GNU bug report logs - #63912
python-scikit-learn can't be imported "module compiled against API version 0x10 but this version of numpy is 0xf"

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Edouard Klein <edk <at> beaver-labs.com>
To: bug-guix <bug-guix <at> gnu.org>
Subject: python-scikit-learn can't be imported "module compiled against API
 version 0x10 but this version of numpy is 0xf"
Date: Mon, 05 Jun 2023 18:50:35 +0200

Dear Guix maintainers,

If I run:
guix shell python-scikit-learn
and in it, run:
python3 -c "from sklearn.feature_extraction.text import CountVectorizer"
I get:
RuntimeError: module compiled against API version 0x10 but this version of numpy is 0xf . Check the section C-API incompatibility at the Troubleshooting ImportError section at https://numpy.org/devdocs/user/troubleshooting-importerror.html#c-api-incompatibility for indications on how to solve this problem .
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/lib/python3.10/site-packages/sklearn/__init__.py", line 82, in <module>
    from .base import clone
  File "/usr/lib/python3.10/site-packages/sklearn/base.py", line 17, in <module>
    from .utils import _IS_32BIT
  File "/usr/lib/python3.10/site-packages/sklearn/utils/__init__.py", line 17, in <module>
    from scipy.sparse import issparse
  File "/usr/lib/python3.10/site-packages/scipy/sparse/__init__.py", line 267, in <module>
    from ._csr import *
  File "/usr/lib/python3.10/site-packages/scipy/sparse/_csr.py", line 10, in <module>
    from ._sparsetools import (csr_tocsc, csr_tobsr, csr_count_blocks,
ImportError: numpy.core.multiarray failed to import

I can't look into it right now, but I'm available to provide any
necessary information.

Cheers,

Edouard.

Message #10 received at 63912-done <at> debbugs.gnu.org (full text, mbox):

From: Edouard Klein <edou <at> rdklein.fr>
To: 63912-done <at> debbugs.gnu.org
Subject: Re: bug#63912: Acknowledgement (python-scikit-learn can't be
 imported "module compiled against API version 0x10 but this version of
 numpy is 0xf")
Date: Wed, 14 Jun 2023 08:38:52 +0200

I found the cause:

.local/lib/python3.10/site-packages/  is part of the interpreter's load
path, and so an old version of numpy was imported in priority over
guix's.

I don't know if this is by design, but if so, it means that any
pip --user installed package will overshadow any guix install package,
even when giving --pure to guix shell. It may not be what we want.

What made me find this is that sklearn worked when in a container, but
not in a shell, that meant that something from the local system was
leaking into the shell.



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