cgpt-r-debugger

name	cgpt-r-debugger
description	Reproducible R debugging, profiling, and edge-case testing for scripts, functions, Quarto analysis chunks, and data pipelines; use when the user asks to diagnose incorrect R output, slow code, brittle behavior, vectorization options, memory use, or runtime failures.

CGPT R Debugger

Use this skill when the user asks to debug, profile, stress test, or optimize R code. Keep the work empirical and reproducible: run the smallest useful test harness, capture the error or timing evidence, and report the exact failure mechanism before proposing changes.

This is not broad R tutoring. Focus on concrete runtime behavior, profiling evidence, edge cases, and safe fixes.

Guardrails

• Do not edit the user's R, QMD, data, or output files unless they explicitly ask for implementation after seeing the diagnosis.
• Prefer temporary scripts in the working directory or a project diagnostics/ or quality_reports/ folder only when the user permits artifacts.
• Do not install packages without approval. If a profiling package is unavailable, fall back to base R tools.
• Preserve project conventions from CLAUDE.md, MEMORY.md, _quarto.yml, renv files, and existing scripts.
• For analysis claims, distinguish observed runtime evidence from inferred causes.

Workflow

1. Identify the target code path, expected output, inputs, side effects, and package/session assumptions.
2. Reproduce the issue with the smallest runnable harness:
   • source the function or script
   • load required inputs
   • set seeds and options when randomness or printing affects results
   • capture sessionInfo(), warnings, errors, and traceback
3. Add edge-case tests based on the code:
   • zero rows, one row, all NA, mixed types, duplicate keys, missing columns, factor versus character, unusual names, date/time boundaries, and larger synthetic inputs
4. Profile only after correctness is understood:
   • use system.time() for a baseline
   • use Rprof() and summaryRprof() for base-R profiling
   • use bench, microbenchmark, or profvis only when already available or approved
5. Classify the issue:
   • correctness bug
   • dependency or environment mismatch
   • data-shape assumption
   • numerical or statistical edge case
   • memory pressure
   • vectorization or algorithmic bottleneck
   • rendering or Quarto execution failure
6. Report the diagnosis with evidence and the smallest safe fix.

R Debugging Patterns

Use base tools first:

tryCatch(
  source("script.R"),
  error = function(e) {
    message("ERROR: ", conditionMessage(e))
    traceback()
  },
  warning = function(w) {
    message("WARNING: ", conditionMessage(w))
    invokeRestart("muffleWarning")
  }
)

sessionInfo()

For profiling:

baseline <- system.time(source("script.R"))
print(baseline)

Rprof("profile.out")
source("script.R")
Rprof(NULL)
print(summaryRprof("profile.out"))

For edge-case checks, build a small table of test inputs and record actual versus expected behavior. Do not treat passing one happy-path run as sufficient when the requested problem concerns fragility.

Performance Triage

Look specifically for:

• growing objects in loops with rbind, cbind, or c(...)
• row-wise loops over data frames where vectorized or grouped operations are clearer
• repeated file I/O inside loops
• repeated joins, filters, or model fits that can be hoisted or cached
• implicit type conversions, factor level loss, and date parsing inside tight loops
• non-deterministic order from joins, grouping, or parallel execution
• memory-heavy copies of large data frames

When recommending a refactor, show the before/after pattern only for the relevant lines and include timing evidence when possible.

Report Format

Use this compact structure:

# R Debugging Report

## Summary
- Target:
- Status: reproduced / not reproduced / partially reproduced
- Main cause:
- Proposed next action:

## Evidence
| Check | Result | Notes |
|---|---|---|

## Edge Cases
| Case | Expected | Actual | Status |
|---|---|---|---|

## Profiling
| Path or function | Time or share | Evidence |
|---|---:|---|

## Recommended Fixes
| Priority | Location | Fix | Rationale |
|---|---|---|---|

If the user asks for implementation, apply only the approved or explicitly scoped edits and rerun the reproduction harness afterward.