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Import Error - dlopen Expected in: flat namespace #19

@lauziere

Description

@lauziere

Hello,

I've been trying to install stardist today.
Mac OSX Mojave 10.14.4

Anaconda 3.6.7
gcc-9 and g++-9 compilers

I run "pip install stardist":

| => pip install stardist
Collecting stardist
Requirement already satisfied: csbdeep>=0.4.0 in /Users/guest/anaconda3/lib/python3.6/site-packages (from stardist) (0.4.1)
Requirement already satisfied: scikit-image in /Users/guest/anaconda3/lib/python3.6/site-packages (from stardist) (0.15.0)
Requirement already satisfied: numba in /Users/guest/anaconda3/lib/python3.6/site-packages (from stardist) (0.43.1)
Requirement already satisfied: numpy in /Users/guest/anaconda3/lib/python3.6/site-packages (from csbdeep>=0.4.0->stardist) (1.16.4)
Requirement already satisfied: matplotlib in /Users/guest/anaconda3/lib/python3.6/site-packages (from csbdeep>=0.4.0->stardist) (3.1.0)
Requirement already satisfied: keras>=2.1.2 in /Users/guest/anaconda3/lib/python3.6/site-packages (from csbdeep>=0.4.0->stardist) (2.2.2)
Requirement already satisfied: tifffile in /Users/guest/anaconda3/lib/python3.6/site-packages (from csbdeep>=0.4.0->stardist) (0.15.1)
Requirement already satisfied: tqdm in /Users/guest/anaconda3/lib/python3.6/site-packages (from csbdeep>=0.4.0->stardist) (4.32.1)
Requirement already satisfied: h5py in /Users/guest/anaconda3/lib/python3.6/site-packages (from csbdeep>=0.4.0->stardist) (2.9.0)
Requirement already satisfied: scipy in /Users/guest/anaconda3/lib/python3.6/site-packages (from csbdeep>=0.4.0->stardist) (1.3.0)
Requirement already satisfied: six in /Users/guest/anaconda3/lib/python3.6/site-packages (from csbdeep>=0.4.0->stardist) (1.12.0)
Requirement already satisfied: networkx>=2.0 in /Users/guest/anaconda3/lib/python3.6/site-packages (from scikit-image->stardist) (2.3)
Requirement already satisfied: pillow>=4.3.0 in /Users/guest/anaconda3/lib/python3.6/site-packages (from scikit-image->stardist) (6.0.0)
Requirement already satisfied: imageio>=2.0.1 in /Users/guest/anaconda3/lib/python3.6/site-packages (from scikit-image->stardist) (2.5.0)
Requirement already satisfied: PyWavelets>=0.4.0 in /Users/guest/anaconda3/lib/python3.6/site-packages (from scikit-image->stardist) (1.0.3)
Requirement already satisfied: llvmlite>=0.28.0dev0 in /Users/guest/anaconda3/lib/python3.6/site-packages (from numba->stardist) (0.28.0)
Requirement already satisfied: python-dateutil>=2.1 in /Users/guest/anaconda3/lib/python3.6/site-packages (from matplotlib->csbdeep>=0.4.0->stardist) (2.8.0)
Requirement already satisfied: cycler>=0.10 in /Users/guest/anaconda3/lib/python3.6/site-packages (from matplotlib->csbdeep>=0.4.0->stardist) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /Users/guest/anaconda3/lib/python3.6/site-packages (from matplotlib->csbdeep>=0.4.0->stardist) (2.4.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /Users/guest/anaconda3/lib/python3.6/site-packages (from matplotlib->csbdeep>=0.4.0->stardist) (1.1.0)
Requirement already satisfied: keras-preprocessing==1.0.2 in /Users/guest/anaconda3/lib/python3.6/site-packages (from keras>=2.1.2->csbdeep>=0.4.0->stardist) (1.0.2)
Requirement already satisfied: pyyaml in /Users/guest/anaconda3/lib/python3.6/site-packages (from keras>=2.1.2->csbdeep>=0.4.0->stardist) (5.1)
Requirement already satisfied: keras-applications==1.0.4 in /Users/guest/anaconda3/lib/python3.6/site-packages (from keras>=2.1.2->csbdeep>=0.4.0->stardist) (1.0.4)
Requirement already satisfied: decorator>=4.3.0 in /Users/guest/anaconda3/lib/python3.6/site-packages (from networkx>=2.0->scikit-image->stardist) (4.4.0)
Requirement already satisfied: setuptools in /Users/guest/anaconda3/lib/python3.6/site-packages (from kiwisolver>=1.0.1->matplotlib->csbdeep>=0.4.0->stardist) (41.0.1)
Installing collected packages: stardist
Successfully installed stardist-0.3.4

Then on command: python -c "import stardist" I get:

Traceback (most recent call last):
File "", line 1, in
File "/Users/guest/anaconda3/lib/python3.6/site-packages/stardist/init.py", line 8, in
from .geometry import star_dist, polygons_to_label, relabel_image_stardist, ray_angles, dist_to_coord
File "/Users/guest/anaconda3/lib/python3.6/site-packages/stardist/geometry/init.py", line 5, in
from .geom2d import star_dist, polygons_to_label, relabel_image_stardist, ray_angles, dist_to_coord
File "/Users/guest/anaconda3/lib/python3.6/site-packages/stardist/geometry/geom2d.py", line 11, in
from ..lib.stardist2d import c_star_dist
ImportError: dlopen(/Users/guest/anaconda3/lib/python3.6/site-packages/stardist/lib/stardist2d.cpython-36m-darwin.so, 2): Symbol not found: _GOMP_loop_nonmonotonic_dynamic_next
Referenced from: /Users/guest/anaconda3/lib/python3.6/site-packages/stardist/lib/stardist2d.cpython-36m-darwin.so
Expected in: flat namespace
in /Users/guest/anaconda3/lib/python3.6/site-packages/stardist/lib/stardist2d.cpython-36m-darwin.so

Any idea what I can do here. Happy to provide other information.

Thank you for the help!

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