scikit-learn install failure / numpy not found / missing numpy headers

Question

When i try to install scikit-learn on a Suse (openSuse 12.2 x86_64) server via:

pip install -U scikit-learn

i get the following error:

(....)

compile options: '-I/usr/lib64/python2.7/site-packages/numpy/core/include -Isklearn/svm/src/libsvm -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c'

gcc: sklearn/svm/libsvm.c

sklearn/svm/libsvm.c:303:31: fatal error: numpy/arrayobject.h: No such file or directory

compilation terminated.

sklearn/svm/libsvm.c:303:31: fatal error: numpy/arrayobject.h: No such file or directory

compilation terminated.

I already tried:

-installing gcc to the latest version
-installing scikit from a downloaded zip, over easy_install (to avoid old repos) -uninstalling and reinstalling numpy (over pip)

When i try to install scipy (which is a requirement of numpy) i get a similar Error:

adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.

adding 'build/src.linux-x86_64-2.7' to include_dirs.

error: file '/usr/lib64/python2.7/site-packages/numpy/f2py/src/fortranobject.c' does not exist

Apparently all the numpy headers in "site-packages/numpy/core/include" are missing. I already reinstalled numpy with pip without any Problems but the headers are still missing.

If you try a `locate arrayobject.h` (or the equivalent for Suse), what does it bring up? — darthbith, Aug 20 '13 at 14:04
i cant find anything. Looks like there are some files missing in numpy. — Dev Icro, Aug 21 '13 at 08:51
Do you have `locate` installed? http://efod.se/blog/archive/2006/01/30/locate-on-suse-based-distributions — darthbith, Aug 21 '13 at 11:53
yes ofc, locate couldnt find the missing numpy object. Apperently (in comparison to an second numpy install) all headers in numpy/core/include are missing — Dev Icro, Aug 21 '13 at 13:13

score 11 · Accepted Answer · answered Aug 21 '13 at 13:37

11

Ok when i installed numpy with pip or normally all the include header were missing.

To fix this i installed the package "python-numpy-devel" (with zypper, stupid suse package names...) which contains the headers.

After that the headers are there and the rest works.

answered Aug 21 '13 at 13:37

Dev Icro

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I am using Docker and Alpine, and so I used: `RUN set -x && apk update && apk add --no-cache --update-cache libexecinfo-dev py3-numpy=1.13.3-r0 py-numpy-dev=1.13.3-r0` – cs94njw Jan 11 '18 at 14:53

scikit-learn install failure / numpy not found / missing numpy headers

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