R Package Check

/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

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## 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.

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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):

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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

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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:

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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:

• 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)

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

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

Phase 5: Source Review

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

The agent is read-only and returns its report; save it to quality_reports/[pkg]_package_review.md. 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:

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## 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. Don't block on them, and don't poll with sleep: start the Monitor tool with a command that runs the check itself, tees the full output to a log, and prints only the lines you would act on, e.g. Rscript -e 'devtools::check("[pkg]", args = "--as-cran")' 2>&1 | tee quality_reports/r-package-check.log | grep --line-buffered -E 'ERROR|WARNING|NOTE|Status:|[Ee]rror'. The watch ends when the check exits; set timeout_ms above the default 5 minutes (max 3600000). The filter must match failure as well as success, because silence looks the same as "still running". If you only need one notice when the check finishes, run it with Bash run_in_background: true instead and read the log when the job reports its exit. Monitor has no job-id parameter, so it cannot attach to a job already running in the background; see data-analysis/SKILL.md for the log-and-tail variant.