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

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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

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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"

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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()

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Common Issues and Solutions

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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)

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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

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Parameters

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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()

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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

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Related Sub-Skills

• create-project: Set up new projects with proper environment
• run-analysis: Execute scripts after fixing environment issues