numpy headers in the include path

[Gael Varoquaux]

Binary package hint: python-numpy

The numpy headers of the Ubuntu are symlinked in /usr/lib. As a result, a Python package compiling with numpy.distutils will always pick up these headers, even if the numpy used is not the system numpy, but a localy installed numpy. Indeed, numpy.distutils will use the following compilation options:

compile options: '-I/usr/include -I/home/varoquau/usr/lib/python2.6/site-packages/numpy/core/include -I/usr/include/python2.6 -c'

Where the second include path points to the numpy headers of the locally-installed numpy, but is overriden by the general include '/usr/include'.

See the following mailing list discussion for more information:
http://mail.scipy.org/pipermail/numpy-discussion/2009-December/047376.html

With the release of numpy 1.4, this problem will become especially crucial, as picking up the wrong header leads to binary incompatibilities.

[WeatherGod (ben-v-root)]

Gael, thank you for bringing this to our attention. Quickly looking through the posted discussion, am I right in assuming that this is a packaging problem, *not* an upstream problem?

[Gael Varoquaux (gael-varoquaux)]

On Fri, Dec 11, 2009 at 10:53:46PM -0000, WeatherGod wrote:
> Gael, thank you for bringing this to our attention. Quickly looking
> through the posted discussion, am I right in assuming that this is a
> packaging problem, *not* an upstream problem?

It is. THe symlink is added by the debian packages. It should either be
removed, or turned into a symlink encoding the numpy version number, ie:

/usr/lib/numpy1.4

Cheers,

Gaël

[WeatherGod (ben-v-root)]

Slight correction to the above post: /usr/include/numpy1.4

Gael, I can confirm this issue with my Jaunty installation. I have also double-checked my Fedora 11 install, and there are no symlinks to the numpy headers from /usr/include. Personally, my vote would be to remove the symlink. But since it is there, it would imply that someone needed that symlink for some purpose and modifying that symlink would break things. I am not a packager, so I will leave it up to them to decide what is best.

[Julian Taylor (jtaylor)]

this should be fixed in recent distributions.