As far as I was able to reconstruct, my scipy install looked like this when it went well: mkdir scipy-bincp ../scipy-svn/site.cfg .export PATH=/Users/adam/repos/scipy.git/scipy-bin:$PATHln -s /usr/bin/g++-4.0 scipy-bin/g++-4.0ln -s /usr/bin/g++-4.0 scipy-bin/c++export CC=/usr/bin/gcc-4.0 ln -s /usr/bin/gcc-4.0 scipy-bin/ln -s /usr/bin/gcc-4.0 scipy-bin/gccln -s /usr/local/bin/gfortran-4.0 scipy-bin/gfortran-4.0ln -s /usr/local/bin/gfortran-4.0 scipy-bin/gfortranln -s /usr/local/bin/g95 scipy-bin/g95ln -s /usr/local/bin/i686-apple-darwin8-gfortran-4.2 scipy-bin/python2.7 setup.py buildpython2.7 setup.py install However, site.cfg included pointers to AMD and UMFPACK that were installed via the incredibly complicated series of steps listed here: http://blog.hyperjeff.net/?p=160 AG