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jackkuo666

Debugging R Environment And Dependencies

by JackKuo666 · GitHub ↗ · v0.1.0
cross-platform ⚠ suspicious
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Install in OpenClaw
/install 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...
README (SKILL.md)

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
Usage Guidance
This skill appears to be what it claims: a troubleshooting guide for R environments. Things to keep in mind before using it: (1) many suggested fixes involve running OS package-manager commands (sudo apt / brew / dnf) and installing compilers—review any commands before executing them and run on a machine where you have permission to install system packages; (2) renv operations and lockfile updates will change project state—commit or back up your repo before making changes; (3) the skill does not ask for API keys or secrets, but some fixes (e.g., rJava) may require installing external software like a JDK—verify sources yourself; (4) if you want extra safety, have the skill produce the exact commands it would run and run them manually rather than allowing autonomous execution.
Capability Analysis
Type: OpenClaw Skill Name: debugging-r-environment-and-dependencies Version: 0.1.0 The skill bundle is designed to diagnose and fix R environment issues, which inherently requires the AI agent to execute system-level commands (e.g., `sudo apt install`, `brew install`) to install missing dependencies and compilers. This capability is explicitly stated in `SKILL.md` and demonstrated with examples in `examples/missing-system-deps/README.md`. While necessary for its stated purpose, the ability to execute arbitrary system commands, potentially with elevated privileges, introduces a significant Remote Code Execution vulnerability. There is no evidence of intentional malicious behavior such as data exfiltration, persistence, or prompt injection for harmful objectives within the provided files, but the inherent high-risk capabilities warrant a 'suspicious' classification.
Capability Assessment
✓ Purpose & Capability
Name/description match the actual instructions: the skill diagnoses R version/package/renv/Bioconductor issues and proposes installing system libraries and compilers when needed. All required actions are proportional to fixing R environment problems.
✓ Instruction Scope
SKILL.md stays within scope: it lists commands to check R and project files (renv.lock), suggests OS-specific package-manager commands, and recommends renv and BiocManager operations. It does not instruct reading unrelated system files, accessing external endpoints, or exfiltrating secrets.
✓ Install Mechanism
Instruction-only skill with no install spec and no code files; nothing is downloaded or written by an installer. Risk from installation is low because the skill only suggests standard OS package-manager commands (apt/brew/dnf) rather than pulling archives from arbitrary URLs.
✓ Credentials
The skill declares no required environment variables, credentials, or config paths. It may suggest system-level installs that require elevated privileges (sudo), which is appropriate for installing compilers or system libs but not a secret-exfiltration risk.
✓ Persistence & Privilege
always is false and the skill does not request persistent agent privileges or modify other skills' configs. Autonomous invocation is allowed by platform default but is not unusual here and does not combine with other red flags.
How to Use
  1. Make sure OpenClaw is installed (local or Docker)
  2. Run the install command in chat: /install debugging-r-environment-and-dependencies
  3. After installation, invoke the skill by name or use /debugging-r-environment-and-dependencies
  4. Provide required inputs per the skill's parameter spec and get structured output
Version History
v0.1.0
- Initial release of the R environment and dependency debugging skill. - Diagnose and resolve package installation failures, version conflicts, and system dependency errors. - Troubleshoot and repair `renv` or Bioconductor environment issues. - Provide guidance for missing compilers, development libraries, and PATH/permission problems. - Restore or rebuild working R project environments to ensure script compatibility. - Offer OS-specific steps for resolving common package and system-level R problems.
Metadata
Slug debugging-r-environment-and-dependencies
Version 0.1.0
License —
All-time Installs 0
Active Installs 0
Total Versions 1
Frequently Asked Questions

What is Debugging R Environment And Dependencies?

Diagnose and fix R environment issues, including package installation failures, dependency conflicts, system library problems, renv errors, and Bioconductor... It is an AI Agent Skill for Claude Code / OpenClaw, with 484 downloads so far.

How do I install Debugging R Environment And Dependencies?

Run "/install debugging-r-environment-and-dependencies" in the OpenClaw or Claude Code chat to install it in one step — no extra setup required.

Is Debugging R Environment And Dependencies free?

Yes, Debugging R Environment And Dependencies is completely free (open-source). You can download, install and use it at no cost.

Which platforms does Debugging R Environment And Dependencies support?

Debugging R Environment And Dependencies is cross-platform and runs anywhere OpenClaw / Claude Code is available (cross-platform).

Who created Debugging R Environment And Dependencies?

It is built and maintained by JackKuo666 (@jackkuo666); the current version is v0.1.0.

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