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:
- Diagnose the environment
- Check R version
- Check installed packages and versions
- Inspect
renv.lock or project library - Identify Bioconductor version compatibility
- 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
- Fix dependency conflicts
- Align package versions
- Reinstall broken packages
- Clean corrupted package libraries
- Repair project environments
- Restore with
renv::restore() - Rebuild
renv.lock - Reinitialize project library if needed
- Bioconductor troubleshooting
- Match Bioconductor version to R version
- Use
BiocManager::install() correctly - Resolve common bioinformatics package errors
- 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