--- name: r-cmd-check-validation description: Use when 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. license: CC-BY-4.0 metadata: edam_operation: http://edamontology.org/operation_0004 edam_topics: - http://edamontology.org/topic_0091 tools: - R - R-CMD-check - GitHub Actions - r-universe - install.packages() - library() derived_from: - doi: 10.3389/fpls.2019.01329 title: tima evidence_spans: - The initial work is available at claims: [] provenance: collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v1 assembled_by: scripts/collect_metabolomics_collection.py sources: - build: coll_tima doi: 10.3389/fpls.2019.01329 title: tima dedup_kept_from: coll_tima schema_version: 0.2.0 --- # 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: "[![R-CMD-check](https://github.com/taxonomicallyinformedannotation/tima/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/taxonomicallyinformedannotation/tima/actions/workflows/R-CMD-c"