GNU bug report logs - #52139
jupyter trying to modify /gnu/store

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Lars-Dominik Braun <lars <at> 6xq.net>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#52139: closed (jupyter trying to modify /gnu/store)
Date: Tue, 21 Dec 2021 13:49:01 +0000

[Message part 1 (text/plain, inline)]

Your message dated Tue, 21 Dec 2021 14:48:04 +0100
with message-id <YcHbFGZm7SeB6YBg <at> noor.fritz.box>
and subject line Re: bug#52139: jupyter trying to modify /gnu/store
has caused the debbugs.gnu.org bug report #52139,
regarding jupyter trying to modify /gnu/store
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)


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52139: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=52139
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Contact help-debbugs <at> gnu.org with problems

[Message part 2 (message/rfc822, inline)]

From: Alexander Asteroth <alexander.asteroth <at> h-brs.de>
To: bug-guix <at> gnu.org
Subject: jupyter trying to modify /gnu/store
Date: Sat, 27 Nov 2021 11:14:07 +0100

Dear all,

yesterday I added jupyter to my profile and it worked perfectly
fine. Overnight I shut down the computer and rebooted today.
Now jupyter refuses to start with the messages below.  It seems that
jupyter-notebook tries to create directories (or modifiy them) in the location it
is installed wich is mounted ro. I have no idea why this didn't happen
yesterday but it seems that there is some misconfiguration somewhere...

Cheers,
Alex

PS: same effect with jupyterlab from the guix-science channel.

-------------------------------
~$  jupyter-notebook 
Traceback (most recent call last):
  File "/gnu/store/1v8dgchnis87a4p3g9i3j1ayv0dfr4ds-python-notebook-6.3.0/bin/.jupyter-notebook-real", line 11, in <module>
    load_entry_point('notebook==6.3.0', 'console_scripts', 'jupyter-notebook')()
  File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py", line 254, in launch_instance
    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
  File "/gnu/store/i037rnmqzwcc7nrgcswzb8dcckfrngzp-python-traitlets-4.3.3/lib/python3.8/site-packages/traitlets/config/application.py", line 663, in launch_instance
    app.initialize(argv)
  File "/gnu/store/f7y0fd230nc6l2qwq58g7q26rlkwjkf3-python-decorator-5.0.9/lib/python3.8/site-packages/decorator.py", line 232, in fun
    return caller(func, *(extras + args), **kw)
  File "/gnu/store/i037rnmqzwcc7nrgcswzb8dcckfrngzp-python-traitlets-4.3.3/lib/python3.8/site-packages/traitlets/config/application.py", line 87, in catch_config_error
    return method(app, *args, **kwargs)
  File "/gnu/store/1v8dgchnis87a4p3g9i3j1ayv0dfr4ds-python-notebook-6.3.0/lib/python3.8/site-packages/notebook/notebookapp.py", line 2122, in initialize
    super().initialize(argv)
  File "/gnu/store/f7y0fd230nc6l2qwq58g7q26rlkwjkf3-python-decorator-5.0.9/lib/python3.8/site-packages/decorator.py", line 232, in fun
    return caller(func, *(extras + args), **kw)
  File "/gnu/store/i037rnmqzwcc7nrgcswzb8dcckfrngzp-python-traitlets-4.3.3/lib/python3.8/site-packages/traitlets/config/application.py", line 87, in catch_config_error
    return method(app, *args, **kwargs)
  File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py", line 229, in initialize
    self.migrate_config()
  File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py", line 155, in migrate_config
    migrate()
  File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/migrate.py", line 244, in migrate
    ensure_dir_exists(env['jupyter_config'])
  File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/utils/__init__.py", line 11, in ensure_dir_exists
    os.makedirs(path, mode=mode)
  File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 213, in makedirs
    makedirs(head, exist_ok=exist_ok)
  File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 213, in makedirs
    makedirs(head, exist_ok=exist_ok)
  File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 213, in makedirs
    makedirs(head, exist_ok=exist_ok)
  [Previous line repeated 7 more times]
  File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 223, in makedirs
    mkdir(name, mode)
OSError: [Errno 30] Read-only file system: '/home/[user]/.guix-profile/etc/jupyter:'

[Message part 3 (message/rfc822, inline)]

From: Lars-Dominik Braun <lars <at> 6xq.net>
To: Alexander Asteroth <alexander.asteroth <at> h-brs.de>
Cc: 52139-done <at> debbugs.gnu.org
Subject: Re: bug#52139: jupyter trying to modify /gnu/store
Date: Tue, 21 Dec 2021 14:48:04 +0100

Hi Alexander,

> [W 13:52:18.502 LabApp] 500 PUT /lab/api/workspaces/lab?1639227138494 (127.0.0.1): [Errno 30] Read-only file system: '[user]/.guix-profile/etc/jupyter/lab'
I’ve fixed this via
https://github.com/guix-science/guix-science/commit/ca5d2b79cc730f6d52f93f4e7347102b620ed988

Cheers,
Lars

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