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gamcil / clinker

Gene cluster comparison figure generator
MIT License
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Conda package errors #91

Closed Anto007 closed 1 year ago

Anto007 commented 1 year ago

Just for the sake of clinker users who might have experienced issues like me- conda installation of clinker was giving me a lot of python errors (for e.g.,too many values to unpack) even when testing with the example .gbk files as input. The pip installed version works fine without errors at my end (on Python 3.7.10; Ubuntu 20.04.2 LTS). Hope this helps somebody!

lm-jkominek commented 1 year ago

I am actually encountering this problem right now, and unfortunately neither the Conda, PIP or Git versions are working. I even went back a few versions, and it's still the same error - "ValueError: too many values to unpack". I know the input files are fine because a colleague run Clinker on them just fine. Maybe it's one of the dependencies that is causing this? I am running Clinker on MacOS 13.0.1, if that helps at all.

EDIT. Ok, I figured it out - turns out the culprit was biopython, for some reason. It errors out when the currently latest version is used, i.e. v1.80. Force-installing an earlier version (e.g. pip install biopython==1.79) resolved the issue.

gamcil commented 1 year ago

Thanks for picking this up. Looks like clinker was a casualty of this change in v1.80 https://github.com/biopython/biopython/issues/4183. I've just released version 0.0.26 of clinker (should be on PyPI shortly) which should fix the issue for pre/post 1.80.

lm-jkominek commented 1 year ago

Lovely, glad you were able to track it down, and thanks for the fix!