Github Action that runs Bioconductor-specific R package checks with BiocCheck.
APACHE-2.0 License
Github Action that implements Bioconductor-specific R package checks with BiocCheck.
Composite
.github/workflows/bioc-check.yaml
and add the following as content:---
name: BiocCheck
on:
push:
branches:
- main
pull_request:
jobs:
bioccheck:
runs-on: ubuntu-latest
name: BiocCheck
steps:
- name: Checkout Repo
uses: actions/checkout@v3
- name: Setup Pandoc
uses: r-lib/actions/setup-pandoc@v2
- name: Setup R
uses: r-lib/actions/setup-r@v2
with:
r-version: release
http-user-agent: release
use-public-rspm: true
- name: Install Deps
uses: r-lib/actions/setup-r-dependencies@v2
with:
cache: true
- name: Run BiocCheck
uses: insightsengineering/bioc-check-action@v1
Note that you may also use the script from this action in standalone mode by running the following:
# Download the script
wget -O BiocCheck.R \
https://raw.githubusercontent.com/insightsengineering/bioc-check-action/main/BiocCheck.R
# Making the script executable
chmod +x BiocCheck.R
# Run the script
./BiocCheck.R --help
You may view an example output of this action here.
path
:
Description: Path to package's root
Required: false
Default: .
new-package
:
Description: enable checks specific to new packages
Required: false
Default: false
post-result-as-comment
:
Description: post the check result as a PR comment
Required: false
Default: true
no-check-dependencies
:
Description: disable check for bad dependencies
Required: false
Default: false
no-check-deprecated
:
Description: disable check for usage of deprecated packages
Required: false
Default: false
no-check-remotes
:
Description: disable check for usage of remote packages other than those hosted on CRAN or Bioconductor
Required: false
Default: false
no-check-version-num
:
Description: disable check for valid version number
Required: false
Default: false
no-check-R-ver
:
Description: disable check for valid R version
Required: false
Default: false
no-check-pkg-size
:
Description: disable check for package tarball size
Required: false
Default: false
no-check-file-size
:
Description: disable check for individual file size
Required: false
Default: false
no-check-bioc-views
:
Description: disable biocViews-specific checks (for non-BioC packages)
Required: false
Default: false
no-check-bbs
:
Description: disable BBS-specific checks (for non-BioC packages). Valid DESCRIPTION
Required: false
Default: false
no-check-description
:
Description: disable DESCRIPTION file checks
Required: false
Default: false
no-check-namespace
:
Description: disable namespace checks
Required: false
Default: false
no-check-vignettes
:
Description: disable vignette checks
Required: false
Default: false
no-check-library-calls
:
Description: disable check usage of functions that install or update packages
Required: false
Default: false
no-check-install-self
:
Description: disable check for require or library of itself
Required: false
Default: false
no-check-coding-practices
:
Description: disable check for some common best coding practices
Required: false
Default: false
no-check-function-len
:
Description: disable check for function length
Required: false
Default: false
no-check-man-doc
:
Description: disable checks for man page documentation
Required: false
Default: false
no-check-news
:
Description: disable checks for NEWS file
Required: false
Default: false
no-check-unit-tests
:
Description: disable checks for unit tests
Required: false
Default: false
no-check-skip-bioc-tests
:
Description: disable check for tests that skip when on bioc
Required: false
Default: false
no-check-formatting
:
Description: disable checks for file formatting
Required: false
Default: false
no-check-CRAN
:
Description: disable check for if package exists in CRAN
Required: false
Default: false
no-check-bioc-help
:
Description: disable check for registration on Bioconductor mailing list and support site
Required: false
Default: false
build-output-file
:
Description: file containing R CMD build output, for additional analysis
Required: false
quit-with-status
:
Description: enable exit code option when performing check
Required: false
Default: false
no-cache
:
Description: disable github action R dependency caching
Required: false
Default: false
cache-version
:
Description: version of cache. To clean cache bump this version
Required: false
Default: cache-v1
allow-failure
:
Description: BiocCheck errors will not fail, but will give a warning
Required: false
Default: false