Issues installing scikit-image

Usage & Issues
#1

Hello, I am having trouble installing scikit-image to my computer. Yesterday, I tried to install by running “pip install scikit-image” It installed fine, but when I run “import skimage” on python, I receive the error:

Traceback (most recent call last):
File “/usr/local/lib/python3.9/site-packages/skimage/init.py”, line 121, in
from ._shared import geometry
ImportError: dlopen(/usr/local/lib/python3.9/site-packages/skimage/_shared/geometry.cpython-39-darwin.so, 2): Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/lib/python3.9/site-packages/skimage/_shared/…/.dylibs/libomp.dylib (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
in /usr/local/lib/python3.9/site-packages/skimage/_shared/…/.dylibs/libomp.dylib

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “”, line 1, in
File “/usr/local/lib/python3.9/site-packages/skimage/init.py”, line 124, in
_raise_build_error(e)
File “/usr/local/lib/python3.9/site-packages/skimage/init.py”, line 102, in _raise_build_error
raise ImportError("""%s
ImportError: dlopen(/usr/local/lib/python3.9/site-packages/skimage/_shared/geometry.cpython-39-darwin.so, 2): Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/lib/python3.9/site-packages/skimage/_shared/…/.dylibs/libomp.dylib (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
in /usr/local/lib/python3.9/site-packages/skimage/_shared/…/.dylibs/libomp.dylib
It seems that scikit-image has not been built correctly.

Your install of scikit-image appears to be broken.
Try re-installing the package following the instructions at:
https://scikit-image.org/docs/stable/install.html

I tried creating a new install of python (version 3.9.1) on pyenv, but I am still having the same issue after installing scikit-image. Thank you

#2

Hi @jtnardin!

what version of macOS are you on? Based on this discussion, I suspect you are on 10.13 or earlier? It might be that our precompiled versions for Python 3.9 don’t work on earlier macOS versions. Some suggestions (all are a bit painful, sorry! :grimacing:):

  • try installing Python 3.8 or even 3.7
  • try building scikit-image from source (pip install -U --no-binary scikit-image). You’ll need to have the XCode Command Line Tools installed.
  • try installing miniforge and installing scikit-image from conda-forge instead of pip
  • try upgrading your OS to 10.15 Catalina :grimacing:
1 Like
#3

Hi @jni ! Thanks so much for your help! I am on 10.13. I tried on python 3.7.1 but had the same issue. Fortunately, I have a conda environment already and installing it through conda appears to work for now. Will let you know if I run into any trouble.