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liguowang / cpgtools

Python package to analyze DNA methylation data
MIT License
39 stars 11 forks source link

installation error #5

Open swvanderlaan opened 1 year ago

swvanderlaan commented 1 year ago

I am installing your tool but I get an error message. What is the best course of action for me?

pip install cpgtools
Collecting cpgtools
  Using cached cpgtools-1.12.0-py3-none-any.whl (5.1 MB)
Requirement already satisfied: numpy in /Users/username/miniconda3/envs/gwaslab/lib/python3.8/site-packages (from cpgtools) (1.24.4)
Requirement already satisfied: scipy in /Users/username/miniconda3/envs/gwaslab/lib/python3.8/site-packages (from cpgtools) (1.10.1)
Collecting sklearn (from cpgtools)
  Using cached sklearn-0.0.post9.tar.gz (3.6 kB)
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [18 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

      If the previous advice does not cover your use case, feel free to report it at
      https://github.com/scikit-learn/sklearn-pypi-package/issues/new
      [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.
liguowang commented 1 year ago

please try:

pip3 install git+https://github.com/liguowang/cpgtools.git

liguowang commented 1 year ago

I just updated the PyPI package. Maybe you could also try: pip install cpgtools