Debug Console module

The Debug Console provides real-time diagnostics and logging capabilities for monitoring SK-Ana’s internal operations and troubleshooting issues.

Overview

This module displays:

• Real-time logs from all SK-Ana processes
• ALS optimization progress and convergence messages
• Ambiguity explorer status updates
• System events and warnings
• Performance metrics

Features

Real-Time Logging

All major operations in SK-Ana write diagnostic messages to the debug console, including:

• Data loading and processing: File format detection, matrix assembly, compression operations

• SVD analysis: Decomposition progress, singular value computations

• ALS optimization:
  • Iteration progress and convergence status
  • Constraint application (positivity, unimodality, etc.)
  • Lack-of-fit evolution
  • Correction spectra coupling (when enabled)

• Ambiguity exploration: Transformation matrix exploration progress

• Kinetic modeling:
  • ODE integration status
  • Parameter optimization progress
  • Global search iterations

System Information

The console displays system information including:

• R version and platform
• Loaded packages and versions
• Memory usage
• Session information

Usage

Accessing the Debug Console

Click the Debug Console tab in the main navigation bar. The console icon (terminal symbol) helps identify this tab quickly.

Reading Log Messages

Log messages are displayed in chronological order with timestamps. Message types include:

• INFO: Normal operation messages
• WARNING: Non-critical issues that may affect results
• ERROR: Critical issues that prevent operation completion
• DEBUG: Detailed diagnostic information for troubleshooting

Troubleshooting with the Console

ALS Convergence Issues

If ALS fails to converge or produces unexpected results:

1. Check the console for warning messages about:
   • Constraint conflicts (e.g., positivity violations)
   • Matrix conditioning issues
   • Initialization problems

2. Look for iteration messages showing lack-of-fit progression

3. Verify that correction spectra coupling is working correctly (if enabled)

Performance Monitoring

The console helps identify performance bottlenecks:

• Long computation times in specific modules
• Memory allocation warnings
• Excessive iterations in optimization loops

Data Loading Problems

If data files fail to load or produce incorrect results:

1. Check console messages for:
   • File format detection results
   • Parsing errors or warnings
   • Matrix dimension mismatches
2. Verify that the correct format parameters were detected

Best Practices

• Keep the console open during long-running operations (ambiguity exploration, global optimization) to monitor progress

• Save console output when reporting bugs: copy the relevant log messages to include in bug reports

• Check for warnings after each analysis step to catch potential issues early

• Use system info to verify package versions when reproducing results

Technical Notes

• The console uses reactive output that updates automatically as new messages are logged

• Console output is stored in memory and cleared when the session ends

• Very long operations may produce extensive logs; the console automatically scrolls to show the most recent messages

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See also:

• About for version information and bug reporting
• ALS for optimization diagnostics
• Kinet for kinetic model troubleshooting