title: Scipy error: numpy.dtype size changed, may indicate binary incompatibility (and associated strange behavior)
body: <p>I am installing numpy/scipy/scikit-learn on OS X 10.9.4, and am getting errors about "numpy.dtype size changed, may indicate binary incompatibility".</p>
  
  <p>Here's what I did to construct the repo:</p>
  
  <pre><code>mkvirtualenv thm
  workon thm
  pip install numpy scipy pandas ipython # and some other stuff
  cd /path/to/our/repo
  # run tests
  </code></pre>
  
  <p>Here's a traceback excerpt of a relevant warning (turned into an error because we use <code>warnings.simplefilter('error')</code> at the beginning of our tests):</p>
  
  <pre><code>======================================================================
  ERROR: Failure: RuntimeWarning (numpy.dtype size changed, may indicate binary in
  compatibility)
  ----------------------------------------------------------------------
  Traceback (most recent call last):
    File "/Users/ben/.virtualenvs/thm/lib/python2.7/site-packages/nose/loader.py",
   line 414, in loadTestsFromName
      addr.filename, addr.module)
    File "/Users/ben/.virtualenvs/thm/lib/python2.7/site-packages/nose/importer.py
  ", line 47, in importFromPath
      return self.importFromDir(dir_path, fqname)
    File "/Users/ben/.virtualenvs/thm/lib/python2.7/site-packages/nose/importer.py
  ", line 94, in importFromDir
      mod = load_module(part_fqname, fh, filename, desc)
    File "/Users/ben/code/thm/alpha/prosper/base/stats/test_auc.py", line 3, in &lt;m
  odule&gt;
      import sklearn.metrics
    File "/Users/ben/.virtualenvs/thm/lib/python2.7/site-packages/sklearn/metrics/
  __init__.py", line 6, in &lt;module&gt;
      from .metrics import (accuracy_score,
    File "/Users/ben/.virtualenvs/thm/lib/python2.7/site-packages/sklearn/metrics/metrics.py", line 27, in &lt;module&gt;
      from scipy.spatial.distance import hamming as sp_hamming
    File "/Users/ben/.virtualenvs/thm/lib/python2.7/site-packages/scipy/spatial/__init__.py", line 90, in &lt;module&gt;
      from .ckdtree import *
    File "__init__.pxd", line 155, in init scipy.spatial.ckdtree (scipy/spatial/ckdtree.c:20570)
  RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility
  </code></pre>
  
  <p>I'm told that this warning is caused by scipy being compiled against a different version of numpy than the one installed. However, I installed them all with pip in what I thought was a pretty standard way, so this shouldn't be a problem, I would think.</p>
  
  <p>Weirdly, although running our entire test suite as a whole (via <code>python -m unittest discover</code>) gives these errors, running the individual tests (via <code>python -m unittest &lt;module&gt;</code>) works fine.</p>
  
  <p>According to the tests, here's some relevant version info:</p>
  
  <pre><code>numpy version 1.9.0 (rev 07601a64cdfeb1c0247bde1294ad6380413cab66)
  scipy version 0.14.0 (built against numpy 1.9.0)
  sklearn version 0.15.2
  pandas version 0.14.1
  </code></pre>
  
  <p>Happy to provide more info on request!</p>