lopatovsky/HMMs

ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

eponraj27392 opened this issue · 11 comments

eponraj27392 commented

I have been using google colab. I would like to work with Hidden markov, so I would like to install a library called hmms On installing pip install hmms, i received the following error.

ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

I also try to install the same library in Pycharm IDE, I received the same error with some call backs.

Command "python setup.py egg_info" failed with error code 1 in C:\Users\eponr\AppData\Local\Temp\pycharm-packaging\hmms\

Collecting hmms
  Using cached https://files.pythonhosted.org/packages/e9/e4/c070c44ec8a391f6d5501316d1ed7615058f1fd365ff4ed65c9636d0bf62/hmms-0.1.tar.gz
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Users\eponr\AppData\Local\Temp\pycharm-packaging\hmms\setup.py", line 22, in <module>
        ext_modules=cythonize(glob.glob('hmms/*.pyx'), language_level=3, include_dirs=[numpy.get_include()]),
      File "C:\Users\eponr\PycharmProjects\untitled1\venv\lib\site-packages\Cython\Build\Dependencies.py", line 955, in cythonize
        c_options = CompilationOptions(**options)
      File "C:\Users\eponr\PycharmProjects\untitled1\venv\lib\site-packages\Cython\Compiler\Main.py", line 563, in __init__
        raise ValueError(message)
    ValueError: got unknown compilation option, please remove: include_dirs


What does it means and how can i rectify this issue ? kindly suggest some solution to get working
mohammeddanishkhan commented

I have been using google colab. I would like to work with Hidden markov, so I would like to install a library called hmms On installing pip install hmms, i received the following error.

ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

I also try to install the same library in Pycharm IDE, I received the same error with some call backs.

Command "python setup.py egg_info" failed with error code 1 in C:\Users\eponr\AppData\Local\Temp\pycharm-packaging\hmms\

Collecting hmms
  Using cached https://files.pythonhosted.org/packages/e9/e4/c070c44ec8a391f6d5501316d1ed7615058f1fd365ff4ed65c9636d0bf62/hmms-0.1.tar.gz
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Users\eponr\AppData\Local\Temp\pycharm-packaging\hmms\setup.py", line 22, in <module>
        ext_modules=cythonize(glob.glob('hmms/*.pyx'), language_level=3, include_dirs=[numpy.get_include()]),
      File "C:\Users\eponr\PycharmProjects\untitled1\venv\lib\site-packages\Cython\Build\Dependencies.py", line 955, in cythonize
        c_options = CompilationOptions(**options)
      File "C:\Users\eponr\PycharmProjects\untitled1\venv\lib\site-packages\Cython\Compiler\Main.py", line 563, in __init__
        raise ValueError(message)
    ValueError: got unknown compilation option, please remove: include_dirs


What does it means and how can i rectify this issue ? kindly suggest some solution to get working

Hey, did you find any solution to this problem?

eponraj27392 commented
shahab-anjum commented

i also got the same issue so plz help me

shahab-anjum commented

i need hmm in my thesis so if u?

eponraj27392 commented
medh61 commented

You install the library hmms from github; and the problem will be solved
The command is :
!python -m pip install git+https://github.com/lopatovsky/HMM
Duplicate of #s#egg=HMMs

medh61 commented

You install the library hmms from github; and the problem will be solved
The command is :
!python -m pip install git+https://github.com/lopatovsky/HMMs#egg=HMMs

  • 👍2
sannicosan commented

Hello! I'm trying to install another github package:

https://github.com/ismrmrd/ismrmrd-python

After trying to install it with the !pip install command, I get the following error:

ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

Can someone hel me further?

yuvipanda commented

Would love to see a release made to PyPI with this patch installed. As of now, installing from PyPI fails with this error for me.

  • 👍1
agicquel commented

The solution of @medh61 worked for me, with python 3.9.

griffinbrookshire commented

Using Python 3.10, had to use: python3 -m pip install git+https://github.com/lopatovsky/HMMs