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Importing scikit-learn==0.24.0 fails on macOS 10.13: "Symbol not found: ____chkstk_darwin"

See original GitHub issue

Describe the bug

Importing scikit-learn==0.24 fails on macOS 10.13.

I believe this is similar to https://github.com/nodegui/nodegui/issues/391, i.e. the prebuilt libomp binary (from 10.15) isn’t compatible with macOS 10.13.

We’re also tracking this issue on the project where we encountered it: https://github.com/neuropoly/spinalcordtoolbox/issues/3121.

Steps/Code to Reproduce

  1. Install scikit-learn==0.24.0 on macOS 10.13 (for us, it appeared as a successful install)
  2. Import scikit-learn (for us, an error was thrown)

Expected Results

No error is thrown.

Actual Results

dlopen(/Users/travis/build/neuropoly/spinalcordtoolbox/python/envs/venv_sct/lib/python3.6/site-packages/sklearn/__check_build/_check_build.cpython-36m-darwin.so, 2): Symbol not found: ____chkstk_darwin
  Referenced from: /Users/travis/build/neuropoly/spinalcordtoolbox/python/envs/venv_sct/lib/python3.6/site-packages/sklearn/__check_build/../.dylibs/libomp.dylib (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib
 in /Users/travis/build/neuropoly/spinalcordtoolbox/python/envs/venv_sct/lib/python3.6/site-packages/sklearn/__check_build/../.dylibs/libomp.dylib
___________________________________________________________________________
Contents of /Users/travis/build/neuropoly/spinalcordtoolbox/python/envs/venv_sct/lib/python3.6/site-packages/sklearn/__check_build:
__init__.py               __pycache__               _check_build.cpython-36m-darwin.so
setup.py
___________________________________________________________________________
It seems that scikit-learn has not been built correctly.

If you have installed scikit-learn from source, please do not forget
to build the package before using it: run `python setup.py install` or
`make` in the source directory.

If you have used an installer, please check that it is suited for your
Python version, your operating system and your platform.

Versions

  • Python: python-3.6.12
  • Numpy: numpy-1.19.4
  • Scipy: scipy-1.5.4
  • Scikit-learn: scikit-learn-0.24.0

Issue Analytics

  • State:closed
  • Created 3 years ago
  • Reactions:6
  • Comments:16 (13 by maintainers)

github_iconTop GitHub Comments

11reactions
ogriselcommented, Dec 24, 2020

Thank you very much for the confirmation. We will include this fix in a 0.24.1 release (soon-ish).

4reactions
ogriselcommented, Jan 21, 2021

This was fixed with the 0.24.1 release a few days ago.

Read more comments on GitHub >

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