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bacpop / unitig-caller

Methods to determine sequence element (unitig) presence/absence
Apache License 2.0
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Fresh conda install throws error (fixed by using older bifrost version) #20

Closed benrhodes26 closed 1 year ago

benrhodes26 commented 1 year ago

If I create a fresh conda environment and then run conda install -c bioconda unitig-caller, followed by unitig-caller --help, I get the following error mesage:

Traceback (most recent call last):
  File "/home/ben/mambaforge/envs/pyseer_env_test/bin/unitig-caller", line 7, in <module>
    from unitig_caller.__main__ import main
  File "/home/ben/mambaforge/envs/pyseer_env_test/lib/python3.10/site-packages/unitig_caller/__main__.py", line 11, in <module>
    import unitig_query
ImportError: /home/ben/mambaforge/envs/pyseer_env_test/lib/python3.10/site-packages/unitig_query.cpython-310-x86_64-linux-gnu.so: undefined symbol: _ZN10GFA_Parser9open_readEv

When debugging, I noticed that bifrost is now at version 1.2.0. I found that pinning the bifrost version to 1.0.6 fixes the above error.

johnlees commented 1 year ago

Ah good, another package broken despite no code changes 🥲

Thanks for the bifrost pinning tip, I'll see if I can update the bioconda build

johnlees commented 1 year ago

Looks like by updating the build with new bifrost I've been able to fix this https://github.com/bioconda/bioconda-recipes/pull/40099

Hopefully that should be added to bioconda shortly