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[macOS] App CLI is not executable Error: EACCES: permission denied #888

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@lewisl

Description

@lewisl

Description

All I do is double-click on the app to start it and then click on new session. Naturally, it fails with "Failed to create session!" and Error:Jupyter Server process terminated before the initialization completed.

Reproduce

  1. Go to '...'
  2. Click on '...'
  3. Scroll down to '...'
  4. See error '...'

Expected behavior

it should work.

Context

  • Operating System and version: MacOS Sequoia 15.3.2
  • JupyterLab-Desktop version: 4.2.5-1
  • Installer: .dmg

Here is the output of trying to launch from the command line. Naturally, us dumb users can't make hide nor tail of this:

Last login: Thu Mar 20 08:27:25 on ttys001
➜ ~ python -m jupyterlab --no-browser --expose-app-in-browser
[I 2025-03-20 15:45:10.052 ServerApp] jupyter_lsp | extension was successfully linked.
[I 2025-03-20 15:45:10.053 ServerApp] jupyter_server_terminals | extension was successfully linked.
[I 2025-03-20 15:45:10.055 ServerApp] jupyterlab | extension was successfully linked.
[W 2025-03-20 15:45:10.056 JupyterNotebookApp] 'ip' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2025-03-20 15:45:10.056 JupyterNotebookApp] 'max_buffer_size' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2025-03-20 15:45:10.056 JupyterNotebookApp] 'password_required' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2025-03-20 15:45:10.057 ServerApp] ServerApp.password_required config is deprecated in 2.0. Use PasswordIdentityProvider.password_required.
[I 2025-03-20 15:45:10.057 ServerApp] notebook | extension was successfully linked.
[I 2025-03-20 15:45:10.206 ServerApp] notebook_shim | extension was successfully linked.
[I 2025-03-20 15:45:10.225 ServerApp] notebook_shim | extension was successfully loaded.
[I 2025-03-20 15:45:10.226 ServerApp] jupyter_lsp | extension was successfully loaded.
[I 2025-03-20 15:45:10.227 ServerApp] jupyter_server_terminals | extension was successfully loaded.
[I 2025-03-20 15:45:10.228 LabApp] JupyterLab extension loaded from /Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-packages/jupyterlab
[I 2025-03-20 15:45:10.228 LabApp] JupyterLab application directory is /Library/Frameworks/Python.framework/Versions/3.13/share/jupyter/lab
[I 2025-03-20 15:45:10.229 LabApp] Extension Manager is 'pypi'.
[I 2025-03-20 15:45:10.261 ServerApp] jupyterlab | extension was successfully loaded.
[I 2025-03-20 15:45:10.263 ServerApp] notebook | extension was successfully loaded.
[I 2025-03-20 15:45:10.263 ServerApp] Serving notebooks from local directory: /Users/lewis
[I 2025-03-20 15:45:10.263 ServerApp] Jupyter Server 2.15.0 is running at:
[I 2025-03-20 15:45:10.263 ServerApp] http://127.0.0.1:8888/lab
[I 2025-03-20 15:45:10.263 ServerApp] http://127.0.0.1:8888/lab
[I 2025-03-20 15:45:10.263 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[I 2025-03-20 15:45:13.749 ServerApp] Skipped non-installed server(s): bash-language-server, dockerfile-language-server-nodejs, javascript-typescript-langserver, jedi-language-server, julia-language-server, pyright, python-language-server, python-lsp-server, r-languageserver, sql-language-server, texlab, typescript-language-server, unified-language-server, vscode-css-languageserver-bin, vscode-html-languageserver-bin, vscode-json-languageserver-bin, yaml-language-server

I can run jupyter lab in a shell and the browser version launches correctly when the browser preference is set manually in jupyter_notebook_config.py as:

c.NotebookApp.browser = u'open -a /Applications/Thorium.app %s'
c.ServerApp.browser = u'open -a /Applications/Thorium.app %s'

This is necessary because jupyter can no longer launch in Safari 18.3 unless one manually changes the url place http:// ahead of the launch url at 127.0.0.1:8888/lab or localhost:8888/lab.

Troubleshoot Output
Paste the output from running `jupyter troubleshoot` from the terminal inside of JupyterLab Desktop here.
You may want to sanitize the paths in the output.

I can't do that because JLD never runs starts a session, I think.

I can connect to the jupyter server I started in a browser, enter the password (this is one way to solve the https issue in safari, but is otherwise inconvenient and seems unnecessary, so I'll end up removing the password.

OK, here you ....

jupyter troubleshoot
$PATH:
        /Users/lewis/nim-2.0.8/bin
        /Applications/Racket v8.10/bin
        /Users/lewis/.local/bin
        /Users/lewis/nim-2.0.8/bin
        /Applications/Racket v8.10/bin
        /Library/Frameworks/Python.framework/Versions/3.13/bin
        /opt/homebrew/bin
        /opt/homebrew/sbin
        /usr/local/bin
        /Users/lewis/.nimble/bin
        /System/Cryptexes/App/usr/bin
        /usr/bin
        /bin
        /usr/sbin
        /sbin
        /var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin
        /var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin
        /var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin
        /opt/X11/bin
        /Library/Apple/usr/bin
        /Library/TeX/texbin
        /usr/local/go/bin

sys.path:
        /Library/Frameworks/Python.framework/Versions/3.13/bin
        /Library/Frameworks/Python.framework/Versions/3.13/lib/python313.zip
        /Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13
        /Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/lib-dynload
        /Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-packages

sys.executable:
        /Library/Frameworks/Python.framework/Versions/3.13/bin/python3.13

sys.version:
        3.13.2 (v3.13.2:4f8bb3947cf, Feb  4 2025, 11:51:10) [Clang 15.0.0 (clang-1500.3.9.4)]

platform.platform():
        macOS-15.3.2-arm64-arm-64bit-Mach-O

which -a jupyter:
        /Library/Frameworks/Python.framework/Versions/3.13/bin/jupyter

pip list:
        Package                   Version
        ------------------------- --------------
        anyio                     4.9.0
        appnope                   0.1.4
        argon2-cffi               23.1.0
        argon2-cffi-bindings      21.2.0
        arrow                     1.3.0
        asttokens                 3.0.0
        async-lru                 2.0.5
        attrs                     25.3.0
        babel                     2.17.0
        beautifulsoup4            4.13.3
        bleach                    6.2.0
        certifi                   2025.1.31
        cffi                      1.17.1
        charset-normalizer        3.4.1
        comm                      0.2.2
        debugpy                   1.8.13
        decorator                 5.2.1
        defusedxml                0.7.1
        executing                 2.2.0
        fastjsonschema            2.21.1
        filelock                  3.18.0
        fqdn                      1.5.1
        fsspec                    2025.3.0
        h11                       0.14.0
        httpcore                  1.0.7
        httpx                     0.28.1
        idna                      3.10
        ipykernel                 6.29.5
        ipython                   9.0.2
        ipython_pygments_lexers   1.1.1
        ipywidgets                8.1.5
        isoduration               20.11.0
        jedi                      0.19.2
        Jinja2                    3.1.6
        json5                     0.10.0
        jsonpointer               3.0.0
        jsonschema                4.23.0
        jsonschema-specifications 2024.10.1
        jupyter                   1.1.1
        jupyter_client            8.6.3
        jupyter-console           6.6.3
        jupyter_core              5.7.2
        jupyter-events            0.12.0
        jupyter-lsp               2.2.5
        jupyter_server            2.15.0
        jupyter_server_terminals  0.5.3
        jupyterlab                4.3.6
        jupyterlab_pygments       0.3.0
        jupyterlab_server         2.27.3
        jupyterlab_widgets        3.0.13
        MarkupSafe                3.0.2
        matplotlib-inline         0.1.7
        mistune                   3.1.3
        mpmath                    1.3.0
        nbclient                  0.10.2
        nbconvert                 7.16.6
        nbformat                  5.10.4
        nest-asyncio              1.6.0
        networkx                  3.4.2
        notebook                  7.3.3
        notebook_shim             0.2.4
        numpy                     2.2.4
        overrides                 7.7.0
        packaging                 24.2
        pandocfilters             1.5.1
        parso                     0.8.4
        pexpect                   4.9.0
        pillow                    11.1.0
        pip                       25.0.1
        platformdirs              4.3.7
        prometheus_client         0.21.1
        prompt_toolkit            3.0.50
        psutil                    7.0.0
        ptyprocess                0.7.0
        pure_eval                 0.2.3
        pycparser                 2.22
        Pygments                  2.19.1
        python-dateutil           2.9.0.post0
        python-json-logger        3.3.0
        PyYAML                    6.0.2
        pyzmq                     26.3.0
        referencing               0.36.2
        requests                  2.32.3
        rfc3339-validator         0.1.4
        rfc3986-validator         0.1.1
        rpds-py                   0.23.1
        Send2Trash                1.8.3
        setuptools                77.0.1
        six                       1.17.0
        sniffio                   1.3.1
        soupsieve                 2.6
        stack-data                0.6.3
        sympy                     1.13.1
        terminado                 0.18.1
        tinycss2                  1.4.0
        torch                     2.6.0
        torchaudio                2.6.0
        torchvision               0.21.0
        tornado                   6.4.2
        traitlets                 5.14.3
        types-python-dateutil     2.9.0.20241206
        typing_extensions         4.12.2
        uri-template              1.3.0
        urllib3                   2.3.0
        wcwidth                   0.2.13
        webcolors                 24.11.1
        webencodings              0.5.1
        websocket-client          1.8.0
        widgetsnbextension        4.0.13
Image
Browser Output (required for interface issues after loading)
Paste the output from the DevTools JavaScript console here, if applicable.
Logs (required for issues with loading, server and startup)
Paste the logs from the `main.log` file here (optionally also from `renderer.log`).
[2025-03-20 15:37:14.342] [error] App CLI is not executable Error: EACCES: permission denied, access '/Applications/JupyterLab.app/Contents/Resources/app/jlab'
    at Object.accessSync (node:fs:262:3)
    at Object. (node:electron/js2c/asar_bundle:2:8579)
    at Object.jlabCLICommandIsSetup (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/utils.js:643:12)
    at setupJLabCommand (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/main.js:146:17)
    at App. (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/main.js:205:9)
[2025-03-20 15:37:14.344] [error] Python path "/Users/lewis/Library/jupyterlab-desktop/jlab_server/bin/python" does not exist.
[2025-03-20 15:37:14.975] [error] Failed to start server Error: Jupyter Server process terminated before the initialization completed
    at ChildProcess. (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/server.js:295:28)
    at ChildProcess.emit (node:events:514:28)
    at Process.onexit (node:internal/child_process:291:12)
[2025-03-20 15:37:18.230] [error] Failed to start server Error: Jupyter Server process terminated before the initialization completed
    at ChildProcess. (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/server.js:295:28)
    at ChildProcess.emit (node:events:514:28)
    at Process.onexit (node:internal/child_process:291:12)
[2025-03-20 15:37:18.235] [error] (node:30707) UnhandledPromiseRejectionWarning: TypeError: Cannot read properties of undefined (reading 'protocol')
    at new LabView (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/labview/labview.js:46:50)
    at SessionWindow._loadLabView (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/sessionwindow/sessionwindow.js:275:25)
    at SessionWindow._updateContentView (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/sessionwindow/sessionwindow.js:873:18)
    at IpcMainImpl. (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/sessionwindow/sessionwindow.js:438:18)
    at process.processTicksAndRejections (node:internal/process/task_queues:95:5)
(Use `JupyterLab --trace-warnings ...` to show where the warning was created)
[2025-03-20 15:37:18.236] [error] (node:30707) UnhandledPromiseRejectionWarning: Unhandled promise rejection. This error originated either by throwing inside of an async function without a catch block, or by rejecting a promise which was not handled with .catch(). To terminate the node process on unhandled promise rejection, use the CLI flag `--unhandled-rejections=strict` (see https://nodejs.org/api/cli.html#cli_unhandled_rejections_mode). (rejection id: 3)
[2025-03-20 15:42:35.347] [error] Failed to start server Error: Jupyter Server process terminated before the initialization completed
    at ChildProcess. (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/server.js:295:28)
    at ChildProcess.emit (node:events:514:28)
    at Process.onexit (node:internal/child_process:291:12)
[2025-03-20 15:43:10.098] [error] Failed to start server Error: Jupyter Server process terminated before the initialization completed
    at ChildProcess. (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/server.js:295:28)
    at ChildProcess.emit (node:events:514:28)
    at Process.onexit (node:internal/child_process:291:12)
[2025-03-20 15:43:28.063] [error] Failed to start server Error: Jupyter Server process terminated before the initialization completed
    at ChildProcess. (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/server.js:295:28)
    at ChildProcess.emit (node:events:514:28)
    at Process.onexit (node:internal/child_process:291:12)
[2025-03-20 15:43:28.074] [error] (node:30784) UnhandledPromiseRejectionWarning: TypeError: Cannot read properties of undefined (reading 'protocol')
    at new LabView (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/labview/labview.js:46:50)
    at SessionWindow._loadLabView (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/sessionwindow/sessionwindow.js:275:25)
    at SessionWindow._updateContentView (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/sessionwindow/sessionwindow.js:873:18)
    at IpcMainImpl. (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/sessionwindow/sessionwindow.js:438:18)
    at process.processTicksAndRejections (node:internal/process/task_queues:95:5)
(Use `JupyterLab --trace-warnings ...` to show where the warning was created)
[2025-03-20 15:43:28.074] [error] (node:30784) UnhandledPromiseRejectionWarning: Unhandled promise rejection. This error originated either by throwing inside of an async function without a catch block, or by rejecting a promise which was not handled with .catch(). To terminate the node process on unhandled promise rejection, use the CLI flag `--unhandled-rejections=strict` (see https://nodejs.org/api/cli.html#cli_unhandled_rejections_mode). (rejection id: 3)
[2025-03-20 15:48:03.148] [error] Failed to start server Error: Jupyter Server process terminated before the initialization completed
    at ChildProcess. (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/server.js:295:28)
    at ChildProcess.emit (node:events:514:28)
    at Process.onexit (node:internal/child_process:291:12)
[2025-03-20 15:48:07.636] [error] Failed to start server Error: Jupyter Server process terminated before the initialization completed
    at ChildProcess. (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/server.js:295:28)
    at ChildProcess.emit (node:events:514:28)
    at Process.onexit (node:internal/child_process:291:12)
[2025-03-20 15:48:07.642] [error] (node:30974) UnhandledPromiseRejectionWarning: TypeError: Cannot read properties of undefined (reading 'protocol')
    at new LabView (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/labview/labview.js:46:50)
    at SessionWindow._loadLabView (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/sessionwindow/sessionwindow.js:275:25)
    at SessionWindow._updateContentView (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/sessionwindow/sessionwindow.js:873:18)
    at IpcMainImpl. (/Applications/JupyterLab.app/Contents/Resources/app.asar/build/out/main/sessionwindow/sessionwindow.js:438:18)
    at process.processTicksAndRejections (node:internal/process/task_queues:95:5)
(Use `JupyterLab --trace-warnings ...` to show where the warning was created)
[2025-03-20 15:48:07.642] [error] (node:30974) UnhandledPromiseRejectionWarning: Unhandled promise rejection. This error originated either by throwing inside of an async function without a catch block, or by rejecting a promise which was not handled with .catch(). To terminate the node process on unhandled promise rejection, use the CLI flag `--unhandled-rejections=strict` (see https://nodejs.org/api/cli.html#cli_unhandled_rejections_mode). (rejection id: 3)
[2025-03-20 16:02:45.247] [warn]  Language pack 'en_US' not installed!
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