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conda-forge / rdkit-feedstock

A conda-smithy repository for rdkit.
BSD 3-Clause "New" or "Revised" License
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Latest build boost-cpp=1.74.0 causes "undefined symbol" error when importing rdkit.Chem from Python #93

Closed greglandrum closed 2 years ago

greglandrum commented 2 years ago

There's a problem with the RDKit and the most recent boost-cpp build. With boost-cpp 1.74.0-h359cf19_5 everything is fine, but with boost-cpp=1.74.0=h359cf19_6 I get the following:

(rdkit_tmp) glandrum@Badger:~$ python -c 'from rdkit import Chem'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/glandrum/miniconda3/envs/rdkit_tmp/lib/python3.9/site-packages/rdkit/Chem/__init__.py", line 23, in <module>
    from rdkit.Chem.rdmolfiles import *
ImportError: /home/glandrum/miniconda3/envs/rdkit_tmp/lib/python3.9/site-packages/rdkit/Chem/../../../../libRDKitmaeparser.so.1: undefined symbol: _ZN5boost9iostreams4zlib8deflatedE

This was originally reported by @guenp in the RDKit repo: https://github.com/rdkit/rdkit/issues/4987

Is it possible to manually trigger a rebuild of this repo to see if it clears that up?

hadim commented 2 years ago

I got the same issue as well. I'll open a PR to trigger a rebuild.

hadim commented 2 years ago

@conda-forge/rdkit: should we mark those packages as broken?

hadim commented 2 years ago

Pretty sure boost-cpp=1.74 build 7 (from https://github.com/conda-forge/boost-cpp-feedstock/pull/115) resolves the issue for me so likely for the others too.

Please confirm.

greglandrum commented 2 years ago

Yep, that resolves it. Thanks for noticing @hadim