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Check on R 4.4 and bioc 3.19 on GHA
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lcolladotor committed May 24, 2024
1 parent f9d7c4b commit cb1591e
Showing 1 changed file with 10 additions and 10 deletions.
20 changes: 10 additions & 10 deletions .github/workflows/check-bioc.yml
Original file line number Diff line number Diff line change
Expand Up @@ -52,9 +52,9 @@ jobs:
fail-fast: false
matrix:
config:
- { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
- { os: macOS-latest, r: '4.3', bioc: '3.18'}
- { os: windows-latest, r: '4.3', bioc: '3.18'}
- { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
- { os: macOS-latest, r: '4.4', bioc: '3.19'}
- { os: windows-latest, r: '4.4', bioc: '3.19'}
## Check https://github.com/r-lib/actions/tree/master/examples
## for examples using the http-user-agent
env:
Expand Down Expand Up @@ -105,16 +105,16 @@ jobs:
uses: actions/cache@v3
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-

- 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_18-r-4.3-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-

# - name: Install Linux system dependencies
# if: runner.os == 'Linux'
Expand Down Expand Up @@ -221,7 +221,7 @@ 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}
Expand Down Expand Up @@ -253,7 +253,7 @@ jobs:
- name: Test coverage
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
run: |
covr::codecov()
covr::codecov(coverage = covr::package_coverage(type = "all"))
shell: Rscript {0}

- name: Install package
Expand Down Expand Up @@ -286,7 +286,7 @@ jobs:
if: failure()
uses: actions/upload-artifact@master
with:
name: ${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-results
name: ${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-results
path: check


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