debug-r-env

name: debug-r-env

description: Check for missing R packages, resolve library conflicts, verify R version compatibility, and suggest fixes for environment issues.

Debug R Environment

A specialized sub-skill for troubleshooting and fixing R environment issues including missing packages, version conflicts, and configuration problems.

Overview

This sub-skill diagnoses and resolves common R environment problems that prevent scripts from running correctly. It analyzes R installations, package dependencies, and system configurations.

Use this sub-skill when the user wants to:

• Check if required packages are installed

• Resolve package version conflicts

• Fix "package not found" errors

• Verify R version compatibility

• Debug library path issues

• Troubleshoot compilation failures

What This Sub-Skill Does

When invoked, this sub-skill will:

1. Analyze R environment

   • Check R version and platform

   • List installed packages and versions

   • Examine library paths

   • Verify package dependencies

2. Identify missing packages

   • Scan scripts for library() and require() calls

   • Check for Bioconductor packages

   • Detect GitHub package dependencies

   • Identify version mismatches

3. Diagnose conflicts

   • Find package masking issues

   • Detect incompatible versions

   • Identify system dependencies

   • Check compilation requirements

4. Provide solutions

   • Generate installation commands

   • Suggest version updates

   • Recommend renv initialization

   • Provide troubleshooting steps

Example User Requests

• "My R script says 'package not found'"

• "Check if all packages for RNA-seq analysis are installed"

• "Fix my R environment - ggplot2 won't load"

• "Why is DESeq2 throwing an error?"

• "Debug the package dependencies in my project"

• "Install all required packages for my analysis"

Diagnostic Checks

Environment Scan

# R version and platform

version

R.version.string



# Library paths

.libPaths()



# Installed packages

installed.packages()[,c("Package", "Version")]



# Package conflicts

sessionInfo()

conflicts()

Missing Package Detection

# Scan scripts for library() calls

grep("library\\(|require\\(", scripts, value = TRUE)



# Check if packages are installed

is_installed <- function(pkg) {

  require(pkg, quietly = TRUE, character.only = TRUE)

}

Dependency Resolution

# Check package dependencies

tools::package_dependencies()



# Verify installation

packageVersion("ggplot2")



# Check for updates

old.packages()

Common Issues and Solutions

| Issue | Diagnosis | Solution |

|-------|-----------|----------|

| "there is no package called" | Package not installed | install.packages("pkgname") |

| Bioconductor package not found | Bioconductor not configured | BiocManager::install("pkgname") |

| Package masked by another | Namespace conflict | library(pkgname) explicitly |

| Compilation error | Missing system dependencies | Install system build tools |

| Version mismatch | Package requires newer R | Update R or use older package |

| renv activation fails | Corrupted lock file | Delete and restore renv.lock |

Installation Command Generator

For different package sources, this sub-skill generates appropriate commands:

CRAN Packages

install.packages("package_name")

Bioconductor Packages

if (!requireNamespace("BiocManager", quietly = TRUE))

    install.packages("BiocManager")

BiocManager::install("package_name")

GitHub Packages

remotes::install_github("username/package")

# or

devtools::install_github("username/package")

Multiple Packages

packages <- c("tidyverse", "ggplot2", "dplyr")

install.packages(packages)

Analysis-Specific Package Lists

Differential Expression

• DESeq2

• edgeR

• limma

• EnhancedVolcano

• pheatmap

Statistical Modeling

• lme4

• broom

• car

• emmeans

• multcomp

Data Visualization

• ggplot2

• patchwork

• scales

• cowplot

• viridis

Bioinformatics

• Biostrings

• GenomicRanges

• biomaRt

• AnnotationDbi

Parameters

| Parameter | Description | Default |

|-----------|-------------|---------|

| script_path | Path to R script to analyze | Current directory |

| required_packages | List of packages to verify | Auto-detect from scripts |

| check_bioc | Check Bioconductor packages | true |

| check_updates | Check for available updates | false |

| fix_issues | Attempt to install missing packages | false |

Diagnostic Report Example

=== R Environment Diagnostic Report ===



R Version: 4.3.2 (2023-10-31)

Platform: x86_64-pc-linux-gnu

Library Path: /home/user/R/x86_64-pc-linux-gnu-library/4.3



--- Installed Packages ---

tidyverse    2.0.0  ✓

ggplot2      3.4.4  ✓

dplyr        1.1.3  ✓



--- Missing Packages ---

DESeq2       ✗     (Bioconductor required)

EnhancedVolcano ✗   (CRAN)

pheatmap     ✗     (CRAN)



--- Installation Commands ---

if (!requireNamespace("BiocManager", quietly = TRUE))

    install.packages("BiocManager")

BiocManager::install("DESeq2")

install.packages(c("EnhancedVolcano", "pheatmap"))



--- Warnings ---

- R 4.3.2 detected; some packages may require R >= 4.4.0

- renv not initialized; consider running renv::init()

Notes

• Always checks both CRAN and Bioconductor sources

• Respects renv.lock if present in project

• Provides safe installation commands (review before running)

• Detects system dependencies for compilation

• Checks for package masking conflicts

Related Sub-Skills

• create-project: Set up new projects with proper environment

• run-analysis: Execute scripts after fixing environment issues