From d2d6670ac8161f745e126d20fc8b0406c58cb42c Mon Sep 17 00:00:00 2001
From: Maria Doyle <maria.doyle@petermac.org>
Date: Wed, 25 May 2022 22:45:23 +0100
Subject: [PATCH] Update github action to Bioc 3.15

---
 .github/workflows/check-bioc.yml | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
index 9855ce9..ed9c4e1 100755
--- a/.github/workflows/check-bioc.yml
+++ b/.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