Running install for scikit-learn ... error

I am using MacOs Mojave and currently trying to run the project available on GitHub on this link. I have installed latest version of python(i.e. python 3.8) and currently facing issues while installing the requirements, mainly in scikit-learn. Either way I am getting the same error.

Kindly help me through out to run this project completely on my machine locally.

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I've also raised an issue on the main GitHub page regarding this and still waiting for an adequate response.

When I tried to install cython according to the given instructions and available answer on stackoverflow I'm getting another big error page with python3.8 using command- pip3 install --upgrade cython as mentioned in an answer. I'm attaching that's error messages here. enter image description here enter image description here enter image description here enter image description here enter image description here enter image description here This is the complete set of error that I'm getting after that. Thanks in advance if anyone can get me through this project with python3.8

2 answers

  • answered 2019-11-14 05:40 VonC

    "no module named Cython" was seen in other projects: CellProfiler/centrosome issue 78 with various workarounds:

    python3 install
    # and/or
    python3.6 -m pip install --upgrade cython
    sudo python3.6 -m pip install --upgrade cython
    # and/or
    pip install --upgrade cython

    If you're using python 2.7 or above, type on terminal: pip install --upgrade cython
    This should work.
    The error is probably because the cython version installed from pip is incompatible to the python version on your system.

    If that leads to:

    xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools)

    Then check this question, and try and update XCode: xcode-select --install

  • answered 2019-11-14 21:51 makis

    You just need to first install scikit-learn. Use:

    pip install -U scikit-learn


    pip3 install -U scikit-learn