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infomap dependency error when importing algorithms

See original GitHub issue

Describe the bug

I’m having problems import algorithms, it seems to be because of a problem with the infomap dependency.

(personal info X’d out)

>>> from cdlib import algorithms
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "XXX/miniconda3/envs/XXX/lib/python3.8/site-packages/cdlib/algorithms/__init__.py", line 2, in <module>
    from .crisp_partition import *
  File "XXX/miniconda3/envs/XXX/lib/python3.8/site-packages/cdlib/algorithms/crisp_partition.py", line 2, in <module>
    import infomap as imp
  File "XXX/miniconda3/envs/XXX/lib/python3.8/site-packages/infomap.py", line 34, in <module>
    import _infomap
ImportError: dlopen(XXX/miniconda3/envs/XXX/lib/python3.8/site-packages/_infomap.cpython-38-darwin.so, 2): Library not loaded: /usr/local/opt/libomp/lib/libomp.dylib
  Referenced from: XXX/miniconda3/envs/XXX/lib/python3.8/site-packages/_infomap.cpython-38-darwin.so
  Reason: image not found

To Reproduce Steps to reproduce the behavior:

CDlib version: 0.2.3
Operating System: macOS-10.16-x86_64-i386-64bit
Python version: 3.8.10

Expected behavior Algorithms to be able to be imported without error.

Additional context from cdlib import ensemble works correctly.

I get issue #181 for cdlib==0.2.0 and cdlib==0.2.1

Issue Analytics

State:
Created 2 years ago
Comments:5 (2 by maintainers)

Top GitHub Comments

2reactions

lizgzilcommented, Jul 2, 2021

hurray 🎉 that made it work. Thank you for your help @GiulioRossetti !

Just for clarity I installed it with:

conda config --add channels giuliorossetti
conda config --add channels conda-forge
conda install cdlib

1reaction

GiulioRossetticommented, Jul 2, 2021

It seems related to a broken installation o f the Infomap dependency. Have you installed cdlib using pip or anaconda? Is this issue common to both installation methodologies (starting from clean python envs)?

Tbh I haven’t tried so far to install Infomap on osx so I don’t know if this is a known issue.

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