Installing extensions at system level (user: `root`, built-in location) throws an error

[benz0li]

Is there an existing issue for this?

• I have searched the existing issues

OS/Web Information

• Web Browser: Safari v18.0.1 (20619.1.26.31.7)
• Local OS: macOS 15.0.1 (24A348)
• Remote OS: Debian 12 (bookworm)
• Remote Architecture: x86_64
• code-server --version: 4.94.2-rc.1 dd2e9fc with Code 1.94.2

Steps to Reproduce

1. Start container:

   docker run --rm -ti \
     -u root \
     -e NB_USER=root \
     -e NB_UID=0 \
     -e NB_GID=0 \
     glcr.b-data.ch/jupyterlab/python/base:3.12.7-code-server-4.94.2-rc.1-linux-amd64 \
     bash

2. Install extension:

   code-server \
     --extensions-dir /opt/code-server/lib/vscode/extensions \
     --install-extension ms-python.python

Expected

Installing extensions...
Installing extension 'ms-python.python'...
Extension 'ms-python.debugpy' v2024.12.0 was successfully installed.
Extension 'ms-python.python' v2024.16.1 was successfully installed.

Actual

Installing extensions...
Installing extensions...
Installing extension 'ms-python.python'...
Installing extension 'ms-python.python'...
[2024-10-19T05:53:53.402Z] error parent:77 Uncaught exception: ENOTEMPTY: directory not empty, rename '/opt/code-server/lib/vscode/extensions/.4361a9d7-c95f-49fb-a7cf-6f4ae4201a3c' -> '/opt/code-server/lib/vscode/extensions/ms-python.debugpy-2024.12.0-linux-x64'
[2024-10-19T05:53:53.403Z] error parent:77 Error: ENOTEMPTY: directory not empty, rename '/opt/code-server/lib/vscode/extensions/.4361a9d7-c95f-49fb-a7cf-6f4ae4201a3c' -> '/opt/code-server/lib/vscode/extensions/ms-python.debugpy-2024.12.0-linux-x64'
    at async Object.rename (node:internal/fs/promises:782:10)
    at async Object.nE (file:///opt/code-server/lib/vscode/out/vs/server/node/server.main.js:45:5381)
    at async yf.G (file:///opt/code-server/lib/vscode/out/vs/server/node/server.main.js:54:24201)
    at async yf.extractUserExtension (file:///opt/code-server/lib/vscode/out/vs/server/node/server.main.js:54:21240)
    at async zc.rb (file:///opt/code-server/lib/vscode/out/vs/server/node/server.main.js:54:14468)
[2024-10-19T05:53:53.962Z] error parent:77 Uncaught exception: ENOTEMPTY: directory not empty, rename '/opt/code-server/lib/vscode/extensions/.0c81ab66-e49a-4744-af2d-3a7ca1755d35' -> '/opt/code-server/lib/vscode/extensions/ms-python.python-2024.16.1-universal'
[2024-10-19T05:53:53.962Z] error parent:77 Error: ENOTEMPTY: directory not empty, rename '/opt/code-server/lib/vscode/extensions/.0c81ab66-e49a-4744-af2d-3a7ca1755d35' -> '/opt/code-server/lib/vscode/extensions/ms-python.python-2024.16.1-universal'
    at async Object.rename (node:internal/fs/promises:782:10)
    at async Object.nE (file:///opt/code-server/lib/vscode/out/vs/server/node/server.main.js:45:5381)
    at async yf.G (file:///opt/code-server/lib/vscode/out/vs/server/node/server.main.js:54:24201)
    at async yf.extractUserExtension (file:///opt/code-server/lib/vscode/out/vs/server/node/server.main.js:54:21240)
    at async zc.rb (file:///opt/code-server/lib/vscode/out/vs/server/node/server.main.js:54:14468)
Error while installing extensions: ENOTEMPTY: directory not empty, rename '/opt/code-server/lib/vscode/extensions/.0c81ab66-e49a-4744-af2d-3a7ca1755d35' -> '/opt/code-server/lib/vscode/extensions/ms-python.python-2024.16.1-universal'
ENOTEMPTY: directory not empty, rename '/opt/code-server/lib/vscode/extensions/.0c81ab66-e49a-4744-af2d-3a7ca1755d35' -> '/opt/code-server/lib/vscode/extensions/ms-python.python-2024.16.1-universal'

Logs

See above.

Screenshot/Video

-

Does this bug reproduce in native VS Code?

This cannot be tested in native VS Code

Does this bug reproduce in GitHub Codespaces?

This cannot be tested in GitHub Codespaces

Are you accessing code-server over a secure context?

• I am using a secure context.

Notes

It seems to work at user level (user: root) by executing code-server --install-extension ms-python.python, but ls -al ~/.local/share/code-server/extensions reveals

drwx------ 4 root root 4096 Oct 19 06:00 .
drwxr-xr-x 9 root root 4096 Oct 19 06:00 ..
drwxr-xr-x 7 root root 4096 Oct 19 06:00 .b88d8567-9056-4934-883b-6ae404444689
-rw-r--r-- 1 root root  804 Oct 19 06:00 extensions.json
drwxr-xr-x 5 root root 4096 Oct 19 06:00 ms-python.debugpy-2024.12.0-linux-x64

which does not look fine.

FYI @code-asher

[benz0li]

Installing extensions using the GUI seem to work fine at user level (user: jovyan):

1. Start container:

   docker run --rm -ti \
     -p 8888:8888 \
     -e GEN_CERT=yes \
     -ti glcr.b-data.ch/jupyterlab/python/base:3.12.7-code-server-4.94.2-rc.1-linux-amd64

2. Open https://127.0.0.1:8888/lab?token=... in a browser

3. Click code-server to start the application

4. Install Python extension using the GUI

[06:09:30] Getting Manifest... ms-python.python
[06:09:31] Installing extension: ms-python.python {
  isMachineScoped: false,
  installPreReleaseVersion: false,
  pinned: false,
  installOnlyNewlyAddedFromExtensionPack: true,
  isApplicationScoped: false,
  profileLocation: un {
    scheme: 'file',
    authority: '',
    path: '/home/jovyan/.local/share/code-server/extensions/extensions.json',
    query: '',
    fragment: '',
    _formatted: 'file:///home/jovyan/.local/share/code-server/extensions/extensions.json',
    _fsPath: '/home/jovyan/.local/share/code-server/extensions/extensions.json'
  },
  productVersion: { version: '1.94.2', date: '2024-10-18T04:36:19.894Z' }
}
[06:09:31] Getting Manifest... ms-python.debugpy
[06:09:31] Installing extension: ms-python.debugpy {
  isMachineScoped: false,
  installPreReleaseVersion: false,
  pinned: false,
  installOnlyNewlyAddedFromExtensionPack: true,
  isApplicationScoped: false,
  profileLocation: un {
    scheme: 'file',
    authority: '',
    path: '/home/jovyan/.local/share/code-server/extensions/extensions.json',
    query: '',
    fragment: '',
    _formatted: 'file:///home/jovyan/.local/share/code-server/extensions/extensions.json',
    _fsPath: '/home/jovyan/.local/share/code-server/extensions/extensions.json'
  },
  productVersion: { version: '1.94.2', date: '2024-10-18T04:36:19.894Z' },
  context: { dependecyOrPackExtensionInstall: true }
}
[06:09:33] Could not load vsce-sign module Cannot find package '@vscode/vsce-sign' imported from /opt/code-server/lib/vscode/out/vs/server/node/server.main.js
[06:09:33] Extension signature verification is not done: ms-python.debugpy
[06:09:33] Could not load vsce-sign module Cannot find package '@vscode/vsce-sign' imported from /opt/code-server/lib/vscode/out/vs/server/node/server.main.js
[06:09:33] Extension signature verification is not done: ms-python.python
[06:09:33] Extracted extension to file:///home/jovyan/.local/share/code-server/extensions/ms-python.debugpy-2024.12.0-linux-x64: ms-python.debugpy
[06:09:33] Renamed to /home/jovyan/.local/share/code-server/extensions/ms-python.debugpy-2024.12.0-linux-x64
[06:09:34] Extracted extension to file:///home/jovyan/.local/share/code-server/extensions/ms-python.python-2024.16.1-universal: ms-python.python
[06:09:34] Renamed to /home/jovyan/.local/share/code-server/extensions/ms-python.python-2024.16.1-universal
[06:09:34] Extension installed successfully: ms-python.debugpy file:///home/jovyan/.local/share/code-server/extensions/extensions.json
[06:09:34] Extension installed successfully: ms-python.python file:///home/jovyan/.local/share/code-server/extensions/extensions.json

[antoinemorcos-bpi]

I'm seeing the same error with other extensions too, (examples include eamodio.gitlens-15.6.1 and mhutchie.git-graph-1.30.0)
Both were ok on version 4.93.1

The repeated lines Installing extensions... and Installing extension 'ms-python.python'... seem like a good hint that it's running twice for some reason, in which case the failure to rename (the second time) makes sense.

My stacktrace is the same when i "download and install", and is slightly different when I install from a vsix file

the common part

lib/vscode/out/vs/server/node/server.main.js:45:5381 -> https://github.com/microsoft/vscode/blob/ffe710dc78580f03d042e404f807a71083f55305/src/vs/base/node/pfs.ts#L499
lib/vscode/out/vs/server/node/server.main.js:54:24201 ->
https://github.com/microsoft/vscode/blob/ffe710dc78580f03d042e404f807a71083f55305/src/vs/platform/extensionManagement/node/extensionManagementService.ts#L822
lib/vscode/out/vs/server/node/server.main.js:54:21240 -> https://github.com/microsoft/vscode/blob/ffe710dc78580f03d042e404f807a71083f55305/src/vs/platform/extensionManagement/node/extensionManagementService.ts#L666

install from vsix file:

lib/vscode/out/vs/server/node/server.main.js:54:16041 -> https://github.com/microsoft/vscode/blob/ffe710dc78580f03d042e404f807a71083f55305/src/vs/platform/extensionManagement/node/extensionManagementService.ts#L383
lib/vscode/out/vs/server/node/server.main.js:54:29045 -> https://github.com/microsoft/vscode/blob/ffe710dc78580f03d042e404f807a71083f55305/src/vs/platform/extensionManagement/node/extensionManagementService.ts#L1050

Download and install

lib/vscode/out/vs/server/node/server.main.js:54:14468 -> https://github.com/microsoft/vscode/blob/ffe710dc78580f03d042e404f807a71083f55305/src/vs/platform/extensionManagement/node/extensionManagementService.ts#L312

EDIT:
Fixed the urls in the stacktrace

[antoinemorcos-bpi]

@benz0li in case you're looking at the urls I posted, one or two of them were wrong, now fixed

[benz0li]

@antoinemorcos-bpi I will wait for the next release and then check again.

Cross reference:

• Update Code to 1.95 #7052

[benz0li]

@code-asher This issue is still present with code-server v4.95.1-rc.1.

[benz0li]

The repeated lines Installing extensions... and Installing extension 'ms-python.python'... seem like a good hint that it's running twice for some reason, in which case the failure to rename (the second time) makes sense.

Yes, it seems to run twice for some reason.