BiocCheck action bla bla bla

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Description

Github Actions to implement Bioconductor-specific R package checks with BiocCheck.

Action Type

Composite

Quick Start

1. Create new action file .github/workflows/bioc-check.yaml and put example content:

---
name: BiocCheck

on:
  push:
    branches:
      - main
  pull_request:

jobs:
  bioc-check:
    runs-on: ubuntu-latest
    name: BiocCheck
    container:
      image: rocker/verse:4.1.0
    steps:
      - name: Checkout repo
        uses: actions/checkout@v2

      - name: Run rcmdcheck
        run: |
          R CMD build .
          R CMD INSTALL *.tar.gz
          R CMD check *.tar.gz

      - name: Run BiocCheck
        uses: insightsengineering/bioc-check-action@v1

2. Create PR to test BiocCheck action.

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