--- name: r-package-installation-and-execution description: Use when when you have a new or updated R package available via a non-CRAN repository (such as r-universe) and need to verify it installs cleanly, passes R-CMD-check compliance, and is ready for downstream workflow execution. license: CC-BY-4.0 metadata: edam_operation: http://edamontology.org/operation_0226 edam_topics: - http://edamontology.org/topic_0091 tools: - R - r-universe - R-CMD-check - GitHub Actions - Docker 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 Package Installation and Execution ## Summary Install an R package from a custom repository and verify successful execution through package loading and validation checks. This skill ensures the package meets build standards and can be reliably invoked in an R environment. ## When to use When you have a new or updated R package available via a non-CRAN repository (such as r-universe) and need to verify it installs cleanly, passes R-CMD-check compliance, and is ready for downstream workflow execution. Use this before attempting to run domain-specific analyses that depend on the package. ## When NOT to use - Package is already installed and loaded in your current session and you only need to use it (no installation step required). - Package is already available on CRAN; use standard `install.packages()` without custom repos instead. - You are working in a containerized environment (Docker or Singularity) where dependencies may be pre-built; prefer pulling the pre-built image. ## Inputs - R installation with network access - Package repository URL (e.g., r-universe host) - Package name and desired version (optional) ## Outputs - Installed R package in library path - Loaded package namespace in R session - R-CMD-check validation report (from CI badge or local run) - Optional: example data files and minimal execution output ## How to apply Configure R to use the target repository URL in its package sources (via the `repos` parameter in `install.packages()`). Install the package using `install.packages()` and verify with `library()` that it loads without errors. If the package provides a secondary setup function (e.g., `tima::install_tima()`), invoke it to ensure all optional dependencies are available. Confirm that the package has passed R-CMD-check on its CI pipeline (check the README badge or GitHub Actions workflow). Load example data if available (e.g., via `tima::get_example_files()`) and attempt a minimal function call to confirm runtime execution succeeds. ## Related tools - **r-universe** (Package repository hosting the compiled R package binaries and source) — https://taxonomicallyinformedannotation.r-universe.dev/tima - **R-CMD-check** (Automated validation workflow that verifies package compliance with CRAN submission standards) — https://github.com/taxonomicallyinformedannotation/tima/actions/workflows/R-CMD-check.yaml - **GitHub Actions** (CI/CD platform that runs R-CMD-check on commits and publishes status badge) — https://github.com/taxonomicallyinformedannotation/tima - **Docker** (Optional containerized environment with pre-installed R package and all dependencies) — https://hub.docker.com/r/adafede/tima-r/ ## Examples ``` install.packages('tima', repos = c('https://taxonomicallyinformedannotation.r-universe.dev', 'https://bioconductor.org/packages/release/bioc', 'https://cloud.r-project.org')); tima::install_tima(); library(tima); tima::get_example_files() ``` ## Evaluation signals - Package loads in R session with no errors or warnings when invoked as `library(package_name)` - R-CMD-check badge in repository README shows passing status (green badge), indicating compliance with CRAN submission checklist - Example data can be retrieved via the package's helper function (e.g., `tima::get_example_files()`) without file-not-found or permission errors - A minimal function call from the package (e.g., `validate_inputs()` or equivalent) executes successfully and produces expected output structure - Package namespace and exported functions are visible when running `ls('package:package_name')` or similar introspection ## Limitations - Package lifecycle is 'experimental' (as indicated by lifecycle badge), meaning API and behavior may change without deprecation notice in future releases. - Secondary dependency installation via a helper function (e.g., `tima::install_tima()`) may fail if upstream package repositories are unavailable or if system-level dependencies (e.g., build tools, system libraries) are not present. - Custom column names in input files are configurable but require manual parameter specification; mismatched column names will cause runtime errors, not installation errors. - No changelog is published in the repository, so version-to-version breaking changes may not be documented; users must inspect GitHub commit history or release notes to track changes. ## Evidence - [readme] Installation method and repository configuration: "install.packages( "tima", repos = c( "https://taxonomicallyinformedannotation.r-universe.dev", "https://bioconductor.org/packages/release/bioc", "https://cloud.r-project.org" ) )" - [readme] Secondary dependency setup function: "Then, you should be able to install the rest with: ``` r tima::install_tima() ```" - [readme] Package loading verification: "Load the installed package into the R environment using library(tima) and confirm no errors occur." - [readme] R-CMD-check validation workflow: "Run R-CMD-check on the installed package to validate against the CRAN submission checklist and verify all tests pass as indicated by the CI badge in the README." - [readme] Example data retrieval for verification: "In case you do not have your data ready, you can obtain some example data using: ``` r tima::get_example_files() ```" - [readme] Lifecycle and experimental status: "[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)]"