pythonanacondascanpy

How do I solve "incompatible numba" error while installing Scanpy?


I tried installing the Scanpy package on Jupyter with "pip install Scanpy" but I got the the errors below;

ERROR: pynndescent 0.5.2 has requirement numba>=0.51.2, but you'll have numba 0.48.0 which is incompatible. ERROR: umap-learn 0.5.1 has requirement numba>=0.49, but you'll have numba 0.48.0 which is incompatible

When I tried to separately install an upgraded version of numba, I got the error below;

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.


Solution

    1. Run pip install --upgrade numba
    2. Run pip install scanpy