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https://github.com/insightsengineering/bioc-check-action
Github Action that runs Bioconductor-specific R package checks with BiocCheck.
https://github.com/insightsengineering/bioc-check-action
actions bioconductor github-actions r
Last synced: about 1 month ago
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Github Action that runs Bioconductor-specific R package checks with BiocCheck.
- Host: GitHub
- URL: https://github.com/insightsengineering/bioc-check-action
- Owner: insightsengineering
- License: apache-2.0
- Created: 2021-11-12T12:17:39.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2024-03-15T15:35:18.000Z (8 months ago)
- Last Synced: 2024-09-30T23:41:13.888Z (about 2 months ago)
- Topics: actions, bioconductor, github-actions, r
- Language: R
- Homepage: https://github.com/marketplace/actions/bioc-check-action
- Size: 21.5 KB
- Stars: 3
- Watchers: 3
- Forks: 2
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Codeowners: .github/CODEOWNERS
Awesome Lists containing this project
README
# BiocCheck Action
[](https://github.com/insightsengineering/bioc-check-action/actions/workflows/test-action.yaml)
[](https://github.com/insightsengineering/bioc-check-action/actions/workflows/linter.yaml)
## Description
Github Action that implements Bioconductor-specific R package checks with [BiocCheck](https://bioconductor.org/packages/release/bioc/html/BiocCheck.html).
## Action Type
Composite
## Quick Start
1. Create a new GitHub Actions workflow file `.github/workflows/bioc-check.yaml` and add the following as content:
```yaml
---
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
```
2. Create a PR against your repository to test and use the action.
## Standalone Usage
Note that you may also use the script from this action in standalone mode by running the following:
```bash
# 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
```
## Example Output
You may view an example output of this action [here](https://github.com/insightsengineering/hermes/pull/166#issuecomment-1016147947).
## Inputs
* `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`