You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
When installing the latest bioconda release in a fresh environment, Python 3.12 will get installed and checkm will fail with the following error:
Traceback (most recent call last):
File "/home/njohner/bin/miniconda3/envs/test_checkm/bin/checkm", line 38, in <module>
from checkm import main
File "/home/njohner/bin/miniconda3/envs/test_checkm/lib/python3.12/site-packages/checkm/main.py", line 22, in <module>
from checkm.defaultValues import DefaultValues
File "/home/njohner/bin/miniconda3/envs/test_checkm/lib/python3.12/site-packages/checkm/defaultValues.py", line 23, in <module>
from checkm.checkmData import DBManager
File "/home/njohner/bin/miniconda3/envs/test_checkm/lib/python3.12/site-packages/checkm/checkmData.py", line 25, in <module>
from pkg_resources import resource_filename
ModuleNotFoundError: No module named 'pkg_resources'
Newer versions of python do not include setuptools anymore, which
breaks checkm. I have also opened an issue with checkm as I think
they should fix that (Ecogenomics/CheckM#403).
When installing the latest bioconda release in a fresh environment, Python 3.12 will get installed and checkm will fail with the following error:
pkg_resources
is deprecated and removed in Python 3.12.I could fix the issue either by setting the python version to 3.7 or lower or by adding a dependency to
setuptools
.The text was updated successfully, but these errors were encountered: