r-package-check

name	r-package-check
description	Run the full R package release gate — regenerate docs, run the test suite, run R CMD check --as-cran, and triage every ERROR / WARNING / NOTE against CRAN policy before a release or submission. Use when the user says "check my R package", "R CMD check", "is this package CRAN-ready", "run devtools::check", "prepare for CRAN submission", or points at a directory containing a DESCRIPTION file. Produces a check report + CRAN-submission checklist in `quality_reports/`.
author	Claude Code Academic Workflow
version	1.0.0
argument-hint	[path to package root, or blank to autodetect from DESCRIPTION]
disable-model-invocation	true
allowed-tools	["Read","Grep","Glob","Bash","Task","Monitor"]
effort	high

/r-package-check — R Package Release Gate

Run the document → test → check → triage pipeline that decides whether an R package is releasable, then review the source for the issues R CMD check cannot see.

Input: $ARGUMENTS — the package root (a directory containing DESCRIPTION). If blank, autodetect by searching upward/within the working directory for DESCRIPTION.

---

Constraints

• Follow .claude/rules/r-package-conventions.md — the CRAN-readiness bar (0 errors, 0 warnings, explained notes) is the gate.
• Treat man/ and NAMESPACE as generated — regenerate with devtools::document(); never hand-edit them.
• Run the r-package-reviewer agent on the source before declaring the package releasable.
• Do not bump the version or write to CRAN. This skill checks; the human decides when to submit.

---

Workflow Phases

Phase 0: Pre-Flight Report

## Pre-Flight Report — R Package Check

**Package:** [name + version from DESCRIPTION]
**Root:** [path]
**Exported functions:** [from NAMESPACE / `@export` count]
**Dependencies:** Imports [list] · Suggests [list] · Depends [list]
**Toolchain available:** devtools [✓/✗], roxygen2 [✓/✗], testthat [✓/✗], R CMD [✓/✗], covr [✓/✗]
**Plan:** document → test → check --as-cran → triage → review

Detect the toolchain with a quick probe; if devtools/R CMD is missing, stop and tell the user what to install.

Rscript -e 'cat("devtools:", requireNamespace("devtools", quietly=TRUE),
               "roxygen2:", requireNamespace("roxygen2", quietly=TRUE),
               "testthat:", requireNamespace("testthat", quietly=TRUE),
               "covr:", requireNamespace("covr", quietly=TRUE), "\n")'

Phase 1: Document

Regenerate man/ + NAMESPACE and detect drift (generated docs that were not committed):

Rscript -e 'devtools::document("[pkg]")'
git -C "[pkg]" status --short man/ NAMESPACE   # any diff = generated docs were stale

If git status shows changes, flag: the committed man//NAMESPACE were out of sync with the roxygen blocks.

Phase 2: Test

Rscript -e 'devtools::test("[pkg]")'

Report failures and (if covr is available, Phase 4) coverage of exported functions.

Phase 3: Check (--as-cran)

Run the full check. This is slow (minutes) — background-launch and stream with the Monitor tool rather than blocking:

Rscript -e 'devtools::check("[pkg]", args = "--as-cran")'
# or: R CMD build [pkg] && R CMD check --as-cran [pkg]_*.tar.gz

Then triage every result into a table:

Result	Tier	CRAN-policy meaning	Action
…	ERROR / WARNING / NOTE	…	fix / justify

• ERROR / WARNING → must fix before submission.
• NOTE → fix if cheap; otherwise write the justification you'd put in cran-comments.md (e.g., "New submission", "Found the following (possibly) invalid URLs … the URL is correct and reachable").

Phase 4: Coverage (optional)

Rscript -e 'covr::package_coverage("[pkg]")'

Report per-function coverage; flag exported functions with 0% coverage.

Phase 5: Source Review

Delegate to the r-package-reviewer agent:
"Review the package source at [pkg]"

Address Critical (CRAN-policy violations) and High (check WARNINGs) findings.

Phase 6: Release Gate + Report

Save a report to quality_reports/[package]_package_check.md and present a verdict:

## Release Gate — [package] [version]
- R CMD check --as-cran: E errors, W warnings, N notes
- Tests: P passed, F failed
- Coverage: X% of exported functions
- r-package-reviewer: C critical, H high
- **Verdict:** RELEASABLE / FIX-FIRST / POLICY-VIOLATION

### CRAN-submission checklist
[ ] 0 errors, 0 warnings; each note justified in cran-comments.md
[ ] Version bumped + NEWS.md updated
[ ] devtools::check_win_devel() / R-hub on other platforms (note: run separately)
[ ] Reverse-dependency check if this is an update (revdepcheck)

---

Important

• --as-cran or it doesn't count. A plain R CMD check misses the policy checks that actually gate submission.
• Generated files are generated. If docs drift, the fix is devtools::document(), not editing .Rd.
• The gate is 0/0/explained. 0 errors, 0 warnings, every remaining note justified — nothing less is "CRAN-ready."
• This skill does not submit. Cross-platform checks (win-devel, R-hub) and the actual devtools::release() are the maintainer's call.

Long-running checks: use the Monitor tool

R CMD check --as-cran and covr can run for several minutes. Background-launch via Bash with run_in_background: true, capture the bash_id, and use the Monitor tool to stream progress (e.g. the checking … lines or process exit) instead of polling. See data-analysis/SKILL.md for the pattern.