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zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
https://zhanghao-njmu.github.io/SCP/
GNU General Public License v3.0
382 stars 82 forks source link

The problem of installation #136

Closed lisch7 closed 1 year ago

lisch7 commented 1 year ago

I have installed the SCP packages in R and created the SCP python environment following the instructions on Github. But in Rstuio, some packages were not installed successfully. So I installed them manually. But it doesn't work. How can I solve this problem? Thanks.

image

pip list in SCP_env Package Version ------------------- ---------` anndata 0.9.1 annoy 1.17.3 backports.zoneinfo 0.2.1 blosc2 2.0.0 click 8.1.5 cmake 3.26.4 contourpy 1.1.0 cycler 0.11.0 Cython 0.29.36 fcsparser 0.2.4 fonttools 4.41.0 future 0.18.3 h5py 3.9.0 igraph 0.10.2 imageio 2.31.1 importlib-metadata 6.8.0 importlib-resources 6.0.0 jax 0.4.13 jaxlib 0.4.13 jaxopt 0.7 joblib 1.3.1 kiwisolver 1.4.4 lazy_loader 0.3 leidenalg 0.10.0 llvmlite 0.38.1 loompy 3.0.7 matplotlib 3.6.3 mellon 1.3.1 ml-dtypes 0.2.0 msgpack 1.0.5 natsort 8.4.0 ndindex 1.7 networkx 3.1 numba 0.55.2 numexpr 2.8.4 numpy 1.21.6 numpy-groupies 0.9.22 opt-einsum 3.3.0 packaging 23.1 palantir 1.3.0 pandas 1.3.5 patsy 0.5.3 Pillow 10.0.0 pip 23.1.2 progressbar2 4.2.0 py-cpuinfo 9.0.0 pygam 0.8.0 pynndescent 0.5.10 pyparsing 3.1.0 python-dateutil 2.8.2 python-igraph 0.10.2 python-utils 3.7.0 pytz 2023.3 PyWavelets 1.4.1 scanpy 1.9.3 scikit-image 0.21.0 scikit-learn 1.1.2 scipy 1.10.1 scrublet 0.2.3 scvelo 0.2.5 seaborn 0.12.2 session-info 1.0.0 setuptools 68.0.0 six 1.16.0 statsmodels 0.14.0 stdlib-list 0.9.0 tables 3.8.0 texttable 1.6.7 threadpoolctl 3.2.0 tifffile 2023.7.10 tqdm 4.65.0 typing_extensions 4.7.1 tzdata 2023.3 tzlocal 5.0.1 umap-learn 0.5.3 versioned-hdf5 1.3.13 wheel 0.38.4 zipp 3.16.1

BenjaminDEMAILLE commented 1 year ago

Same for me on M1 Max

Lijuming33 commented 1 year ago

pip install palantir==1.2就可以安装了，但是有些包会升级，例如numpy会升级到1.24

Lijuming33 commented 1 year ago

Python 3.8.17 pip 23.2.1

pip install setuptools==68.0.0 wheel==0.41.0 numpy==1.21.6 numba==0.55.2 scikit-learn==1.1.2 pandas==1.3.5 python-igraph==0.10.2 matplotlib==3.6.3 scipy==1.10.1 versioned-hdf5==1.3.14 leidenalg==0.10.1 scanpy==1.9.3 scvelo==0.2.5 palantir==1.2

zhanghao-njmu commented 1 year ago

The package conflict issues caused by the Palantir Python package have been resolved in SCP v0.5.1, with Palantir being forced to version 1.0.1