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Medaka v1.11.3 ImportError - undefined symbol: libdeflate_free_compressor #504

Closed nbel15 closed 1 month ago

nbel15 commented 2 months ago

Hi, I tried installing the latest medaka version (1.11.3) from the source, everything went smoothly during the installation. However, I got the error below when I tried to use it.

Traceback (most recent call last): File "medaka/venv/bin/medaka", line 5, in from medaka.medaka import main File "medaka/venv/lib/python3.10/site-packages/medaka/medaka.py", line 7, in import medaka.common File "medaka/venv/lib/python3.10/site-packages/medaka/common.py", line 17, in import libmedaka ImportError: medaka/venv/lib/python3.10/site-packages/libmedaka.abi3.so: undefined symbol: libdeflate_free_compressor

I tried with a conda environment, and the latest version I could get is "1.7.0", despite the specification of the latest version during the installation. Could you please assist in sorting out this issue?

PS: Python 3.10, ubuntu 22.04

cjw85 commented 2 months ago

Is there a particular reason you wish to compile medaka from source? The recommended installation method is through the binary wheels available on PyPI.

It seems you have managed to compile the code linked to libdeflate but don't have this present on your system. The Makefile only optionally links to libdeflate and notes what needs to be done to use it at runtime. Alternatively you may just wish to install libdeflate on your system with apt.

nbel15 commented 2 months ago

Thanks for your prompt reply. Problem solved.