Setting up scikit-learn - numpy errors on import

Question

I'm trying to set up scikit-learn, but after installing numpy and scikit-learn (using pip) that's what I get when trying to imort sklearn:

import sklearn
RuntimeError: module compiled against API version 8 but this version of numpy is 7
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python2.7/site-packages/sklearn/__init__.py", line 32, in <module>
  from .base import clone
File "/usr/local/lib/python2.7/site-packages/sklearn/base.py", line 10, in <module>
  from scipy import sparse
File "/Library/Python/2.7/site-packages/scipy-0.13.0.dev_c31f167_20130304-py2.7-macosx-10.8-intel.egg/scipy/sparse/__init__.py", line 182, in <module>
from .csr import *
File "/Library/Python/2.7/site-packages/scipy-0.13.0.dev_c31f167_20130304-py2.7-macosx-10.8-intel.egg/scipy/sparse/csr.py", line 15, in <module>
from .sparsetools import csr_tocsc, csr_tobsr, csr_count_blocks, \
File "/Library/Python/2.7/site-packages/scipy-0.13.0.dev_c31f167_20130304-py2.7-macosx-10.8-intel.egg/scipy/sparse/sparsetools/__init__.py", line 5, in <module>
from .csr import *
File "/Library/Python/2.7/site-packages/scipy-0.13.0.dev_c31f167_20130304-py2.7-macosx-10.8-intel.egg/scipy/sparse/sparsetools/csr.py", line 26, in <module>
_csr = swig_import_helper()
File "/Library/Python/2.7/site-packages/scipy-0.13.0.dev_c31f167_20130304-py2.7-macosx-10.8-intel.egg/scipy/sparse/sparsetools/csr.py", line 22, in swig_import_helper
_mod = imp.load_module('_csr', fp, pathname, description)
ImportError: numpy.core.multiarray failed to import

Tried to reinstall things without success

It looks like you have the wrong version of numpy - are you positive you installed the correct one? — thegrinner
– thegrinner, Commented Mar 7, 2013 at 21:32
@thegrinner Well, I have version 7 while the traceback mentions version 8. But is there a numpy 1.8 out there? This sourceforge.net/projects/numpy/files/NumPy confirms that I have the newest one — smogg
– smogg, Commented Mar 7, 2013 at 21:36
Hmmm... this github issue suggets 1.7.0b2 should work: github.com/jsalvatier/scikits.bvp_solver/issues/2 I assume you grabbed 1.7.0? — thegrinner
– thegrinner, Commented Mar 7, 2013 at 21:41
Or perhaps it's related to this issue on macports where the system numpy is being prioritized over the new version: trac.macports.org/ticket/31891 — thegrinner
– thegrinner, Commented Mar 7, 2013 at 21:42

thegrinner · Accepted Answer · 2013-03-07 21:57:20Z

1

Looking at this issue on github, it sounds like it might require a specific version of numpy - they used 1.7.0b2.

answered Mar 7, 2013 at 21:57

thegrinner

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2 Comments

Andreas Mueller Over a year ago

This issue is not related to scikit-learn at all as far as I can tell.

thegrinner Over a year ago

@AndreasMueller I think root cause might actually be related to this issue where the wrong library version is being given priority and installing a specific version just happened to fix that.

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