Cannot import correct version of numpy on OS X Mavericks

Question

I have upgraded from Mountain Lion to Mavericks ande also updated Macports and its outdated packages. I have installed numpy 1.7, but the problem is the one used by python is still numpy 1.6. The following are some information about my system.

>> python -c 'import numpy; print numpy.__version__' gives

1.6.2

which shows the active numpy version is 1.6.2

>> port installed | grep numpy gives

py27-numpy @1.7.1_0 (active)

which shows the active numpy version is 1.7.1_0

>> port installed | grep python gives

gnome-doc-utils @0.20.10_0+python27 (active)
gtk-doc @1.18_0+python27 (active)
ipython_select @0.3_1 (active)
opencv @2.4.6.1_2+python27 (active)
py27-ipython @0.13.2_0+notebook+parallel+scientific
py27-ipython @1.1.0_0+scientific
py27-ipython @1.1.0_0+notebook+parallel+scientific (active)
py27-wxpython-3.0 @2.9.5.0_0 (active)
py27-wxpython-devel @2.9.4.0_0
python24 @2.4.6_10 (active)
python27 @2.7.5_0
python27 @2.7.5_1 (active)
python_select @0.3_2
python_select @0.3_3 (active)
swig-python @2.0.9_0
swig-python @2.0.10_0 (active)
xorg-libxcb @1.9.1_0+python27 (active)
xorg-xcb-proto @1.8_0+python27 (active)

which shows, the active python version is python27.

Also, port select python gives

Available versions for python:
    none
    python24
    python25-apple
    python26-apple
    python27
    python27-apple (active)

And what is numpy.__file__? You're probably picking up the system one. Does which python tells you it's in /opt/local? — user707650
– user707650, Commented Oct 31, 2013 at 12:42
On the command line, run which python or ls -l $(which python) to check for links. Also, please type port select python, to see which python port is telling the system to use. — askewchan
– askewchan, Commented Oct 31, 2013 at 13:22
@void: what is wrong with macports? I am using it because it is suggested as similar tool as apt in Ubuntu. Actually, I start to use Mac only a few months ago. — skyuuka
– skyuuka, Commented Oct 31, 2013 at 13:30
@Evert:numpy.__file__=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/__init__.pyc and which python gives /opt/local/bin/python — skyuuka
– skyuuka, Commented Oct 31, 2013 at 13:34

askewchan · Accepted Answer · 2013-10-31 14:23:58Z

1

You're using the apple-installed version of python, you can see this by the fact that

port select python

gives you

python27-apple (active)

Remedy this with:

sudo port select python python27

If this:

import sys
print sys.path

still shows that python is looking in /System/Library instead of (or before) /opt/local/Library for packages, then the apple versions of packages might be imported. To solve this, you might be able to fix it by using a .pth file with site to modify your sys.path.

edited Oct 31, 2013 at 14:23

answered Oct 31, 2013 at 13:46

askewchan

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4 Comments

skyuuka Over a year ago

Thanks, but it does not solve the problem. I tried to switch the python version, it never works.

askewchan Over a year ago

Can you switch to python27 (not -apple) and then run python, and import sys; print sys.path and see if it's looking in /opt/local/Library or /System/Library? IT could be related to trac.macports.org/ticket/34763

skyuuka Over a year ago

Sure, I am using the one without -apple, but sys.path is looking into both opt/local/Library and /System/Library.

askewchan Over a year ago

So that's the problem, the old numpy is in /System/Library and due to that bug, that path must come first before the /opt/local/Library. You might be able to fix it by using site to modify your sys.path.

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