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AGENTS

Overview

This repository contains the CodeAndRoll2 R package, a collection of utility functions for vector, matrix, and list manipulations.

Structure

  • R/ – core package functions.
    • CodeAndRoll2.R exposes the main utilities.
    • deprecated.R lists legacy helpers that should not be used in new code.
  • man/ – roxygen2-generated documentation.
  • DESCRIPTION & NAMESPACE – package metadata.
  • Development/ – auxiliary scripts used for building and maintenance; not required for package use.
  • README.md – package description, installation instructions, and an extensive function catalogue.

Development Workflow

  1. Use R (>= 4.0).
  2. After editing code in R/, keep roxygen2-style comments and regenerate documentation with: 
    devtools::document()
  3. Run checks before committing: 
    R CMD build .
R CMD check CodeAndRoll2_*.tar.gz
    (or in R: devtools::check()).
  4. Delete the generated CodeAndRoll2_*.tar.gz archive and CodeAndRoll2.Rcheck directory after the check.
  5. Commit only when checks complete without errors or warnings.

Getting Started for New Contributors

  • Read README.md for a package overview and list of available functions.
  • Explore R/CodeAndRoll2.R to see implementation style and naming conventions.
  • Review DESCRIPTION to understand package dependencies (e.g., Stringendo, ReadWriter).
  • Check deprecated.R to avoid relying on obsolete functions.
  • Suggested next steps: learn roxygen2 for documentation, devtools for package development, and review dependent packages (MarkdownReports, ggExpress, Seurat.utils) to see CodeAndRoll2 in action.