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cellgeni / sceasy

A package to help convert different single-cell data formats to each other
GNU General Public License v3.0
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No module named 'numpy.core._multiarray_umath' #80

Open chrarnold opened 10 months ago

chrarnold commented 10 months ago

I followed the install instructions today, created a new sceasy conda env with anndata etc. When I check my conda env, all looks good:

$ which python ~/miniconda3/envs/sceasy/bin/python

$ python Python 3.11.5 | packaged by conda-forge | (main, Aug 27 2023, 03:34:09) [GCC 12.3.0] on linux import numpy numpy.core._multiarray_umath <module 'numpy.core._multiarray_umath' from '~/miniconda3/envs/sceasy/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-x86_64-linux-gnu.so'> (sceasy)

So far, so good. In R:

library(sceasy) library(reticulate) use_python('~/miniconda3/envs/sceasy/bin/python') use_condaenv('sceasy')

sceasy::convertFormat("Global_raw-counts.h5ad", from="anndata", to="seurat", outFile='Global_raw-counts.rds')

However, in R, I receive this error:

Error: ImportError:

...

Please note and check the following:

  • The Python version is: Python3.11 from "~/miniconda3/envs/sceasy/bin/python"
  • The NumPy version is: "1.24.2"

...

Original error was: No module named 'numpy.core._multiarray_umath'