R. David Murray <rdmur...@bitdance.com> added the comment:

I'm not sure I understand your confusion, but perhaps what you are missing is 
that we don't support installing 3rd party packages inside a source tree, only 
into an installed Python, and installing Python creates the site-packages 
directory in $prefix.

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nosy: +r.david.murray

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<http://bugs.python.org/issue12246>
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