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Update check-bioc.yml #260

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merged 3 commits into from
Nov 14, 2022
Merged

Update check-bioc.yml #260

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3dc5647
Update check-bioc.yml
mblue9 Nov 14, 2022
caef835
Update actions/cache to v3
Nov 14, 2022
435eca5
Update to Bioc 3.16
Nov 14, 2022
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26 changes: 13 additions & 13 deletions .github/workflows/check-bioc.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -51,9 +51,9 @@ jobs:
fail-fast: false
matrix:
config:
- { 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'}
- { 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: macOS-latest, r: '4.2', bioc: '3.16'}
- { os: windows-latest, r: '4.2', bioc: '3.16'}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
Expand Down Expand Up @@ -81,14 +81,14 @@ jobs:
## R is already included in the Bioconductor docker images
- name: Setup R from r-lib
if: runner.os != 'Linux'
uses: r-lib/actions/setup-r@master
uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}

## pandoc is already included in the Bioconductor docker images
- name: Setup pandoc from r-lib
if: runner.os != 'Linux'
uses: r-lib/actions/setup-pandoc@master
uses: r-lib/actions/setup-pandoc@v2

- name: Query dependencies
run: |
Expand All @@ -98,19 +98,19 @@ jobs:

- name: Cache R packages
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ${{ env.R_LIBS_USER }}
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-
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-

- name: Cache R packages on Linux
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: /home/runner/work/_temp/Library
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-
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-

- name: Install Linux system dependencies
if: runner.os == 'Linux'
Expand Down Expand Up @@ -272,7 +272,7 @@ jobs:

- name: Upload check results
if: failure()
uses: actions/upload-artifact@master
uses: actions/upload-artifact@v3
with:
name: ${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-results
name: ${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-results
path: check