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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 14 forks source link

Errors on import #8

Closed DarylWM closed 5 years ago

DarylWM commented 5 years ago

I did a plain Python install on Python 2.7, and when I do the import I get these errors:

>>> import ms_deisotope
No module named composition
(ImportError('No module named averagine',), 'averagine')
No module named scoring

Have I missed a step somewhere?

mobiusklein commented 5 years ago

Those indicate that the C-extensions for one or more libraries failed to import. This looks like the brainpy and ms_deisotope C extensions failed to import. Do you know if there were errors during their compilation?

DarylWM commented 5 years ago

To get going I was aiming for a plain Python install - the C extensions weren't compiled. I missed the ms_peak_picker and brainpy dependencies, but all good now. Thanks!

DarylWM commented 5 years ago

I went back and installed ms_peak_picker, brainpy, and ms_deisotope with C extensions compiled, and I still get an error on import. I'm using Python 2.7.15

>>> import ms_deisotope
No module named composition
(ImportError('No module named composition',), 'averagine')
No module named composition

Update: I also get 'Segmentation fault (core dumped)' from the deconvolute method now.

mobiusklein commented 5 years ago

That looks like the brainpy C extensions still aren't being found. To confirm, try running python -c "from brainpy._c import composition"

DarylWM commented 5 years ago

It seems I messed up my environment along the way. I scratched it and started again, and now it's fine. Thanks for your help Joshua.