Appsilon/bioc-check-action

Github Action that runs Bioconductor-specific R package checks with BiocCheck.

BiocCheck Action

Description

Github Action that implements Bioconductor-specific R package checks with BiocCheck.

Action Type

Composite

Quick Start

1. 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

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:

# 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

Example Output

You may view an example output of this action here.

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