scverse / scanpy

Single-cell analysis in Python. Scales to >1M cells.
https://scanpy.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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cannot read file data #2441

Closed ghost closed 1 year ago

ghost commented 1 year ago

Hi all,

I encountered a problem that it keeps saying : "Please install skmisc package via `pip install --user scikit-misc", but I have checked pip/conda and it is already installed.

I followed the instructions here: #2073

checked the ouput of "from skmisc.loess import loess".

Does anyone know how to solve this problem?

Thanks!

Minimal code sample (that we can copy&paste without having any data)

from skmisc.loess import loess
sc.pp.highly_variable_genes(all_exp_merged_bins_ad, n_top_genes=2000, flavor='seurat_v3', span=1.0)
  File "/ldfssz1/ST_BI/USER/ywu/.conda/envs/scs/lib/python3.9/site-packages/scanpy/preprocessing/_highly_variable_genes.py", line 419, in highly_variable_genes
    return _highly_variable_genes_seurat_v3(
  File "/ldfssz1/ST_BI/USER/ywu/.conda/envs/scs/lib/python3.9/site-packages/scanpy/preprocessing/_highly_variable_genes.py", line 55, in _highly_variable_genes_seurat_v3
    raise ImportError(
ImportError: Please install skmisc package via `pip install --user scikit-misc

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/wyu/.local/lib/python3.9/site-packages/skmisc/loess/__init__.py", line 51, in <module>
    from ._loess import (loess, loess_model, loess_inputs, loess_control,
ImportError: /home/wyu/.local/lib/python3.9/site-packages/skmisc/loess/../../scikit_misc.libs/libopenblasp-r0-085ca80a.3.9.so: cannot read file data

Versions

WARNING: If you miss a compact list, please try `print_header`! ----- anndata 0.7.5 scanpy 1.8.2 sinfo 0.3.1 ----- PIL 9.4.0 anndata 0.7.5 beta_ufunc NA binom_ufunc NA cffi 1.15.1 colorama 0.4.6 cycler 0.10.0 cython_runtime NA dateutil 2.8.2 defusedxml 0.7.1 google NA h5py 3.8.0 hypergeom_ufunc NA joblib 1.2.0 kiwisolver 1.4.4 llvmlite 0.39.1 matplotlib 3.5.0 mpl_toolkits NA natsort 8.3.1 nbinom_ufunc NA numba 0.56.4 numexpr 2.8.3 numpy 1.22.4 packaging 23.0 pandas 1.5.3 pkg_resources NA psutil 5.9.4 pyexpat NA pyparsing 3.0.9 pytz 2022.7.1 scanpy 1.8.2 scipy 1.8.0 setuptools_scm NA sinfo 0.3.1 six 1.16.0 sklearn 1.0.1 skmisc 0.1.4 tables 3.6.1 threadpoolctl 3.1.0 typing_extensions NA yaml 6.0 ----- Python 3.9.7 | packaged by conda-forge | (default, Sep 29 2021, 19:20:46) [GCC 9.4.0] Linux-3.10.0-1127.el7.x86_64-x86_64-with-glibc2.17 8 logical CPU cores, x86_64
Zethson commented 1 year ago

Could you please open this issue here? https://github.com/has2k1/scikit-misc