Known Issues

This page documents current limitations, bugs, and workarounds. We update this list as issues are resolved.

Active Issues

Installation

Issue	Platform	Workaround	Status
Network Block	All	Request access to ports `443`, `8080`, and `873`.	Ongoing
macOS Permissions	macOS	Manual `synthetic.conf` and system reboot.	Permanent
Legacy Rosetta	Apple Silicon	Install Rosetta 2: `softwareupdate --install-rosetta`.	Ongoing

Software-Specific

Issue	Software	Workaround	Status
CUDA Mismatch	GPU Tools	Ensure system driver supports required CUDA version.	Investigating
Java Memory	GATK, IGV	Set `JAVA_OPTS="-Xmx8g"` manually.	Testing Fix
R Dependencies	Bioconductor	Install specific system libraries via OS manager.	Documentation

Troubleshooting Tools

If you encounter an issue not listed above, run these diagnostic commands:

# Check your system health
biogrids-cli diag

# Reset a corrupted environment
biogrids-reset --full

Reporting a New Issue

Before reporting, please check our FAQ and ensure your System Requirements are met.

Report a New Issue

How to Report

Please include: 1. System Info: uname -a and biogrids-cli --version. 2. Reproduction: Clear steps to trigger the bug. 3. Logs: Attach relevant files from ~/.biogrids/logs/.

Planned Improvements

Short Term

Enhanced error messages for installation failures.
Better CUDA version detection.
Expanded Linux distribution support.

Long Term

Native Apple Silicon builds for all major packages.
Automated cloud deployment templates.
Advanced dependency resolution engine.

Status Legend

Fixed: Resolved in latest release.
Investigating: Confirmed bug, solution being researched.
Ongoing: Complex issue with active development.
Won't Fix: Limited by external constraints (e.g., OS security).