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Published 20 hours ago • verified publisher icon deeptools

can't use hicDetectLoops

Open jrw510 opened this issue 3 years ago • 6 comments

hello, i used conda to install hicexplorer in a new environment, but i can't use hicDetectLoops or hicHyperoptDetectLoops,

$ hicDetectLoops -h Traceback (most recent call last): File "/data/jerry/software/miniconda3/envs/hicexplorer/bin/hicDetectLoops", line 4, in from hicexplorer.hicDetectLoops import main File "/data/jerry/software/miniconda3/envs/hicexplorer/lib/python3.9/site-packages/hicexplorer/hicDetectLoops.py", line 22, in from hicexplorer.lib import cnb File "/data/jerry/software/miniconda3/envs/hicexplorer/lib/python3.9/site-packages/hicexplorer/lib/init.py", line 2, in from .tadClassifier import TADClassifier File "/data/jerry/software/miniconda3/envs/hicexplorer/lib/python3.9/site-packages/hicexplorer/lib/tadClassifier.py", line 41, in from cleanlab.classification import LearningWithNoisyLabels ImportError: cannot import name 'LearningWithNoisyLabels' from 'cleanlab.classification' (/data/jerry/software/miniconda3/envs/hicexplorer/lib/python3.9/site-packages/cleanlab/classification.py)

$ hicHyperoptDetectLoops -h Traceback (most recent call last): File "/data/jerry/software/miniconda3/envs/hicexplorer/bin/hicHyperoptDetectLoops", line 4, in from hicexplorer.hicHyperoptDetectLoops import main File "/data/jerry/software/miniconda3/envs/hicexplorer/lib/python3.9/site-packages/hicexplorer/hicHyperoptDetectLoops.py", line 11, in from hicexplorer import hicDetectLoops File "/data/jerry/software/miniconda3/envs/hicexplorer/lib/python3.9/site-packages/hicexplorer/hicDetectLoops.py", line 22, in from hicexplorer.lib import cnb File "/data/jerry/software/miniconda3/envs/hicexplorer/lib/python3.9/site-packages/hicexplorer/lib/init.py", line 2, in from .tadClassifier import TADClassifier File "/data/jerry/software/miniconda3/envs/hicexplorer/lib/python3.9/site-packages/hicexplorer/lib/tadClassifier.py", line 41, in from cleanlab.classification import LearningWithNoisyLabels ImportError: cannot import name 'LearningWithNoisyLabels' from 'cleanlab.classification' (/data/jerry/software/miniconda3/envs/hicexplorer/lib/python3.9/site-packages/cleanlab/classification.py)

thanks for your help!

jrw510 avatar Jul 23 '22 07:07 jrw510

$ hicexplorer --version hicexplorer 3.7.2 $ python --version Python 3.9.13

jrw510 avatar Jul 23 '22 07:07 jrw510

Seems that a dependency changed its API. Please try to install HiCExplorer with a fixed version number for this dependency: conda install hicexplorer cleanlab=0.1 -c bioconda -c conda-forge

Best,

Joachim

joachimwolff avatar Jul 25 '22 07:07 joachimwolff

it works. thank you!

jrw510 avatar Jul 25 '22 09:07 jrw510

I had similar issue and I solved installing this exact version of cleanlab in my conda env:

conda install -c conda-forge 'cleanlab=1.0.1=pyhd8ed1ab_0'

sebastian-gregoricchio avatar Aug 05 '22 11:08 sebastian-gregoricchio

The same is true when installing HiCExplorer by cloning the repository it's not working with the current version of cleanlab 2.0.0 but when switching to 1.0.1 it's working fine.

Norbittner avatar Aug 23 '22 08:08 Norbittner

Had this same error message but used "conda install hicexplorer cleanlab=0.1 -c bioconda -c conda-forge" as suggested and it worked. Can you update the main page to make it clearer for others?

Thank you so much!

tolender avatar Aug 24 '22 16:08 tolender