Building numpy/scipy for Python3 on Mac OS Lion - macos

Question

I can't get Numpy or Scipy to work with Python3 on MAC OSX Lion.
I have used pip successfully to install numpy, scipy and matplotlib, and they work well with Python2.7, but in Python3 typing import numpy brings up No module named numpy. I've tried downloading the source code directly and then running 'python3 setup.py build', but I get various error warnings, some in red that have to do with fortran (e.g. 'Could not locate executable f95'). The error message that appears to fail in the end is 'RuntimeError: Broken toolchain: cannot link a simple C program', and appears to be related to the previous line 'sh: gcc-4.2: command not found'.
The Scipy website suggests that there may be issues with the c compiler, but the same problems didn't arise using pip to install for python2.7. I have followed the instructions on the website regarding changing the compiler but this has not made any difference.
I have also tried installing from a virtual environment:
mkvirtualenv -p python3.2 test1
pip install numpy
But this fails with Command python setup.py egg_info failed with error code 1 in /Users/Eddy/.virtualenvs/test1/build/numpy
I've considered making python3 default, and then I thought a pip install might work, but I don't know how to do that. Does anyone have any suggestions for how I might proceed? Thanks.

Answer 1

I ran into the same issue of
scipy/sparse/linalg/dsolve/superlumodule.c:268:9: error: non-void function 'PyInit_superlu' should return a value [-Wreturn-type]
someone on the scipy mailing list suggested the following:
what happens if you change the line 268 ( in scipy/sparse/linalg/dsolve/_superlumodule.c)
from
return;
to
return NULL;
sure enough it worked

Answer 2

I've made some progress with this problem, with much assistance from Ned Deily on the pythonmac mailing list. I can now build numpy for python3, but scipy still won't build.
To install numpy:
The scipy website (http://www.scipy.org/Installing_SciPy/Mac_OS_X) suggests working around the C compiler problem with three typed commands, but these are insufficient, you need one more:
$ export CC=clang
$ export CXX=clang
$ export FFLAGS=-ff2c
$ export LDSHARED='clang -bundle -undefined dynamic_lookup \
-arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk -g'
After this building from source should work. See here for details.
Problem building scipy:
I don't know what the issue here is, something with the C compiler again though I think. Here are the error messages. I'd greatly appreciate any thoughts on this matter.
Thanks, Eddy
error messages:
compiling C sources
C compiler: clang -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk
compile options: '-DNO_ATLAS_INFO=3 -DUSE_VENDOR_BLAS=1 -I/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include -I/Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m -c'
extra options: '-msse3'
clang: scipy/sparse/linalg/dsolve/_superlumodule.c
In file included from scipy/sparse/linalg/dsolve/_superlumodule.c:18:
In file included from /Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy/arrayobject.h:15:
In file included from /Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy/ndarrayobject.h:17:
In file included from /Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy/ndarraytypes.h:1972:
/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API"
^
scipy/sparse/linalg/dsolve/_superlumodule.c:268:9: error: non-void function 'PyInit__superlu' should return a value [-Wreturn-type]
return;
^
1 warning and 1 error generated.
In file included from scipy/sparse/linalg/dsolve/_superlumodule.c:18:
In file included from /Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy/arrayobject.h:15:
In file included from /Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy/ndarrayobject.h:17:
In file included from /Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy/ndarraytypes.h:1972:
/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API"
^
scipy/sparse/linalg/dsolve/_superlumodule.c:268:9: error: non-void function 'PyInit__superlu' should return a value [-Wreturn-type]
return;
^
1 warning and 1 error generated.
error: Command "clang -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk -DNO_ATLAS_INFO=3 -DUSE_VENDOR_BLAS=1 -I/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include -I/Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m -c scipy/sparse/linalg/dsolve/_superlumodule.c -o build/temp.macosx-10.6-intel-3.2/scipy/sparse/linalg/dsolve/_superlumodule.o -msse3" failed with exit status 1

Answer 3

I had this problem and one of these sorted it - not sure which one but I include both for completeness:
I had this in my .bash_profile "export CC=gcc-4.2" which was probably some kind of hack from previous OS X compilation problems, I removed it.
Installed the standalone GCC from here https://github.com/kennethreitz/osx-gcc-installer/ over my XCode install
booted up a new terminal window and pip install numpy worked fine