Removing printing from configure #131
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on: | |
push: | |
branches: | |
- devel | |
- use-sys-libs | |
pull_request: | |
branches: | |
- master | |
- 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 }}, System Libs: ${{ matrix.config.sys-libs }})' | |
strategy: | |
fail-fast: false | |
matrix: | |
config: | |
- { os: windows-2022, bioc-version: 'devel', bioc-mirror: 'https://ftp.gwdg.de/pub/misc/bioconductor', sys-libs: 'false'} | |
- { os: macOS-12, bioc-version: 'devel', bioc-mirror: 'https://ftp.gwdg.de/pub/misc/bioconductor', sys-libs: 'false'} | |
- { os: ubuntu-22.04, bioc-version: 'devel', bioc-mirror: 'https://ftp.gwdg.de/pub/misc/bioconductor', sys-libs: 'false'} | |
- { os: ubuntu-22.04, bioc-version: 'devel', bioc-mirror: 'https://ftp.gwdg.de/pub/misc/bioconductor', sys-libs: 'true'} | |
- { os: ubuntu-22.04, bioc-version: 'release', bioc-mirror: 'https://packagemanager.posit.co/bioconductor', sys-libs: 'true'} | |
steps: | |
## R CMD check complains about Windows line endings without this | |
- name: Configure git | |
run: | | |
git config --global core.autocrlf false | |
- uses: actions/checkout@v3 | |
- name: Install system dependencies | |
if: ${{ runner.os == 'linux' && matrix.config.sys-libs == 'true' }} | |
run: sudo apt-get update && sudo apt-get install -y libblosc-dev libbz2-dev libzstd-dev liblzf-dev | |
- name: Remove system dependencies | |
if: ${{ runner.os == 'linux' && matrix.config.sys-libs == 'false' }} | |
run: sudo apt-get update && sudo apt-get remove -y libblosc-dev libbz2-dev libzstd-dev liblzf-dev | |
- name: Setup R and Bioconductor | |
uses: grimbough/bioc-actions/setup-bioc@v1 | |
with: | |
bioc-version: ${{ matrix.config.bioc-version }} | |
bioc-mirror: ${{ matrix.config.bioc-mirror }} | |
- uses: r-lib/actions/setup-pandoc@v2 | |
- name: Install dependencies | |
uses: r-lib/actions/setup-r-dependencies@v2 | |
with: | |
extra-packages: | | |
covr | |
rcmdcheck | |
- name: Bioc - 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: Test coverage | |
if: runner.os == 'Windows' | |
run: | | |
covr::codecov() | |
shell: Rscript {0} |