cellgeni/sceasy

No module named 'numpy.core._multiarray_umath'

chrarnold opened this issue · 0 comments

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'