can't import gdalnumeric (numpy version mismatch)

[saultdon]

I've built gdal against the 2.2 release branch and running 2.2.r39208.

In python I can't import gdalnumeric. It complains about the module conflicting with the numpy version.

>>> from osgeo import gdal
>>> import numpy
>>> import gdalnumeric
RuntimeError: module compiled against API version 0xb but this version of numpy is 0xa
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.7/site-packages/gdalnumeric.py", line 5, in <module>
    from osgeo.gdal_array import *
  File "/usr/lib/python2.7/site-packages/osgeo/gdal_array.py", line 28, in <module>
    _gdal_array = swig_import_helper()
  File "/usr/lib/python2.7/site-packages/osgeo/gdal_array.py", line 24, in swig_import_helper
    _mod = imp.load_module('_gdal_array', fp, pathname, description)
ImportError: numpy.core.multiarray failed to import
>>> import osgeo.gdalnumeric
RuntimeError: module compiled against API version 0xb but this version of numpy is 0xa
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.7/site-packages/osgeo/gdalnumeric.py", line 1, in <module>
    from osgeo.gdal_array import *
  File "/usr/lib/python2.7/site-packages/osgeo/gdal_array.py", line 28, in <module>
    _gdal_array = swig_import_helper()
  File "/usr/lib/python2.7/site-packages/osgeo/gdal_array.py", line 24, in swig_import_helper
    _mod = imp.load_module('_gdal_array', fp, pathname, description)
ImportError: numpy.core.multiarray failed to import
>>> import numpy.core.multiarray
>>>

This is on Linux and I have the following installed:

python2-numpy 1.13.0
python2-scipy 0.19.0
python2-pillow 4.1.1
gdal 2.2.r39205

I tried to recompile the packages above in the same order they're listed, but still can't get the GDAL python module to import gdalnumeric (this is needed for a QGIS plugin).

[Even Rouault]

Which distribution is this ?

[saultdon]

Hey Even, it's Arch Linux 64-bit.

[Even Rouault]

That works fine for me on Ubuntu 16.04 with a manually built numpy 1.13

Here's my procedure.

Build and install numpy 1.13

unzip numpy-1.13.0.zip
cd numpy-1.13.0
./setup.py build
PYTHONPATH=$HOME/install-numpy-1.13.0/lib/python ./setup.py install --home=$HOME/install-numpy-1.13.0

Build GDAL python bindings against numpy 1.13:

cd gdal/swig/python
PYTHONPATH=$HOME/install-numpy-1.13.0/lib/python make clean
PYTHONPATH=$HOME/install-numpy-1.13.0/lib/python make
cd ../..

Test :

PYTHONPATH=$HOME/install-numpy-1.13.0/lib/python:$HOME/gdal/swig/python/build/lib.linux-x86_64-2.7 python

>>> from osgeo import gdal
>>> import numpy
>>> numpy.__version__
'1.13.0'
>>> import gdalnumeric

Are you sure you don't have several numpy versions installed in your system, and you built against a recent one but run against an older one ?

[saultdon]

Ah, that's it.

Looks like numpy is installed system wide in /usr/lib/python2.7 (1.13.0) and also at $HOME/.local/lib/python2.7 (1.10.4)!

It was placed in .local while grabbing a module with pip2 install --user landsat-util which grabbed numpy as a dependency.

Looks like when I drop to python2 terminal it looks for modules in $HOME/.local/lib/python2.7 first instead of the system ones in /usr/lib/python2.7

Not sure how to fix it, will have to do some research for a remedy here. Would be nice to tell pip2 that when it installs a module or package to $HOME/.local/lib/python2.7 to only install dependencies there if they aren't already found in /usr/lib/python2.7