Update workflows #178
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on: | |
push: | |
branches-ignore: | |
- mac-conda | |
pull_request: | |
branches: | |
- devel | |
name: R-CMD-check | |
env: | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
jobs: | |
R-CMD-check: | |
runs-on: ${{ matrix.config.os }} | |
name: ${{ matrix.config.os }} (${{ matrix.config.bioc-version }}) | |
strategy: | |
fail-fast: false | |
matrix: | |
config: | |
- { os: windows-2022, bioc-version: 'devel', Ncpus: 4} | |
- { os: macOS-13, bioc-version: 'devel', Ncpus: 4} | |
- { os: macOS-14, bioc-version: 'devel', Ncpus: 3} | |
- { os: ubuntu-20.04, bioc-version: 'devel', Ncpus: 4, system-libs: 'libcurl4-gnutls-dev libaec-dev'} | |
- { os: ubuntu-22.04, bioc-version: 'devel', Ncpus: 4, system-libs: 'libcurl4-openssl-dev'} | |
steps: | |
- name: Configure git | |
run: | | |
git config --global core.autocrlf false | |
- name: Install Linux system libraries | |
if: ${{ runner.os == 'Linux' }} | |
run: | | |
sudo apt-get update && sudo apt-get install ${{ matrix.config.system-libs }} | |
- name: Install Mac system libraries | |
if: ${{ matrix.config.os == 'macOS-latest' }} | |
run: | | |
source("https://mac.R-project.org/bin/install.R") | |
install.libs("openssl") | |
shell: Rscript {0} | |
- uses: actions/checkout@v4 | |
- name: Setup R and Bioconductor | |
uses: grimbough/bioc-actions/setup-bioc@v1 | |
with: | |
bioc-version: ${{ matrix.config.bioc-version }} | |
bioc-mirror: https://ftp.gwdg.de/pub/misc/bioconductor | |
Ncpus: ${{ matrix.config.Ncpus }} | |
- uses: r-lib/actions/setup-pandoc@v2 | |
- name: Install dependencies | |
uses: r-lib/actions/setup-r-dependencies@v2 | |
with: | |
## install BiocCheck here so it is cached | |
extra-packages: | | |
bioc::BiocCheck | |
- name: Bioc - Build, Install, Check | |
id: build-install-check | |
uses: grimbough/bioc-actions/build-install-check@v1 | |
- name: Run BiocCheck | |
uses: grimbough/bioc-actions/run-BiocCheck@v1 | |
with: | |
error-on: 'never' | |
arguments: '--no-check-bioc-help' | |
- name: Session info | |
run: | | |
sessionInfo() | |
shell: Rscript {0} | |
- name: Upload check results | |
if: always() | |
uses: actions/upload-artifact@v4 | |
with: | |
name: ${{ matrix.config.os }}-results | |
path: ${{ steps.build-install-check.outputs.check-dir }} | |
- name: Upload check results | |
if: ${{ failure() }} | |
uses: actions/upload-artifact@v4 | |
with: | |
name: ${{ matrix.config.os }}-${{ matrix.config.r }}-hdf5_config.log | |
path: check/*.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/config.log |