8000 kage installation error · Issue #14 · kage-genotyper/kage · GitHub
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kage installation error #14

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cgroza opened this issue Aug 2, 2024 · 4 comments
Open

kage installation error #14

cgroza opened this issue Aug 2, 2024 · 4 comments

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@cgroza
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cgroza commented Aug 2, 2024

I install kage via pip3 which works fine:

pip3 install kage-genotyper

However, when I try to run it I get:

cgroza@ubuntu:~$ kage
Traceback (most recent call last):
  File "/home/cgroza/.local/bin/kage", line 5, in <module>
    from kage.command_line_interface import main
  File "/home/cgroza/.local/lib/python3.10/site-packages/kage/command_line_interface.py", line 29, in <module>
    from kmer_mapper.command_line_interface import map_bnp
  File "/home/cgroza/.local/lib/python3.10/site-packages/kmer_mapper/command_line_interface.py", line 12, in <module>
    warnings.filterwarnings("ignore", category=np.VisibleDeprecationWarning) 
  File "/home/cgroza/.local/lib/python3.10/site-packages/numpy/__init__.py", line 410, in __getattr__
    raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'VisibleDeprecationWarning'
@ivargr
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ivargr commented Aug 7, 2024

Hi!

Thanks for asking. I think this might be related to numpy recently having released version 2.0.0, and we have unfortunately not specified that KAGE requires version 1. Could you try force installing Numpy version 1 and see if that solves the issue? I.e. run pip3 install numpy==1.24 and then trying to run kage again.

If that solves the issue, I'll release a fix when I'm back from vacation next week.

@baozg
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baozg commented Aug 27, 2024

It resolved in my part!

@eblerjana
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I'm getting the same error, is there an update on this?

@ivargr
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ivargr commented Mar 14, 2025

Hi!

I think force installing numpy less than version 2 should solve this issue. I've pushed an update to the kage-genotyper pip package now that solves this (so a force install of kage-genotyper==2.0.7) should also fix it.

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@cgroza @ivargr @baozg @eblerjana
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