Github Action that implements Bioconductor-specific R package checks with BiocCheck.
Composite
- Create a new GitHub Actions workflow file
.github/workflows/bioc-check.yaml
and add the following as content:
---
name: BiocCheck
on: push
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: false
pak-version: 'devel'
- name: Run BiocCheck
uses: Appsilon/bioc-check-action@v1.2
with:
new-package: true
no-cache: true
allow-failure: true
- Create a PR against your repository to test and use the action.
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/Appsilon/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