Merge pull request #42 from stemangiola/update-action-to-bioc3.15

Update github action to Bioc 3.15

Author: mblue9

.github/workflows/check-bioc.yml

@@ -51,9 +51,9 @@ jobs:
  fail-fast: false
  matrix:
  config:
- - { os: ubuntu-latest, r: '4.1', bioc: '3.14', cont: "bioconductor/bioconductor_docker:RELEASE_3_14", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
- - { os: macOS-latest, r: '4.1', bioc: '3.14'}
- - { os: windows-latest, r: '4.1', bioc: '3.14'}
+ - { os: ubuntu-latest, r: '4.2', bioc: '3.15', cont: "bioconductor/bioconductor_docker:RELEASE_3_15", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+ - { os: macOS-latest, r: '4.2', bioc: '3.15'}
+ - { os: windows-latest, r: '4.2', bioc: '3.15'}
  env:
  R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
  RSPM: ${{ matrix.config.rspm }}
@@ -101,16 +101,16 @@ jobs:
  uses: actions/cache@v2
  with:
  path: ${{ env.R_LIBS_USER }}
- key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-${{ hashFiles('.github/depends.Rds') }}
- restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-
+ key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }}
+ restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-
 
  - name: Cache R packages on Linux
  if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
  uses: actions/cache@v2
  with:
  path: /home/runner/work/_temp/Library
- key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-${{ hashFiles('.github/depends.Rds') }}
- restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-
+ key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }}
+ restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-
 
  - name: Install Linux system dependencies
  if: runner.os == 'Linux'
@@ -256,6 +256,9 @@ jobs:
  - name: Deploy package
  if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
  run: |
+ ## Temporary workaround for https://github.com/actions/checkout/issues/766
+ git config --global --add safe.directory "$GITHUB_WORKSPACE"
+ 
  git config --local user.email "actions@github.com"
  git config --local user.name "GitHub Actions"
  Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
@@ -269,6 +272,6 @@ jobs:
  if: failure()
  uses: actions/upload-artifact@master
  with:
- name: ${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-results
+ name: ${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-results
  path: check