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MSingerLab / COMETSC

COMET Single-Cell Marker Detection tool
BSD 3-Clause "New" or "Revised" License
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Unable to install COMETSC #13

Closed mdidish closed 2 years ago

mdidish commented 3 years ago

Dear, I failed to install locally COMETSC, on Ubuntu 20.04 with Python 3.6.8: pip3 install COMETSC give this error :

ERROR: Cannot install cometsc==0.1.10, cometsc==0.1.11, cometsc==0.1.12, cometsc==0.1.13, cometsc==0.1.5, cometsc==0.1.6, cometsc==0.1.7 and cometsc==0.1.9 because these package versions have conflicting dependencies.

The conflict is caused by:
    cometsc 0.1.13 depends on scikit-learn==0.21.0
    cometsc 0.1.12 depends on scikit-learn==0.21.0
    cometsc 0.1.11 depends on scikit-learn==0.21.0
    cometsc 0.1.10 depends on scikit-learn==0.21.0
    cometsc 0.1.9 depends on scikit-learn==0.21.0
    cometsc 0.1.7 depends on scikit-learn==0.21.0
    cometsc 0.1.6 depends on scikit-learn==0.21.0
    cometsc 0.1.5 depends on scikit-learn==0.21.0

On scikit-learn github, we can read this: "Also we removed the 0.21.0 tarball from pypi because it lacked a metadata that made it explicit that it was not compatible with python 2."

So how do you recommend installing COMETSC?

Best, Marc

XinLi-0419 commented 3 years ago

@mdidish

Hi, do you happen to have a solution for this now? I am running into the same error. Thanks!

mdidish commented 3 years ago

No I didn't, I still use the web version. Tell me if you find one! Best

⁣Télécharger TypeApp pour Android ​

Le 2 nov. 2021 à 20:38, à 20:38, Shinlee419 @.> a écrit: @.

Hi, do you happen to have a solution for this now? I am running into the same error. Thanks!

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/MSingerLab/COMETSC/issues/13#issuecomment-958108288

XinLi-0419 commented 3 years ago

No I didn't, I still use the web version. Tell me if you find one! Best ⁣Télécharger TypeApp pour Android ​ Le 2 nov. 2021 à 20:38, à 20:38, Shinlee419 @.> a écrit: @. …

Sure thing.

Sadly, the web version is not working for me. I am okay with downsampling but it is saying Internal Server Error after I submit.

mdidish commented 3 years ago

Concerning the web version, cluster's names have to be number. The contact indicated on their website answered to my questions and helped me.

⁣Télécharger TypeApp pour Android ​

Le 2 nov. 2021 à 22:08, à 22:08, Shinlee419 @.***> a écrit:

No I didn't, I still use the web version. Tell me if you find one! Best ⁣Télécharger TypeApp pour Android ​ Le 2 nov. 2021 à 20:38, à 20:38, Shinlee419 @.> a écrit: @. …

Sure thing.

Sadly, the web version is not working for me. I am okay with downsampling but it is saying Internal Server Error after I submit.

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/MSingerLab/COMETSC/issues/13#issuecomment-958167672

oshahid commented 2 years ago

Hi all,

I was able to fix the Internal Server Error on the COMET website. I'll leave this thread open if you'd like to diagnose any problems you may still have with local installation of COMET on your computer.

desmondramirez commented 2 years ago

Hi,

I have the same issue trying to install comet on my cluster. Is it possible to change the requirements for a version of scikit-learn that hasn't been replaced with a different name by the developer? I happen to have scikit-learn 0.21 installed on my home computer, but looks like it would take over 3 days running on my laptop-- not ideal. I am running on the web server, but would like to be able to run them independently.

Thanks for the program though, it's very useful!

oshahid commented 2 years ago

Hi desmondramirez,

Can you tell me which version of Python you are using? I've noticed that even with some version of Python 3.6 (like 3.6.8, for example), scikit-learn gives a few issues. Using Python 3.6.0 or 3.6.2 should resolve the issue. Otherwise, a temporary work-around that I've tried is the following, which works if you have conda or anaconda installed already:

1.) Create a temporary environment using Anaconda called "COMET" which uses Python 3.6:

conda create -n COMET python=3.6.2

2.) Activate the environment

conda activate COMET

3.) Now your computer should see you using Python 3.6 in the COMET environment. To check, do the following:

python -V

4.) You should end up with Python 3.6.2. Now use this version of Python to install your COMET virtual environment::

pip install COMETSC

In the meantime, I will try changing the requirements for scikit-learn so that a more current version will be available. Please let me know if this solution works for you, or if you still run into issues.

mdidish commented 2 years ago

@oshahid Perfect, it works for me! Best,