From: Konrad Hinsen <konrad.hinsen@fastmail.net>
To: 53258@debbugs.gnu.org
Subject: bug#53258: Python unable to find modules within a Singularity container created with guix pack
Date: Thu, 04 Jan 2024 13:35:28 +0100 [thread overview]
Message-ID: <m1v889jmy7.fsf@fastmail.net> (raw)
In-Reply-To: <67e7d225-f824-b691-7125-6b37abef8bb0@felsoci.sk>
Hi everyone,
I found this issue while investigating a related one (the error
message). It looks like the core problem discussed here has been solved
in the meantime:
Singularity> python3 -m numpy
Error in sitecustomize; set PYTHONVERBOSE for traceback:
ValueError: '/gnu/store/kx98dz2vc3gdpjficy4nbd7rscnkvz4s-profile/bin/../../h855kddqbay0pcbwr8a7i8m6ilz67cfn-python-3.10.7/lib/python3.10/site-packages' is not in list
/gnu/store/kx98dz2vc3gdpjficy4nbd7rscnkvz4s-profile/bin/python3: No module named numpy.__main__; 'numpy' is a package and cannot be directly executed
This error message is to be expected, and NumPy can be imported:
Singularity> python3
Error in sitecustomize; set PYTHONVERBOSE for traceback:
ValueError: '/gnu/store/kx98dz2vc3gdpjficy4nbd7rscnkvz4s-profile/bin/../../h855kddqbay0pcbwr8a7i8m6ilz67cfn-python-3.10.7/lib/python3.10/site-packages' is not in list
Python 3.10.7 (main, Jan 1 1970, 00:00:01) [GCC 11.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>>
What remains is the error message, which comes from a bug in Guix'
sitecustomize.py. It compares a raw path (sys.prefix) with paths that
have been normalized (os.path.normpath). That comparison fails if
sys.prefix contains "../", as it does when run from a Singularity
container. I will submit a patch for this.
Cheers,
Konrad
next prev parent reply other threads:[~2024-01-04 12:36 UTC|newest]
Thread overview: 13+ messages / expand[flat|nested] mbox.gz Atom feed top
2022-01-14 14:20 bug#53258: Python unable to find modules within a Singularity container created with guix pack Marek Felšöci
2022-01-14 17:45 ` Ludovic Courtès
2022-02-04 20:50 ` Ludovic Courtès
2022-02-05 22:28 ` Josselin Poiret via Bug reports for GNU Guix
2022-02-05 22:30 ` Josselin Poiret via Bug reports for GNU Guix
2022-03-07 8:25 ` Ludovic Courtès
2023-02-02 14:44 ` Josselin Poiret via Bug reports for GNU Guix
2023-02-02 15:40 ` Maxim Cournoyer
2023-02-06 17:34 ` Simon Tournier
2024-01-04 12:35 ` Konrad Hinsen [this message]
2024-01-04 13:01 ` Konrad Hinsen
2024-01-05 15:23 ` Konrad Hinsen
2024-01-21 18:31 ` Maxim Cournoyer
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