R cmd check validation

r-cmd-check-validation

Summary

Automated validation of R package build integrity and CRAN compliance using the R-CMD-check test suite, typically run via GitHub Actions CI/CD workflows. This skill verifies that a package installs successfully, loads without errors, and passes all checks against the CRAN submission checklist.

When to use

Apply this skill after installing an R package from a non-CRAN repository (such as r-universe) to confirm the package build is sound, dependencies resolve correctly, and no warnings or errors are introduced. Use it as a gate before relying on the package for downstream analysis or distribution.

When NOT to use

• Package is already on CRAN; use CRAN's native check infrastructure instead.
• Package installation has not yet been attempted; first confirm basic install.packages() works before running R-CMD-check.
• Local development environment lacks R development tools (Rtools on Windows, build-essential on Linux) needed for R-CMD-check.

Inputs

• R package source code (GitHub repository)
• Package repository URL (e.g., r-universe registry)
• GitHub Actions workflow configuration (.github/workflows/R-CMD-check.yaml)

Outputs

• R-CMD-check test report (pass/fail status)
• CI badge status (displayed in README)
• Installation verification (no error/warning log)
• Package load confirmation (library() call succeeds)

How to apply

First, configure R to use the r-universe repository as a package source by specifying the repository URL in install.packages(). Install the target package (e.g., tima) using install.packages() with the configured repository, then load it into the R environment with library(package_name) and verify no errors occur. Finally, run R-CMD-check on the installed package to validate against the CRAN submission checklist. The R-CMD-check workflow should be configured in the package's GitHub Actions (typically in .github/workflows/R-CMD-check.yaml) and the results tracked via a CI badge in the README. A passing check indicates all tests pass and the package meets CRAN standards.

Related tools

• R-CMD-check (Automated test harness validating package build, dependencies, and CRAN compliance) — https://github.com/r-lib/rcmdcheck
• GitHub Actions (CI/CD workflow engine executing R-CMD-check on every commit/PR and publishing badge status) — https://github.com/features/actions
• r-universe (Package repository providing pre-built binaries and automated R-CMD-check results) — https://r-universe.dev
• install.packages() (R base function to download and install package from specified repository)
• library() (R base function to load installed package into environment and verify no load-time errors)

Examples

install.packages("tima", repos = c("https://taxonomicallyinformedannotation.r-universe.dev", "https://bioconductor.org/packages/release/bioc", "https://cloud.r-project.org")); library(tima)

Evaluation signals

• R-CMD-check workflow in GitHub Actions completes successfully (all checks pass) with green status badge visible in README.
• install.packages(package_name, repos=c('r-universe_url', ...)) completes without errors or unresolved dependency warnings.
• library(package_name) executes without errors or critical warnings in R console.
• No unexpected NOTE, WARNING, or ERROR messages appear in R-CMD-check report logs.
• Package version badge from r-universe updates in sync with repository releases, confirming automated build pipeline is active.

Limitations

• R-CMD-check validates against CRAN standards but does not guarantee functional correctness or scientific validity of the package's algorithms.
• CI workflows depend on GitHub Actions availability and correct .yaml configuration; misconfigured workflows may report false negatives.
• r-universe automatic builds require the repository to be registered and may lag behind local development if CI/CD is not actively configured.
• Tests passed on GitHub Actions (Linux container) do not guarantee cross-platform compatibility on Windows or macOS without explicit platform-specific workflow steps.

Evidence

• [other] research_question: "Does the tima R package install successfully from the r-universe repository and pass its R-CMD-check test suite?"
• [other] workflow_confirmation: "Install the TIMA package using install.packages() with the configured repository. 3. Load the installed package into the R environment using library(tima) and confirm no errors occur. 4. Run"
• [readme] installation_instruction: "As the package is not (yet) available on CRAN, you will need to install with: install.packages( "tima", repos = c( "https://taxonomicallyinformedannotation.r-universe.dev","
• [readme] load_verification: "Then, you should be able to install the rest with: tima::install_tima()"
• [readme] ci_badge_confirmation: "[](https://github.com/taxonomicallyinformedannotation/tima/actions/workflows/R-CMD-c"