Description
Description
This issue would appear to be very similar to Importing scikit-learn==0.24.0 fails on macOS 10.13: "Symbol not found: ____chkstk_darwin" #19063, which was fixed.
Running on OS X High Sierra 10.13.6. On Python 3.7 and 3.9.
The highlight of the error message is this line
Referenced from: /Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/skimage/_shared/../.dylibs/libomp.dylib (which was built for Mac OS X 10.15)
It appears that binaries built on 10.15 are incompatible with 10.13.6.
Way to reproduce
# In PyCharm, create new project, add these packages (you actually don't need to manually add all of them, only imgaug and the dependencies will load the rest automatically):
# opencv-python
# matplotlib
# pandas
# sklearn
# imgaug
# tensorflow
# Then create a new Python file with just this line, on its own, and run it. No other code is required to repro the issue
from imgaug import augmenters as iaathis will result in
/Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/bin/python /Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/TestCrash.py
Traceback (most recent call last):
File "/Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/skimage/__init__.py", line 121, in <module>
from ._shared import geometry
ImportError: dlopen(/Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/skimage/_shared/geometry.cpython-37m-darwin.so, 2): Symbol not found: ____chkstk_darwin
Referenced from: /Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/skimage/_shared/../.dylibs/libomp.dylib (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
in /Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/skimage/_shared/../.dylibs/libomp.dylib
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/TestCrash.py", line 2, in <module>
from imgaug import augmenters as iaa
File "/Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/imgaug/__init__.py", line 7, in <module>
from imgaug.imgaug import * # pylint: disable=redefined-builtin
File "/Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/imgaug/imgaug.py", line 22, in <module>
import skimage.draw
File "/Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/skimage/__init__.py", line 124, in <module>
_raise_build_error(e)
File "/Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/skimage/__init__.py", line 104, in _raise_build_error
%s""" % (e, msg))
ImportError: dlopen(/Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/skimage/_shared/geometry.cpython-37m-darwin.so, 2): Symbol not found: ____chkstk_darwin
Referenced from: /Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/skimage/_shared/../.dylibs/libomp.dylib (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
in /Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/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
Process finished with exit code 1
Version information - Python 3.7
# Paste the output of the following python commands
from __future__ import print_function
import sys; print(sys.version)
import platform; print(platform.platform())
import skimage; print("scikit-image version: {}".format(skimage.__version__))
import numpy; print("numpy version: {}".format(numpy.__version__))# your output here
/Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/bin/python /Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/CrashInfo.py
3.7.10 (default, May 1 2021, 23:35:31)
[Clang 10.0.0 (clang-1000.10.44.4)]
Darwin-17.7.0-x86_64-i386-64bit
Traceback (most recent call last):
File "/Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/skimage/__init__.py", line 121, in <module>
from ._shared import geometry
ImportError: dlopen(/Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/skimage/_shared/geometry.cpython-37m-darwin.so, 2): Symbol not found: ____chkstk_darwin
Referenced from: /Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/skimage/_shared/../.dylibs/libomp.dylib (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
in /Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/skimage/_shared/../.dylibs/libomp.dylib
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/CrashInfo.py", line 4, in <module>
import skimage; print("scikit-image version: {}".format(skimage.__version__))
File "/Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/skimage/__init__.py", line 124, in <module>
_raise_build_error(e)
File "/Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/skimage/__init__.py", line 104, in _raise_build_error
%s""" % (e, msg))
ImportError: dlopen(/Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/skimage/_shared/geometry.cpython-37m-darwin.so, 2): Symbol not found: ____chkstk_darwin
Referenced from: /Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/site-packages/skimage/_shared/../.dylibs/libomp.dylib (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
in /Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/lib/python3.7/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
Process finished with exit code 1With this line
# import skimage; print("scikit-image version: {}".format(skimage.__version__))
commented out, the output is:
/Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/venv/bin/python /Users/macbook/PycharmProjects/SelfDrivingSimulatorv3/CrashInfo.py
3.7.10 (default, May 1 2021, 23:35:31)
[Clang 10.0.0 (clang-1000.10.44.4)]
Darwin-17.7.0-x86_64-i386-64bit
numpy version: 1.21.0
Process finished with exit code 0
Version information - Python 3.9
# Paste the output of the following python commands
from __future__ import print_function
import sys; print(sys.version)
import platform; print(platform.platform())
# import skimage; print("scikit-image version: {}".format(skimage.__version__))
import numpy; print("numpy version: {}".format(numpy.__version__))/Users/macbook/PycharmProjects/scikit-image-test/venv3.9/bin/python /Users/macbook/PycharmProjects/scikit-image-test/CrashInfo.py
3.9.4 (default, Apr 17 2021, 22:46:43)
[Clang 10.0.0 (clang-1000.10.44.4)]
macOS-10.13.6-x86_64-i386-64bit
numpy version: 1.21.0
Process finished with exit code 0
FWIW, Installing scikit-image via the terminal gives the same end result. This output shows the version number at the bottom:
pip3 install -U --no-cache-dir --no-binary :all scikit-image
Collecting scikit-image
Downloading scikit_image-0.18.2-cp37-cp37m-macosx_10_9_x86_64.whl (12.7 MB)
|████████████████████████████████| 12.7 MB 1.4 MB/s
Requirement already satisfied: pillow!=7.1.0,!=7.1.1,>=4.3.0 in ./venv/lib/python3.7/site-packages (from scikit-image) (8.3.1)
Requirement already satisfied: tifffile>=2019.7.26 in ./venv/lib/python3.7/site-packages (from scikit-image) (2021.7.2)
Requirement already satisfied: PyWavelets>=1.1.1 in ./venv/lib/python3.7/site-packages (from scikit-image) (1.1.1)
Requirement already satisfied: networkx>=2.0 in ./venv/lib/python3.7/site-packages (from scikit-image) (2.5.1)
Requirement already satisfied: matplotlib!=3.0.0,>=2.0.0 in ./venv/lib/python3.7/site-packages (from scikit-image) (3.4.2)
Requirement already satisfied: numpy>=1.16.5 in ./venv/lib/python3.7/site-packages (from scikit-image) (1.21.0)
Requirement already satisfied: imageio>=2.3.0 in ./venv/lib/python3.7/site-packages (from scikit-image) (2.9.0)
Requirement already satisfied: scipy>=1.0.1 in ./venv/lib/python3.7/site-packages (from scikit-image) (1.7.0)
Requirement already satisfied: kiwisolver>=1.0.1 in ./venv/lib/python3.7/site-packages (from matplotlib!=3.0.0,>=2.0.0->scikit-image) (1.3.1)
Requirement already satisfied: cycler>=0.10 in ./venv/lib/python3.7/site-packages (from matplotlib!=3.0.0,>=2.0.0->scikit-image) (0.10.0)
Requirement already satisfied: python-dateutil>=2.7 in ./venv/lib/python3.7/site-packages (from matplotlib!=3.0.0,>=2.0.0->scikit-image) (2.8.1)
Requirement already satisfied: pyparsing>=2.2.1 in ./venv/lib/python3.7/site-packages (from matplotlib!=3.0.0,>=2.0.0->scikit-image) (2.4.7)
Requirement already satisfied: six in ./venv/lib/python3.7/site-packages (from cycler>=0.10->matplotlib!=3.0.0,>=2.0.0->scikit-image) (1.16.0)
Requirement already satisfied: decorator<5,>=4.3 in ./venv/lib/python3.7/site-packages (from networkx>=2.0->scikit-image) (4.4.2)
Installing collected packages: scikit-image
Successfully installed scikit-image-0.18.2
(venv) MacBook-Pro-van-Macbook:SelfDrivingSimulatorv3 macbook$