check-r-package.yml

Bundles the standard check suite for R package repositories (such as Morrison-Lab/rpt). Replaces individual hygiene and R code review checks with a single composite action or reusable workflow call.

What it runs

Runs the full Morrison-Lab repository hygiene pass plus R package-specific checks:

check-junk-files.yml: OS and editor detritus (.DS_Store, Thumbs.db, .Rhistory, etc.)
check-secrets.yml: Gitleaks scan of git history for committed credentials and tokens
check-non-standard-chars.yml: flags non-standard unicode characters, curly quotes, and smart dashes
check-new-line-breaks.yml: enforces semantic line breaks on modified lines in diffs
check-typos.yml: crate-ci/typos CLI scan for spelling errors on modified files
check-ai-tells.yml: scans narrative prose (*.md, *.Rmd, *.qmd) for AI cliches and tells
lint-yaml.yml: yamllint over tracked YAML files
lint-workflows.yml: actionlint and zizmor over GitHub Actions workflows
lint-markdown.yml: markdownlint-cli2 over tracked Markdown files
check-duplicate-roxygen.yml: detects duplicated @param documentation across R/ files
check-one-function-per-file.yml: enforces single function definition per file in R/
check-formatting.yml: verifies R code formatting via Air (posit-dev/setup-air)
check-extra.yml: runs extra checks (warnings as errors, readme freshness) when opt-in

Every check is enabled by default (except check-extra, which is opt-in). Opt out of any specific check by passing its boolean flag as false.

PR metadata governance workflows that inspect pull request labels (check-news.yml, version-check.yml) remain dedicated standalone workflows because they require pull-requests: read permissions to inspect live labels from the GitHub API.

Inputs

Input	Type	Default	Description
`fail`	boolean	`true`	Fail the job on findings (else warn only).
`check-junk-files`	boolean	`true`	Enable junk files check.
`junk-patterns`	string	see `check-junk-files.qmd`	Gitignore patterns naming junk files.
`junk-paths-ignore`	string	`''`	Paths to exempt from junk files scan.
`check-secrets`	boolean	`true`	Enable gitleaks secrets scan.
`secrets-config`	string	`''`	Custom gitleaks config file path.
`secrets-paths-ignore`	string	`''`	Regex paths to exempt from secrets scan.
`check-non-standard-chars`	boolean	`true`	Enable non-standard character check.
`non-standard-chars-extensions`	string	`'.R, .qmd, .md'`	File extensions to check for non-standard characters.
`check-new-line-breaks`	boolean	`true`	Enable semantic line break check.
`new-line-breaks-base-ref`	string	`''`	Base ref for diff-scoping new line breaks.
`new-line-breaks-globs`	string	`''`	Globs to check for new line breaks.
`check-typos`	boolean	`true`	Enable typos check.
`typos-config`	string	`''`	Typos configuration file path.
`typos-base-ref`	string	`''`	Base ref for diff-scoping typo checks.
`check-ai-tells`	boolean	`true`	Enable AI tells check on prose.
`ai-tells-threshold`	string	`'10'`	Maximum allowed tell density (per 1,000 words).
`ai-tells-ignore`	string	`''`	Comma- or space-separated list of tells to ignore.
`lint-yaml`	boolean	`true`	Enable YAML linting.
`yaml-config-file`	string	`''`	Custom yamllint config file path.
`yaml-paths-ignore`	string	`''`	Patterns to exclude from YAML linting.
`lint-workflows`	boolean	`true`	Enable workflow linting.
`workflows-path`	string	`'.'`	Path to workflow files.
`lint-markdown`	boolean	`true`	Enable Markdown linting.
`markdown-config-file`	string	`''`	Markdownlint config file path.
`markdown-globs`	string	`'*.md'`	Git pathspecs of Markdown files to lint.
`markdown-paths-ignore`	string	`''`	Paths to exempt from Markdown linting.
`markdown-base-ref`	string	`''`	Base ref for list-item splice checks.
`check-duplicate-roxygen`	boolean	`true`	Enable duplicate roxygen documentation check.
`duplicate-roxygen-path`	string	`'.'`	Directory path to scan for duplicate roxygen docs.
`check-one-function-per-file`	boolean	`true`	Enforce one function per file in `R/`.
`one-function-per-file-path`	string	`'R'`	Path to R directory.
`check-extra`	boolean	`false`	Run extra R checks (`warnings`, `random-order`, `readme`).
`extra-check`	string	`'warnings'`	Extra check type to run.
`check-formatting`	boolean	`true`	Enable Air R code formatting check.
`air-version`	string	`'0.11.0'`	Air release version to install.
`air-path`	string	`'.'`	Path to format-check.

Example

name: Check R package

on:
  push:
    branches: [main]
  pull_request:

jobs:
  check:
    permissions:
      contents: read
    uses: Morrison-Lab/gha/.github/workflows/check-r-package.yml@v3