check-extra.yml

Extra R-package checks that R CMD check passes over. Adapted from IndrajeetPatil/workflows check-extra.yaml (MIT).

Three jobs run in parallel so every failure surfaces at once instead of short-circuiting at the first – the extra R-install cost is the point, not an accident. Disable any job with the matching check-* input if a package has no tests, no vignettes, or no README.Rmd.

What it catches

Warnings as errors on three surfaces, all under options(warn = 2L). Examples run in a fresh R session with run_dontrun and run_donttest on (the devtools::run_examples(fresh = TRUE, ...) equivalent), because a parent warn=2 does not reach callr’s child. Tests use a per-file sweep: testthat::test_file() inside withr::local_options(list(warn = 2L)). A session-wide warn=2 crashes parallel testthat workers (testthat#1912); this is the workaround that issue closed on. Vignettes render via fs::dir_ls("vignettes/", glob = "*.Rmd", recurse = TRUE). A deprecation warning from a dependency is the motivating case: it is invisible in a normal green check until the deprecation becomes an error a release later.
Random test order. testthat::test_dir("tests/testthat", shuffle = TRUE) with a randomly drawn seed that is logged, so a failure is reproducible. TESTTHAT_PARALLEL=FALSE via withr::local_envvar, because shuffling is meaningless if tests run in parallel anyway. This catches a test that only passes because an earlier one left state behind. A missing tests/testthat fails this job; disable it with check-random-order: false if the package has no tests.
README render, also with warnings as errors. When check-readme-freshness is on (the default), the job also fails if README.md is modified or untracked after the render – so a consumer does not need a second workflow for that half. Only an explicit false opts out of freshness. A missing README.Rmd fails this job; disable it with check-readme: false if the package has none.

A missing tests/testthat or vignettes/*.Rmd inside the combined warnings job is a skip with a log line, not a failure, so a package that has only examples still gets those checked.

.qmd vignettes and README.qmd are out of scope: the vignette glob is *.Rmd, matching upstream, and a Quarto README would need Quarto, which this check does not install.

purrr, withr, fs, cli, and pkgload are declared in extra-packages rather than arriving transitively via devtools.

Inputs

Input	Type	Default	Description
`path`	string	`'.'`	Path to the R package root (the directory holding `DESCRIPTION`).
`extra-packages`	string	`''`	Extra R packages forwarded to `setup-r-dependencies`. Use this for packages a README or example needs that are not in `DESCRIPTION`.
`install-quarto`	boolean	`false`	Install Quarto when setting up R dependencies.
`check-warnings`	boolean	`true`	Run examples, tests, and vignettes with warnings as errors.
`check-random-order`	boolean	`true`	Run testthat with `shuffle = TRUE` and a logged seed.
`check-readme`	boolean	`true`	Render `README.Rmd` with warnings as errors.
`check-readme-freshness`	boolean	`true`	When the README job runs, fail if `README.md` is modified or untracked after the render.

Pin @v2: this capability was added after @v1 was frozen, so it does not exist at that tag.

Permissions

Only contents: read (the default), so no permissions: block is needed.

Example

# Copy to .github/workflows/check-extra.yml in your repo.
name: Extra R-package checks

on:
  push:
    branches:
      - main
  pull_request:
  workflow_dispatch:

jobs:
  extra:
    uses: Morrison-Lab/gha/.github/workflows/check-extra.yml@v2
    # with:
    #   path: '.'
    #   extra-packages: 'any::ggthemes'
    #   install-quarto: false
    #   check-warnings: true
    #   check-random-order: true
    #   check-readme: true
    #   check-readme-freshness: true

See check-extra.yml in examples/ for the full caller stub. (Linked to the directory rather than the file, for the reason check-secrets.qmd records: a blob/main/... link to a capability’s own example 404s on the pull request that introduces it, and check-links rightly fails it.)