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R-CMD-check-bioc

R-CMD-check-bioc #748

Workflow file for this run

# 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}