R-CMD-check-bioc #748
Workflow file for this run
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# Based on | |
# - https://lcolladotor.github.io/biocthis/reference/use_bioc_github_action | |
# - https://github.com/tidyverse/ggplot2/blob/master/.github/workflows/R-CMD-check.yaml | |
# - https://github.com/r-lib/actions/tree/master/examples | |
# - https://github.com/maxheld83/ghactions | |
# - https://github.com/seandavi/BiocActions | |
on: | |
push: | |
branches-ignore: | |
- gh-pages | |
pull_request: | |
branches-ignore: | |
- gh-pages | |
schedule: | |
- cron: "0 7 * * 1,3,5" # Run every Monday/Wednesday/Friday at 07:00 UTC | |
name: R-CMD-check-bioc | |
# Increment to clear the cache or include "/nocache" in commit message | |
env: | |
cache-version: v5 | |
jobs: | |
R-CMD-check-r-lib: | |
runs-on: ${{ matrix.config.os }} | |
name: ${{ matrix.config.os }} (bioc-${{ matrix.config.biocversion }}) | |
strategy: | |
fail-fast: false | |
matrix: | |
config: | |
# - {os: windows-latest, biocversion: "release"} | |
# - {os: windows-latest, biocversion: "devel"} | |
- {os: macOS-latest, biocversion: "release"} | |
# - {os: macOS-latest, biocversion: "devel"} | |
- {os: ubuntu-latest, biocversion: "release"} | |
# - {os: ubuntu-latest, biocversion: "devel"} | |
env: | |
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
TZ: UTC | |
NOT_CRAN: true | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
BIOCVERSION: ${{ matrix.config.biocversion }} | |
steps: | |
# https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml | |
- uses: actions/checkout@v3 | |
- name: Find R version to run | |
run: | | |
# Define R version to use | |
config="https://bioconductor.org/config.yaml" | |
rversion=$(curl ${config} | \ | |
grep r_version_associated_with_${BIOCVERSION} | \ | |
grep -o "[0-9]*\.[0-9]*\.[0-9]*") | |
echo "Using R ${rversion}..." | |
echo "rversion=${rversion}" >> $GITHUB_ENV | |
shell: | |
bash {0} | |
- uses: r-lib/actions/setup-r@v2 | |
with: | |
r-version: ${{ env.rversion }} | |
- uses: r-lib/actions/setup-pandoc@v2 | |
- uses: r-lib/actions/setup-r-dependencies@v2 | |
with: | |
extra-packages: | | |
any::rcmdcheck | |
any::BiocCheck | |
needs: check | |
- uses: r-lib/actions/check-r-package@v2 | |
with: | |
args: 'c("--no-build-vignettes", "--no-manual", "--timings")' | |
build_args: 'c("--no-manual", "--no-resave-data")' | |
error-on: '"warning"' | |
check-dir: '"check"' | |
- name: R CMD BiocCheck | |
run: | | |
# Continue even if BiocCheck finds an error | |
BiocCheck::BiocCheck(dir('check', 'tar.gz$', full.names = TRUE), `no-check-R-ver` = TRUE, `no-check-bioc-help` = TRUE) | |
# For more options: http://bioconductor.org/packages/release/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html | |
shell: Rscript {0} | |
- name: Upload check results | |
if: failure() | |
uses: actions/upload-artifact@master | |
with: | |
name: ${{ runner.os }}-bioc-${{ matrix.config.biocversion }}-r-${{ env.rversion }}-results | |
path: check | |
- name: Test coverage | |
if: runner.os == 'macOS' && matrix.config.biocversion == 'release' | |
run: | | |
install.packages("remotes") | |
remotes::install_cran("covr") | |
covr::codecov() | |
shell: Rscript {0} |