Describe the bug

I followed the steps mentioned in the docs(https://github.com/github/github-mcp-server/blob/main/docs/installation-guides/install-claude.md) from claude-desktop section to connect to github mcp. But I am getting "Message from client: {"jsonrpc":"2.0","method":"notifications/cancelled","params":{"requestId":0,"reason":"McpError: MCP error -32001: Request timed out"}} { metadata: undefined }" error. Docker was in running state too and the PAT was valid as well.

Steps to reproduce the behavior

1. Generate a github PAT granting permissions to public repo
2. Ensure docker is running.
3. have the github config in claude_desktop_changes.json:
   "github": { "command": "docker", "args": [ "run", "-i", "--rm", "-e", "GITHUB_PERSONAL_ACCESS_TOKEN", "ghcr.io/github/github-mcp-server" ], "env": { "GITHUB_PERSONAL_ACCESS_TOKEN": "github_pat_abc" } }
4. restart claude desktop

Expected vs actual behavior

Expected behavior was to see the list of github tools in the UI. But got the timeout error instead after 20-25 seconds. Initially it showed running state in the settings after few more seconds it went to failed state due to time out error

Logs

2025-07-22T06:40:33.124Z [github] [info] Initializing server... { metadata: undefined }
2025-07-22T06:40:33.177Z [github] [info] Using MCP server command: C:\Program Files\Docker\Docker\resources\bin\docker.exe with args and path: {
metadata: {
args: [
'run',
'-i',
'--rm',
'-e',
'GITHUB_PERSONAL_ACCESS_TOKEN',
'ghcr.io/github/github-mcp-server',
[length]: 6
],
paths: [
'C:\Program Files\nodejs',
'C:\Scripts\',
'C:\',
'c:\Users\hp\AppData\Local\Programs\cursor\resources\app\bin',
'C:\Program Files\Microsoft SDKs\Azure\CLI2\wbin',
'C:\Users\hp\AppData\Local\Programs\Python\Python39\Scripts\',
'C:\Users\hp\AppData\Local\Programs\Python\Python39\',
'C:\Python311\Scripts\',
'C:\Python311\',
'C:\Program Files\Common Files\Oracle\Java\javapath',
'C:\Windows\system32',
'C:\Windows',
'C:\Windows\System32\Wbem',
'C:\Windows\System32\WindowsPowerShell\v1.0\',
'C:\Windows\System32\OpenSSH\',
'C:\Program Files\MongoDB\mongosh-1.10.1-win32-x64\bin',
'C:\Program Files\MongoDB\Server\6.0\bin',
'C:\Program Files\Git\cmd',
'C:\Program Files\Docker\Docker\resources\bin',
'C:\minikube',
'C:\Program Files\Java\jdk-17',
'C:\Program Files\Common Files\Oracle\Java\javapath_target_169341296',
'C:\Program Files\OpenSSL-Win64\bin',
'C:\Users\hp\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\Scripts',
'C:\Program Files\nodejs\',
'C:\ProgramData\chocolatey\bin',
'C:\Program Files\Tesseract-OCR',
'C:\Windows\System32\OpenSSH\',
'C:\Program Files (x86)\Google\Cloud',
'c:\Users\hp\AppData\Local\Programs\cursor\resources\app\bin',
'C:\Program Files (x86)\ngrok',
'C:\Program Files\Amazon\AWSCLIV2\',
'C:\Users\hp\.local\bin',
'C:\Users\hp\AppData\Local\Programs\Python\Python310\Scripts\',
'C:\Users\hp\AppData\Local\Programs\Python\Python310\',
'C:\Users\hp\AppData\Local\Programs\Python\Python39\Scripts\',
'C:\Users\hp\AppData\Local\Programs\Python\Python39\',
'C:\Program Files\MySQL\MySQL Shell 8.0\bin\',
'C:\Users\hp\AppData\Local\Microsoft\WindowsApps',
'C:\Users\hp\AppData\Local\Programs\Microsoft VS Code\bin',
'C:\Program Files\JetBrains\IntelliJ IDEA 2023.1.3\bin',
'',
'C:\Program Files\MongoDB\mongosh-1.10.1-win32-x64\bin',
'C:\Program Files\MongoDB\Server\6.0\bin',
'C:\Program Files\JetBrains\PyCharm 2023.2.1\bin',
'',
'C:\Users\hp\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\Scripts',
'C:\Users\hp\AppData\Roaming\npm',
'C:\Users\hp\Documents\notebooks\chrome-win64\chrome-win64',
'C:\Users\hp\AppData\Local\JetBrains\DataSpell 2023.2.2\bin',
'',
'C:\Program Files\Tesseract-OCR',
'C:\Program Files\JetBrains\DataGrip 2023.3.4\bin',
'',
'C:\Users\hp\AppData\Local\Programs\Ollama',
'C:\Program Files\JetBrains\PyCharm Community Edition 2024.1\bin',
'',
[length]: 57
]
}
} %o
2025-07-22T06:40:33.182Z [github] [info] Server started and connected successfully { metadata: undefined }
2025-07-22T06:40:33.190Z [github] [info] Message from client: {"method":"initialize","params":{"protocolVersion":"2025-06-18","capabilities":{},"clientInfo":{"name":"claude-ai","version":"0.1.0"}},"jsonrpc":"2.0","id":0} { metadata: undefined }
2025-07-22T06:41:33.185Z [github] [info] Message from client: {"jsonrpc":"2.0","method":"notifications/cancelled","params":{"requestId":0,"reason":"McpError: MCP error -32001: Request timed out"}} { metadata: undefined }
2025-07-22T06:41:33.186Z [github] [info] Client transport closed { metadata: undefined }
2025-07-22T06:41:33.186Z [github] [info] Server transport closed { metadata: undefined }
2025-07-22T06:41:33.186Z [github] [info] Client transport closed { metadata: undefined }
2025-07-22T06:41:33.186Z [github] [info] Server transport closed unexpectedly, this is likely due to the process exiting early. If you are developing this MCP server you can add output to stderr (i.e. console.error('...') in JavaScript, print('...', file=sys.stderr) in python) and it will appear in this log. { metadata: undefined }
2025-07-22T06:41:33.186Z [github] [error] Server disconnected. For troubleshooting guidance, please visit our debugging documentation { metadata: { context: 'connection', stack: undefined } }
2025-07-22T06:41:33.192Z [github] [info] Server transport closed { metadata: undefined }
2025-07-22T06:41:33.192Z [github] [info] Client transport closed { metadata: undefined }