erron on import about ms_deisotope HOT 5 CLOSED

Could you post any messages you get during installation? It looks like the C extensions weren't compiled.

Are you installing ms_peak_picker from source as well?

from ms_deisotope.

Hi, thanks for your reply!

Yes, I have installed ms_peak_picker from source first, and brainpy just before installing ms_deisotope. I have also tried with the latest releases (rather than cloning the repos, but the result was the same.

The output is here: https://gist.github.com/infusini/836118414f3b52f37262ccb91deeed2f

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Hmm. I wasn't testing on Py3.7, but I've just updated my Travis config and it seems to build fine there. What kind of environment are you running this on? An AWS hosted instance?

Are you running Python directly from the source directory for ms_deisotope?

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I have tried on both an Ubuntu instance on AWS, and a CentOS here on our internal VMs

Yes, I did run python from within the source directory of ms_deisotope (sorry). It didn't occur to me to try from somewhere else to check... and, of course, it works perfectly fine now. Thanks for your help :(

buntu@ip-172-31-24-45:~/ms_deisotope$ python
Python 3.7.3 (default, Mar 27 2019, 22:11:17)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import ms_deisotope
No module named 'ms_deisotope._c.averagine' averagine
No module named 'ms_deisotope._c.scoring'
No module named 'ms_deisotope._c.deconvoluter_base'
No module named 'ms_deisotope._c.deconvoluter_base'
No module named 'ms_deisotope._c.deconvoluter_base'
>>>
ubuntu@ip-172-31-24-45:~/ms_deisotope$ cd ..
ubuntu@ip-172-31-24-45:~$ python
Python 3.7.3 (default, Mar 27 2019, 22:11:17)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import ms_deisotope
>>>

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Glad it was resolved. I've spent days of investigation to only find that was the culprit. When run from the source directory, Python tries to import from the local directory first, where it finds the source (without the compiled C extensions), and never looks in site-packages.

If you find yourself needing to do that, or to tweak things, you can install it with python setup.py develop or pip install -e, which will compile the C extensions and then place the .so files alongside the source code. These "editable" installations have some downsides for package metadata introspection, but I rarely have an issue with that.

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