shell: Rscript {0}
-
       - name: Install dependencies pass 1
         run: |
           ## Try installing the package dependencies in steps. First the local
@@ -301,7 +295,7 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-devel-r-devel-results
+          name: ${{ runner.os }}-biocversion-devel-results
           path: check
 
         ## Note that DOCKER_PASSWORD is really a token for your dockerhub