install error: 'numpy/arrayobject.h' file not found

audy commented 8 years ago

Can anyone help with this error?

🚀 pip install numpy --upgrade
Requirement already up-to-date: numpy in /usr/local/lib/python2.7/site-packages

🚀 python --version
Python 2.7.11

🚀 pip install biom-format

...

biom/_filter.c:258:10: fatal error: 'numpy/arrayobject.h' file not found
...

On Mac OS El Capitan w. Python installed via homebrew.

wasade commented 8 years ago

Is the directory corresponding to np.get_include() empty?

audy commented 8 years ago

🐶  tree /usr/local/lib/python2.7/site-packages/numpy/core/include/                                                                         kraken-wgs-qc
/usr/local/lib/python2.7/site-packages/numpy/core/include/
└── numpy
    ├── __multiarray_api.h
    ├── __ufunc_api.h
    ├── _neighborhood_iterator_imp.h
    ├── _numpyconfig.h
    ├── arrayobject.h
    ├── arrayscalars.h
    ├── halffloat.h
    ├── multiarray_api.txt
    ├── ndarrayobject.h
    ├── ndarraytypes.h
    ├── noprefix.h
    ├── npy_1_7_deprecated_api.h
    ├── npy_3kcompat.h
    ├── npy_common.h
    ├── npy_cpu.h
    ├── npy_endian.h
    ├── npy_interrupt.h
    ├── npy_math.h
    ├── npy_no_deprecated_api.h
    ├── npy_os.h
    ├── numpyconfig.h
    ├── old_defines.h
    ├── oldnumeric.h
    ├── ufunc_api.txt
    ├── ufuncobject.h
    └── utils.h

audy commented 8 years ago

Stack Overflow says do this which you've already done.

... I bet it's just my machine. I'm going to try stock ubuntu.

wasade commented 8 years ago

Very weird... does a conda install work?

audy commented 8 years ago

Works on fresh Ubuntu. I'll just close this.

Thanks for your help 😸

wasade commented 8 years ago

np, glad it's working :)

gawbul commented 7 years ago

I'm having this issue too - please see this fix https://github.com/epruesse/biom-format/commit/b72a0381ef6af8af2e9efb7535d068c410b2489a.

biocore / biom-format

install error: 'numpy/arrayobject.h' file not found #702