debugging-r-environment-and-dependencies

# 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 --- ## 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 --- ## 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" --- ## 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 --- ## 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 | --- ## 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