I was trying to run scanpy's neighbors function with my genes expression dataset:
import scanpy as sc
sc.pp.pca(adata)
sc.pp.neighbors(adata)
and got this error:
C:\Users\User\anaconda3\lib\site-packages\numba\core\cpu.py:77: UserWarning: Numba extension module 'sparse._numba_extension' failed to load due to 'ContextualVersionConflict((llvmlite 0.33.0+1.g022ab0f (c:\users\User\anaconda3\lib\site-packages), Requirement.parse('llvmlite<0.38,>=0.37.0rc1'), {'numba'}))'. numba.core.entrypoints.init_all()
I then Tried to update my llvmlite==0.33 version due to this error using
pip install llvmlite --upgrade
and got another error:
ERROR: -umba 0.50.1 has requirement llvmlite<0.34,>=0.33.0.dev0, but you'll have llvmlite 0.37.0 which is incompatible. ERROR: Cannot uninstall 'llvmlite'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.
Python doesn't let me to upgrade llvmlite to the newer version and therefore I cannot use scanpy's functions. I tried to update numba, I tried to reinstall everything, but nothing worked.
What should be done in order to solve this problem?