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name: debugging-r-environment-and-dependencies description: Diagnose and fix R environment issues, including package installation failures, dependency conflicts, system library problems, renv errors, and Bioconductor version mismatches.

Debugging R Environment and Dependencies

This skill focuses on resolving problems related to R environments rather than analysis logic. It helps restore a working setup so that R scripts and projects can run successfully.

Use this skill when the user encounters:

• Package installation failures
• Version conflicts between packages
• renv or packrat environment issues
• Bioconductor version mismatches
• System dependency errors (e.g., missing compilers or libraries)
• R failing to start or load packages

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What This Skill Does

When activated, this skill will:

1. Diagnose the environment

   • Check R version
   • Check installed packages and versions
   • Inspect renv.lock or project library
   • Identify Bioconductor version compatibility

2. Resolve package installation issues

   • Suggest correct CRAN/Bioconductor repositories
   • Install missing system dependencies (e.g., libxml2, curl, openssl)
   • Handle compilation failures on Linux/macOS/Windows

3. Fix dependency conflicts

   • Align package versions
   • Reinstall broken packages
   • Clean corrupted package libraries

4. Repair project environments

   • Restore with renv::restore()
   • Rebuild renv.lock
   • Reinitialize project library if needed

5. Bioconductor troubleshooting

   • Match Bioconductor version to R version
   • Use BiocManager::install() correctly
   • Resolve common bioinformatics package errors

6. System-level troubleshooting

   • Install missing compilers (e.g., gcc, gfortran)
   • Install development libraries required for R packages
   • Fix PATH or permission issues

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Example User Requests That Should Trigger This Skill

• "I can't install tidyverse"
• "This package fails with a compilation error"
• "renv restore is broken"
• "Bioconductor says my version is incompatible"
• "library() fails even though the package is installed"
• "R says shared object cannot be loaded"

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Example Workflow

User: I get an error when installing sf.

Skill actions:

• Detect missing system libraries (GEOS, GDAL, PROJ)
• Provide OS-specific install commands
• Retry R package installation
• Confirm successful library loading

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Common Problem Categories

Category	Examples
Missing system libs	xml2, curl, openssl, sf, rJava
Compiler issues	gfortran missing, Xcode tools missing
Version mismatch	old R vs new package
Bioconductor mismatch	wrong Bioc version for R
renv problems	corrupted cache, lockfile mismatch
Permission issues	cannot write to library path

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Notes

• Do not modify analysis code unless necessary
• Prefer fixing the environment over rewriting scripts
• Always aim to make the project reproducible
• Recommend renv for future environment stability