pip install -e SCARlink not working
Closed this issue · 5 comments
Hello there
I'm try to install SCARlink but when I run :
pip install -e SCARlink
I get :
distutils.errors.LinkError: command '/home/david/anaconda3/envs/scarlink-env/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.
I try to update/upgrade everything I could but nothing work. Do you have an idea why ?
Best
David
Could you share list of packages installed in your environment?
Hello
It's indeed a python incompatibility problem. I'm trying with a virtual env and I will see if it's working
Best
David
Hi there
I reinstalled everything in a clean new virtual env and preprocessing seems to work on the tutorial data
When running scarlink, I got the output but I have this kind of messages popping :
scarlink -o multiome_outTest -g hg38 -c celltype
2024-08-29 09:39:07.382326: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-08-29 09:39:07.522831: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
I get those everytime I use python3.8 (and never with other python version)
I tried to reinstall Tensorflow and rebuild it but to no end so I'm just ignoring the message.
Is scarlink running after displaying the message? In that case, you can ignore the message.
It's working on the tutorial data :)
Thanks a lot for this very nice analysis package !
Best
D