/rforge:thorough - Comprehensive R Package Analysis

Deep, comprehensive analysis using background R processes. Takes 2-5 minutes but provides publication-quality insights.

Usage

# Thorough analysis
/rforge:thorough

# With context
/rforge:thorough "Prepare RMediation for CRAN"

# Specific analysis type
/rforge:thorough --type full_check
/rforge:thorough --type coverage
/rforge:thorough --type performance

What It Does

Runs comprehensive R analysis in background:

Launch Phase (5 sec)
- Start background R process
- Return task ID immediately
- Show estimated duration
Monitoring Phase (2-5 min)
- Poll task every 10 seconds
- Show progress updates
- Display intermediate results
Results Phase (5 sec)
- Retrieve complete results
- Synthesize comprehensive report
- Provide detailed recommendations

Output Example

🔬 Launching thorough analysis...

Background R analysis started (task: abc123)
Estimated duration: 3-5 minutes

You can:
- Wait here (I'll show progress)
- Do other work (run /rforge:results abc123 later)
- Cancel anytime (Ctrl+C)

[10s] 📊 Running R CMD check...
[20s] 📊 Still running checks (platform: ubuntu)...
[30s] 📊 Checking examples...
[45s] ✅ R CMD check complete: 0 errors, 0 warnings, 0 notes
[60s] 📊 Running test suite...
[75s] 📊 Calculating coverage...
[90s] ✅ Coverage analysis complete: 94.2%
[120s] 📊 Running performance benchmarks...
[150s] ✅ Performance analysis complete

✅ Thorough analysis complete! (2m 35s)

═══════════════════════════════════════════════════

🎯 COMPREHENSIVE ANALYSIS: RMediation

📦 PACKAGE INFO:
  • Version: 2.0.1
  • R dependency: >= 3.5.0
  • Imports: 3 packages
  • Suggests: 5 packages

🔍 R CMD CHECK: ✅ PASS
  • Errors: 0
  • Warnings: 0
  • Notes: 0
  • Platforms tested: ubuntu-latest, macos-latest, windows-latest
  • Time: 45 seconds

🧪 TEST RESULTS: ✅ EXCELLENT
  • Tests: 187/187 passing
  • Coverage: 94.2%
  • Test files: 12
  • Assertions: 1,245
  • Performance: 2.3 seconds

📊 COVERAGE BREAKDOWN:
  • R/: 96.1% (138/143 lines)
  • R/ci_mediation.R: 98.5%
  • R/bootstrap.R: 92.3% ⚠️ (needs 2 more tests)
  • R/utils.R: 100%

⚡ PERFORMANCE:
  • ci_mediation(): 2.3ms (fast)
  • bootstrap_ci(): 145ms (acceptable)
  • Benchmarked: 1000 iterations
  • No regressions detected

🎯 DEPENDENCY IMPACT:
  • Reverse dependencies: 5 packages
  • All passing with current version
  • 2 packages would be affected by API change

📝 DOCUMENTATION:
  • Roxygen: ✅ Up to date
  • Vignettes: 3 found, all build successfully
  • Examples: All run without errors
  • NEWS.md: Last entry 2.0.0 (needs update for 2.0.1)
  • README badges: All current

🌐 CRAN STATUS:
  • Current CRAN version: 2.0.0
  • Check results: All OK (last check: 2 days ago)
  • Incoming: No submissions pending
  • Reverse check results: All passing

💯 OVERALL HEALTH SCORE: 95/100 (A)

Grade breakdown:
  • Code quality: 96/100 (excellent test coverage)
  • Documentation: 92/100 (minor NEWS update needed)
  • CRAN compliance: 100/100 (perfect)
  • Performance: 94/100 (good)
  • Maintenance: 91/100 (active development)

═══════════════════════════════════════════════════

📋 DETAILED RECOMMENDATIONS:

🔥 BEFORE RELEASE:
  1. Update NEWS.md with 2.0.1 changes
  2. Add 2 tests to R/bootstrap.R (coverage < 95%)
  3. Update version badge in README
  4. Run final check: R CMD check --as-cran

🎯 FOR THIS CHANGE:
  1. Implement bootstrap algorithm update (3 hours)
  2. Update algorithm vignette
  3. Benchmark new vs old performance
  4. Update 2 affected packages (mediate, sensitivity)

⭐ OPTIONAL IMPROVEMENTS:
  1. Add performance benchmarks to vignettes
  2. Create pkgdown site
  3. Add code coverage badge

═══════════════════════════════════════════════════

Next steps:
[1] Generate release checklist
[2] Create cascade plan for dependents
[3] Export report to markdown
[4] Something else

Analysis Types

full_check (Default)

R CMD check --as-cran
Full test suite
Coverage analysis
Basic performance
Time: 3-5 minutes

coverage

Detailed coverage by file
Identify untested code
Generate coverage report
Time: 2-3 minutes

performance

Benchmark key functions
Compare to baseline
Memory profiling
Time: 2-4 minutes

Background Task Management

Check Task Status

# While analysis running in background
/rforge:status abc123

Get Results Later

# If you closed Claude or interrupted
/rforge:results abc123

Cancel Task

# Stop background R process
/rforge:cancel abc123

When to Use

Use /rforge:thorough when:

✅ Preparing for CRAN submission
✅ Need comprehensive coverage report
✅ Want performance benchmarks
✅ Release readiness check
✅ Detailed dependency analysis
✅ Can wait 2-5 minutes

Don't use when:

❌ Just need quick status (use /rforge:quick)
❌ Iterating rapidly (use /rforge:analyze)
❌ In a hurry

Options

--type <type> - Analysis type (full_check, coverage, performance)
--package <path> - Explicit package path
--platforms <list> - Test platforms (ubuntu, macos, windows)
--wait - Wait for completion (default: true)
--background - Return immediately, check later
--json - Raw JSON output

Output to File

# Export comprehensive report
/rforge:thorough --export report.md

# Or JSON for CI/CD
/rforge:thorough --export report.json --json

CI/CD Integration

Perfect for automated checks:

# .github/workflows/rforge-check.yml
- name: Thorough RForge Check
  run: |
    npx rforge-mcp
    claude-code "/rforge:thorough --json --export results.json"
    # Parse results.json for pass/fail

ADHD Considerations

Challenges:

⏰ Takes 2-5 minutes (long wait)
🎯 Risk of distraction during wait

Mitigations:

📊 Live progress updates every 10s
🔔 Can do other work, come back later
⏱️ Clear time estimates upfront
✅ Incremental result streaming
💾 Results saved if interrupted

Comparison

Feature	Quick	Analyze	Thorough
Time	10s	30s	2-5min
R CMD check	❌	❌	✅
Test suite	Status only	✅	✅ Full
Coverage	Last run	✅	✅ Detailed
Performance	❌	❌	✅
CRAN check	❌	Status	✅ Full
Depth	Surface	Medium	Deep
Use case	Quick check	Daily dev	Pre-release

Related Skills

/rforge:quick - Ultra-fast (10s)
/rforge:analyze - Balanced (30s)
/rforge:status <task> - Check background task
/rforge:results <task> - Get background results

Perfect for: Pre-release validation, comprehensive audits, CRAN preparation Trade-off: Depth over speed (worth the wait for releases!)

Pro tip: Run /rforge:thorough at end of day, review results in morning. Or run in background while you work on something else.

/thorough