Scipy Error: Numpy.dtype Size Changed, May Indicate Binary Incompatibility (and Associated Strange Behavior)

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'. Here's what I did to construct

Solution 1:

How did you build sklearn 0.14.1? Did you build it against the same version of numpy as you did for scipy?

Recent versions of scikit-learn, scipy and numpy have prebuilt-packages. In particular scikit-learn 0.15.2 should be binary compatible with numpy 1.7+. I think the same is true with scipy 0.14.0 but you said you built it yourself from source, which is not what pip should do by default (it should just install the prebuilt whl package).

Edit: have you tried to do:

pip install -U scipy scikit-learn pandas

to make sure that you are using the latest stable versions of the whl for those packages?

Edit: The comment below has the actual answer that works and is presumably why this answer was accepted. Namely:

pip uninstall -y scipy scikit-learn
pip install --no-binary scipy scikit-learn