Skip to content

Commit

Permalink
Update GHA for bioc 3.20
Browse files Browse the repository at this point in the history
  • Loading branch information
lcolladotor committed Dec 12, 2024
1 parent fff2ebd commit b8a1580
Showing 1 changed file with 15 additions and 15 deletions.
30 changes: 15 additions & 15 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: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
- { os: macOS-latest, r: '4.3', bioc: '3.17'}
- { os: windows-latest, r: '4.3', bioc: '3.17'}
- { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:RELEASE_3_20", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
- { os: macOS-latest, r: '4.4', bioc: '3.20'}
- { os: windows-latest, r: '4.4', bioc: '3.20'}
## Check https://github.com/r-lib/actions/tree/master/examples
## for examples using the http-user-agent
env:
Expand Down Expand Up @@ -105,23 +105,23 @@ jobs:
uses: actions/cache@v3
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_20-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_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-

- name: Install Linux system dependencies
if: runner.os == 'Linux'
run: |
sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
echo $sysreqs
sudo -s eval "$sysreqs"
# - name: Install Linux system dependencies
# if: runner.os == 'Linux'
# run: |
# sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
# echo $sysreqs
# sudo -s eval "$sysreqs"

- name: Install macOS system dependencies
if: matrix.config.os == 'macOS-latest'
Expand Down Expand Up @@ -252,7 +252,7 @@ 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 @@ -285,7 +285,7 @@ jobs:
if: failure()
uses: actions/upload-artifact@master
with:
name: ${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-results
name: ${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-results
path: check


Expand Down

0 comments on commit b8a1580

Please sign in to comment.