z5: symbol not found

it is probably some library version conflict in my environment. When I installed z5py, libboost 1.77 was installed. has anyone seen this error and has a solution?

import z5py
  File "/Users/jwu/opt/anaconda3/envs/cf/lib/python3.9/site-packages/z5py/__init__.py", line 1, in <module>
    from .file import File, N5File, ZarrFile, S3File
  File "/Users/jwu/opt/anaconda3/envs/cf/lib/python3.9/site-packages/z5py/file.py", line 6, in <module>
    from . import _z5py
ImportError: dlopen(/Users/jwu/opt/anaconda3/envs/cf/lib/python3.9/site-packages/z5py/_z5py.cpython-39-darwin.so, 2): Symbol not found: __ZN5boost10filesystem4path25m_path_iterat
or_incrementERNS1_8iteratorE
  Referenced from: /Users/jwu/opt/anaconda3/envs/cf/lib/python3.9/site-packages/z5py/_z5py.cpython-39-darwin.so
  Expected in: /Users/jwu/opt/anaconda3/envs/cf/lib/python3.9/site-packages/z5py/../../../libboost_filesystem.dylib
 in /Users/jwu/opt/anaconda3/envs/cf/lib/python3.9/site-packages/z5py/_z5py.cpython-39-darwin.so

About this issue

Original URL
State: closed
Created 3 years ago
Comments: 15 (4 by maintainers)

Most upvoted comments

I just tried, it works! thanks a lot! @constantinpape @jakirkham

jingpengw on Nov 6, 2021

conda-forge mirrors packages to a CDN (hence the delay)

jakirkham on Nov 5, 2021

It’s listed here: https://anaconda.org/conda-forge/z5py/files. But was only added ~ 30 minutes ago. It sometimes takes a while for new packages to become available fully (not sure why, maybe some caches need to be updated). Could you please try again tomorrow or next week and report back?

constantinpape on Nov 5, 2021

It looks like this mixing packages from defaults and conda-forge in an incompatible way. That is likely leading to these symbol loading errors. Would set strict channel priority and create a fresh environment

jakirkham on Nov 5, 2021