[error: subprocess-exited-with-error] error with sklearn

[chanhee22kim]

Hello, thank you for providing a great tool with deep learning in tandem repeat (TR).

While using this tool, I encountered the following error code.

format for machine learning
Done
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [15 lines of output]
      The 'sklearn' PyPI package is deprecated, use 'scikit-learn'
      rather than 'sklearn' for pip commands.
      
      Here is how to fix this error in the main use cases:
      - use 'pip install scikit-learn' rather than 'pip install sklearn'
      - replace 'sklearn' by 'scikit-learn' in your pip requirements files
        (requirements.txt, setup.py, setup.cfg, Pipfile, etc ...)
      - if the 'sklearn' package is used by one of your dependencies,
        it would be great if you take some time to track which package uses
        'sklearn' instead of 'scikit-learn' and report it to their issue tracker
      - as a last resort, set the environment variable
        SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True to avoid this error
      
      More information is available at
      https://github.com/scikit-learn/sklearn-pypi-package
      [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.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

From what I understand, it indicates that I should use the scikit-learn package instead of sklearn. I would like to know if this error is acceptable and if it can be ignored.

Even though this error occurs, the two result files (RExPRTscores.txt, and TRsAnnotated_RExPRTscores.txt) are generated successfully. I am curious if it is okay for the error to occur.

I have included the entire program log in the attached file. I would appreciate your response regarding this issue.

RExPRT_log_error.log

Best regards,
Chanhee

[sxf710]

This could be an environment issue, if the two output files are generated successfully, it seems to be a warning rather than an actual error with running the program.

[jessicanoya]

Hello!

I ran into the same issue here. I created a conda env. to install all of the pip dependencies so its isolated, though, in my case it didn't generate TRsAnnotated_RExPRTscores.txt and RExPRTscores.txt.

Best,
Jess

[vaguiarpulido]

Hi, they changed the libraries as as suggested you should be using scikit-learn instead of sklearn now to install the package through pip.