[SciPy-User] Install scipy in virtualenv under OS X Snow Leopard with Python 3

[Chris Waigl]

Good morning! 

I am setting up my first scientific Python environment with Python 3 (3.3.3, from python.org). My production stuff is running under 2.7.5, where I installed scipy globally via the .dmg file from scipy.org. Now, I have set up a virtual environment (with --no-site-packages) and am installing packages with pip. Scipy is the first to give me trouble, though. (Numpy and matplotlib are already installed.)

pip install scipy 

errors out while compiling _umfpack_wrap.c. The final error message is 

error: Command "gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk -g -DSCIPY_UMFPACK_H -DSCIPY_AMD_H -DNO_ATLAS_INFO=3 -I/usr/local/include -I/Users/cwaigl/.virtualenvs/science3/lib/python3.3/site-packages/numpy/core/include -I/Library/Frameworks/Python.framework/Versions/3.3/include/python3.3m -c build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c -o build/temp.macosx-10.6-intel-3.3/build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.o -msse3 -I/System/Library/Frameworks/vecLib.framework/Headers" failed with exit status 1

This happens with gcc 4.2. I also installed gcc4.6, in case, but the makefile still picks up gcc4.2. 

Is this a known issue? Any advice how to resolve it? (I could force it to use 4.6 if that would help.)

Thanks,

Chris Waigl


Error log excerpt:

build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c: In function ‘PySwigPacked_repr’:

build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c:1715: warning: return makes pointer from integer without a cast

build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c:1717: warning: return makes pointer from integer without a cast

build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c: In function ‘PySwigPacked_str’:

build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c:1726: warning: return makes pointer from integer without a cast

build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c:1728: warning: return makes pointer from integer without a cast

build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c: In function ‘_PySwigPacked_type’:

build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c:1773: warning: missing braces around initializer

build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c:1773: warning: (near initialization for ‘tmp.ob_base.ob_base’)

build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c:1775: warning: initialization makes integer from pointer without a cast

build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c:1778: warning: initialization from incompatible pointer type

build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c:1779: warning: initialization from incompatible pointer type

build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c:1780: warning: initialization from incompatible pointer type

build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c:1782: error: ‘cmpfunc’ undeclared (first use in this function)

build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c:1782: error: expected ‘}’ before ‘PySwigPacked_compare’

build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c:1829: error: ‘PyTypeObject’ has no member named ‘ob_type’

build/src.macosx-10.6-intel-3.3/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c:1767: warning: unused variable ‘swigpacked_doc’