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simon-anders / htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
https://htseq.readthedocs.io/en/release_0.11.1/
GNU General Public License v3.0
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HTSeq: Failed to import 'numpy'. when building snap #25

Closed dmnfarrell closed 7 years ago

dmnfarrell commented 7 years ago

Hi

I am trying to build a snap package on Ubuntu that includes HTSeq. It seems to be the only thing that won't work. I get the following error:

Setup script for HTSeq: Failed to import 'numpy'.
Please install numpy and then try again to install HTSeq.

Obviously numpy and other dependencies are being installed as well and the package is installed on my normal system. This is using python 2.7. Could there be something else missing that is falsely flagged as a numpy error? You might not be familiar with snaps but I do think it's a HTSeq problem as all the other packages build ok. Any ideas?

iosonofabio commented 7 years ago

Hi Damien, Thanks for your efforts! Have you checked the Travis CI tests for HTSeq to get a sense whether you are missing something in the dependency chain?

I am not familiar with snaps, a link would help. However, I have included HTSeq in a number of docker images without problems... Maybe the numpy shared libs or header files? HTSeq does need both to compile.

Can you provide a link to an automated build that's making the snap or is it you typing the commands manually in a shell?

Thanks!

On May 11, 2017 4:37:12 AM PDT, Damien Farrell notifications@github.com wrote:

Hi

I am trying to build a snap package on Ubuntu that includes HTSeq. It seems to be the only thing that won't work. I get the following error:

Setup script for HTSeq: Failed to import 'numpy'.
Please install numpy and then try again to install HTSeq.

Obviously numpy and other dependencies are being installed as well and the package is installed on my normal system. This is using python 2.7. Could there be something else missing that is falsely flagged as a numpy error? You might not be familiar with snaps but I do think it's a HTSeq problem as all the other packages build ok. Any ideas?

-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/simon-anders/htseq/issues/25

dmnfarrell commented 7 years ago

Hi Fabio Yes I must have missed some dependency that is present on my main system. snaps can build a python package using the setup.py but you can also specify ubuntu apt packages (i.e. python-numpy) before installing the pypi dependencies and that seems to work. I'll mark this as fixed. cheers.

https://snapcraft.io/docs/reference/plugins/python

iosonofabio commented 7 years ago

Thanks for the link!

On May 12, 2017 4:59:28 AM PDT, Damien Farrell notifications@github.com wrote:

Hi Fabio Yes I must have missed some dependency that is present on my main system. snaps can build a python package using the setup.py but you can also specify ubuntu apt packages (i.e. python-numpy) before installing the pypi dependencies and that seems to work. I'll mark this as fixed. cheers.

https://snapcraft.io/docs/reference/plugins/python

-- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/simon-anders/htseq/issues/25#issuecomment-301057998