liana_tensor_c2c error

[estherwon]

Hello,

Thankyou for your work on this package. I have been trying to run tensor decomposition on my data after successfully running the liana_bysample. But when I try to run liana_tensor_c2c it has been giving me error related to setup.py as shown below. I tried to update setup.py but it did not work. I converted all my dataset(seurat objects) to SingleCellExperiment object before using this package. I am not sure if this error is related to setting up the conda environment, I also tried to update conda but it did not work either. Please let me know if you have any suggestions or solutions on this issue. I really appreciate your help. Thankyou.

Collecting h5py>=3 (from anndata->anndatari==1.0.6)
Using cached h5py-3.11.0-cp38-cp38-macos×_10_9_x86_64.whl.metadata (2.5 kB)
Collecting natsort (from anndata->anndatari=-1.0.6)
Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Collecting dunamai (from get_version->anndata2ri==1.0.6)
Using cached dunamai-1.21.2-py3-none-any.whl.metadata (10 kB)
Collecting get-annotations (from scanpy->cell2cell==0.6.8)
Using cached get_annotations-0.1.2-py3-none-any.whl.metadata (3.3 kB)
Collecting joblib (from scanpy->cell2cell==0.6.8)
Using cached joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB)
INFO: pip is looking at multiple versions of scany to determine which version is compatible with other requir
Collecting scapy (from cell2cell==0.6.8)
Using cached scanpy-1.9.7-py3-none-any.whl.metadata (6.0 kB)
Using cached scanpy-1.9.6-py3-none-any.whl.metadata (6.0 kB)
Collecting numba>=0.41.0 (from scanpy->cell2cell==0.6.8)
Using cached numba-0.58.1-cp38-cp38-macosx_10_9_x86_64.whl.metadata (2.7 kB)
Collecting patsy (from scanpy->cell2cell==0.6.8)
Using cached patsy-0.5.6-py2.py3-none-any.whl.metadata (3.5 kB)
Collecting session-info (from scanpy->cel12cell==0.6.8)
Using cached session_info-1.0.0.tar.gz (24 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'error' error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully.
I exit code: 1
L> [1 lines of output]
ERROR: Can not execute setup.py since setuptools is not available in the build environment.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed
× Encountered error while generating package metadata.
L> See above for output.
note: This is an issue with the package mentioned above, not pip. hint: See above for details.
Error in setupBasiliskEnvenvpath, packages = .getPackages(en), channels = •getChannels(env), failed to install additional packages via pip

[dbdimitrov]

Hi @estherwon,

This seems to be a recurring issue when trying to install the automatically setup environment by liana. I will try to resolve it, in the meantime, you could check setting up the environment as done here: https://github.com/saezlab/ccc_protocols/tree/main/env_setup

Honestly, I recommend following those tutorials also :)

Best wishes,
Daniel