Error running Basic Memory in Claude Code on fedora

[phernandez]

Installed with uv on Fedora 42.

I've added the following to .mcp.json in my root project:

{
    "basic-memory": {
      "command": "uvx",
      "args": ["basic-memory", "mcp"],
      "env": {}
    }
  }
}

• I made sure I was on the main project
• I tested basic-memory tool to write a simple md and it worked.
• I deleted the 2 folders related to the package in ~ and relaunched in case it was corruption somehow

Terminal:

$ basic-memory tool write-note --title "First!" --folder "test" --content "Write your first note"
/home/user/.local/share/uv/tools/basic-memory/lib/python3.13/site-packages/aiosqlite/core.py:105: DeprecationWarning: The default datetime adapter is deprecated as of Python 3.12; see the sqlite3 documentation for suggested replacement recipes
  result = function()
# Created note
file_path: test/First!.md
permalink: test/first
checksum: a0c1d2a0

derek@pc:~$ basic-memory project default main
/home/user/.local/share/uv/tools/basic-memory/lib/python3.13/site-packages/sqlalchemy/sql/schema.py:3624: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).
  return util.wrap_callable(lambda ctx: fn(), fn)  # type: ignore
Project 'main' set as default successfully
Project activated for current session

derek@pc:~$ uv tool update basic-memory
Nothing to upgrade

derek@pc:~$ uvx basic-memory mcp
[06/30/25 19:54:27] INFO     Starting MCP server 'Basic Memory' with transport 'stdio'                                                                                                                                             server.py:1307
/home/user/.local/share/uv/tools/basic-memory/lib/python3.13/site-packages/aiosqlite/core.py:105: DeprecationWarning: The default datetime adapter is deprecated as of Python 3.12; see the sqlite3 documentation for suggested replacement recipes
  result = function()

derek@pc:~$ basic-memory sync
Syncing project: main
Project path: /home/user/basic-memory
Project 'main': Everything up to date

Claude Code

╭───────────────────────────────────────────────────╮
│ Basic-memory MCP Server                           │
│                                                   │
│ Status: ✘ failed                                  │
│ Command: uvx                                      │
│ Args: basic-memory mcp                            │
│                                                   │
│ ❯ 1. Back                                         │
╰───────────────────────────────────────────────────╯

Any suggestions on what I can try next ?

Originally posted by @Extarys in https://github.com/basicmachines-co/basic-memory/discussions/196

[Extarys]

Thanks for that!

Operating System: Fedora Linux 42
KDE Plasma Version: 6.4.2
KDE Frameworks Version: 6.15.0
Qt Version: 6.9.1
Kernel Version: 6.15.4-200.fc42.x86_64 (64-bit)
Graphics Platform: Wayland
Processors: 24 × AMD Ryzen 9 5900X 12-Core Processor
Memory: 64 GiB of RAM (62.7 GiB usable)
Graphics Processor: AMD Radeon RX 6650 XT

$ uv --version
uv 0.7.17
$ python --version
Python 3.13.5

[phernandez]

@claude can you see the github discussion at https://github.com/basicmachines-co/basic-memory/discussions/196 and try to see what the problem is?

[claude]

Claude finished @phernandez's task —— View job

---

Analyzing Basic Memory MCP Server Issue on Fedora

I'm investigating why the Basic Memory MCP server works when run manually but fails in Claude Code on Fedora.

Todo List:

• Read repository context and MCP server implementation
• Analyze the GitHub discussion for additional details
• Investigate potential differences between manual vs Claude Code execution
• Check for Fedora/uv-specific issues
• Provide diagnostic steps and solutions

Root Cause Analysis:

Based on the codebase analysis and the issue description, I've identified several potential causes:

1. Python 3.13 Compatibility Issues

• The deprecation warnings indicate Python 3.13 compatibility problems with SQLite datetime handling
• These warnings might be causing the MCP server to fail in Claude Code's stricter environment

2. Environment Differences

• Claude Code may not have the same environment variables or PATH as the user's shell
• The uvx execution context might differ between manual and Claude Code execution

3. Process Communication

• The MCP server uses stdio transport, which requires proper stdin/stdout handling
• Claude Code's process management might interfere with stdio communication

Diagnostic Steps & Solutions:

Solution 1: Fix Python 3.13 Compatibility
Try downgrading to Python 3.12 temporarily:

# Install with Python 3.12
uv tool install --python 3.12 basic-memory

Solution 2: Use Full Path Configuration
Update your .mcp.json to use the full path:

{
  "basic-memory": {
    "command": "/home/user/.local/share/uv/tools/basic-memory/bin/basic-memory",
    "args": ["mcp"],
    "env": {
      "PYTHONPATH": "/home/user/.local/share/uv/tools/basic-memory/lib/python3.13/site-packages"
    }
  }
}

Solution 3: Environment Variables
Add required environment variables to your .mcp.json:

{
  "basic-memory": {
    "command": "uvx", 
    "args": ["basic-memory", "mcp"],
    "env": {
      "BASIC_MEMORY_PROJECT": "main",
      "PYTHONWARNINGS": "ignore"
    }
  }
}

Solution 4: Debug Mode
Create a debug wrapper script:

#!/bin/bash
echo "Starting Basic Memory MCP server..." >&2
echo "Environment: $(env)" >&2
echo "Python version: $(python --version)" >&2
exec uvx basic-memory mcp

Immediate Next Steps:

1. Try Solution 1 (Python 3.12) first - this is most likely to work
2. If that doesn't work, try Solution 2 with full paths
3. Add environment variables as in Solution 3
4. Use the debug wrapper if you need to troubleshoot further

The core issue appears to be Python 3.13 compatibility combined with Claude Code's process execution environment. The deprecation warnings suggest the application may be failing silently in Claude Code's stricter environment.

---

[phernandez]

The Python 3.13 deprecation warnings that were causing stderr output on startup have been fixed:

1. SQLite datetime adapter warning - Fixed in previous commits by updating SQLite datetime handling
2. datetime.utcnow() warning - Fixed by migrating to timezone-aware datetime objects

These warnings were likely causing Claude Code to interpret the MCP server as "failed" even though it was working correctly. The server should now start cleanly without any deprecation warnings.

We've also added Python 3.13 to our CI test matrix (#331) to catch these issues proactively going forward.

If you're still experiencing issues with Claude Code after updating to the latest version, please reopen this issue or create a new one with the specific error details.