Issue 1:
This was closed improperly.

New wheels were placed on PyPI on 6/28. numpy wheels are new as of 6/19. I just reinstalled on 8/4, which picked up both new wheels. One or the other is the problem. This is OPEN. Whenever binary builds are placed in a public place for widespread download, great caution and extensive testing of dependencies is in order.

Rebuilding these seems to cause:

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/_continuous_distns.py:24: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility

from . import vonmises_cython

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/_continuous_distns.py:24: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility

from . import vonmises_cython

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/stats.py:188: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility

from ._rank import rankdata, tiecorrect

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/stats.py:188: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility

from ._rank import rankdata, tiecorrect

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/interpolate/interpolate.py:28: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility

from . import _ppoly

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/interpolate/interpolate.py:28: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility

from . import _ppoly

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/spatial/init.py:90: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility

from .ckdtree import *

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/spatial/init.py:90: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility

from .ckdtree import *

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/spatial/init.py:91: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility

from .qhull import *

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/spatial/init.py:91: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility

from .qhull import *

Issue 2:
Two days I reinstalled everything (Python plus all modules) and started getting these warnings:

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/_continuous_distns.py:24: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility

from . import vonmises_cython

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/_continuous_distns.py:24: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility

from . import vonmises_cython

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/stats.py:188: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility

from ._rank import rankdata, tiecorrect

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/stats.py:188: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility

from ._rank import rankdata, tiecorrect

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/interpolate/interpolate.py:28: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility

from . import _ppoly

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/interpolate/interpolate.py:28: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility

from . import _ppoly

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/spatial/init.py:90: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility

from .ckdtree import *

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/spatial/init.py:90: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility

from .ckdtree import *

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/spatial/init.py:91: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility

from .qhull import *

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/spatial/init.py:91: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility

from .qhull import *

I had never experienced this before. Was there recently a rev of scipy? Big time regression perhaps?

Or is there an order of installation problem.

My config is python 2.7.8 from Python.org. On Mac OS X 10.9.4

pip list:

altgraph (0.12)

argparse (1.2.1)

astroid (1.2.0)

backports.ssl-match-hostname (3.4.0.2)

certifi (14.05.14)

Cython (0.20.2)

docutils (0.12)

gnureadline (6.3.3)

ipython (2.1.0)

jdcal (1.0)

Jinja2 (2.7.3)

logilab-common (0.62.1)

macholib (1.7)

MarkupSafe (0.23)

matplotlib (1.3.1)

mock (1.0.1)

modulegraph (0.12)

nose (1.3.3)

numexpr (2.4)

numpy (1.8.1)

openpyxl (2.0.4)

pandas (0.14.1)

patsy (0.3.0)

pep8 (1.5.7)

Pillow (2.5.1)

pip (1.5.6)

psutil (2.1.1)

py (1.4.23)

py2app (0.9)

pyflakes (0.8.1)

Pygments (1.6)

pylint (1.3.0)

pyparsing (2.0.2)

pytest (2.6.0)

python-dateutil (2.2)

pytz (2014.4)

pyzmq (14.3.1)

rope (0.10.2)

Scidoc (1.8.0)

scikit-learn (0.15.1)

scipy (0.14.0)

seaborn (0.3.1)

setuptools (5.4.2)

simplejson (3.6.0)

six (1.7.3)

Sphinx (1.2.2)

spyder (2.3.0)

statsmodels (0.5.0)

stevedore (0.15)

sympy (0.7.5)

tornado (4.0)

virtualenv (1.11.6)

virtualenv-clone (0.2.5)

virtualenvwrapper (4.3.1)

wsgiref (0.1.2)

xlrd (0.9.3)

XlsxWriter (0.5.6)

xlwt (0.7.5)

I am trying to perfect an automated installer script and I want to get the right order of installation to prevent this (I've used this script many times and not had this problem previously.).