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mobiusklein / ms_deisotope

A library for deisotoping and charge state deconvolution of complex mass spectra
https://mobiusklein.github.io/ms_deisotope
Apache License 2.0
33 stars 13 forks source link

Installing ms_deisotope, get warning "The C extension could not be compiled" #4

Closed azzamallow closed 6 years ago

azzamallow commented 6 years ago

I am trying to install ms_deisotope on my ubuntu machine, using python3.6. I checkout the code and run:

python3 setup.py install

results in:

Version is: '0.0.6'
local variable 'macros' referenced before assignment
Version is: '0.0.6'
/usr/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'project_urls'
  warnings.warn(msg)
running install
running bdist_egg
running egg_info

...

Using /home/ubuntu/.local/lib/python3.6/site-packages
Finished processing dependencies for ms-deisotope==0.0.6
***************************************************************************
WARNING: The C extension could not be compiled, speedups are not enabled.
Plain-Python build succeeded.
***************************************************************************

How do I install ms_deisotope on my machine, with C extensions compiled?

mobiusklein commented 6 years ago

Thank you for reporting this. I had a mistake in my setup.py script. I'll fix that shortly. In the meantime, you can work around the problem by installing Cython when building from source.

mobiusklein commented 6 years ago

I've included the fix in commit d97f0e679d1e38eed40888f1b5b6009572ba4f6e.

mobiusklein commented 6 years ago

@azzamallow can you confirm whether that change fixed the problem, please?

azzamallow commented 6 years ago

@mobiusklein sorry for the late reply, yes the changes fixed the problem. Thanks!