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thouis / homebrew

The missing package manager for OS X.
http://mxcl.github.com/homebrew
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Numpy installation confused by old system install of numpy #4

Open ljosa opened 12 years ago

ljosa commented 12 years ago

I tried to follow the wiki instructions on a virgin Lion machine. All went well until the cellprofiler-dev recipe failed to install numpy:

compiling C sources

C compiler: /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I/Users/ljosa/tmp/homebrew/Cellar/libhdf5-universal/1/include -isystem /Users/ljosa/tmp/homebrew/include

creating build/temp.macosx-10.6-intel-2.7/numpy/core/blasdot

compile options: '-DNO_ATLAS_INFO=3 -Inumpy/core/blasdot -Inumpy/core/include -Ibuild/src.macosx-10.6-intel-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -Ibuild/src.macosx-10.6-intel-2.7/numpy/core/src/multiarray -Ibuild/src.macosx-10.6-intel-2.7/numpy/core/src/umath -c'

extra options: '-faltivec -I/System/Library/Frameworks/vecLib.framework/Headers'

clang: numpy/core/blasdot/_dotblas.c

clang: error: invalid argument '-faltivec' only allowed with 'ppc/ppc64'

clang: error: invalid argument '-faltivec' only allowed with 'ppc/ppc64'

clang: error: invalid argument '-faltivec' only allowed with 'ppc/ppc64'

clang: error: invalid argument '-faltivec' only allowed with 'ppc/ppc64'

error: Command "/usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I/Users/ljosa/tmp/homebrew/Cellar/libhdf5-universal/1/include -isystem /Users/ljosa/tmp/homebrew/include -DNO_ATLAS_INFO=3 -Inumpy/core/blasdot -Inumpy/core/include -Ibuild/src.macosx-10.6-intel-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -Ibuild/src.macosx-10.6-intel-2.7/numpy/core/src/multiarray -Ibuild/src.macosx-10.6-intel-2.7/numpy/core/src/umath -c numpy/core/blasdot/_dotblas.c -o build/temp.macosx-10.6-intel-2.7/numpy/core/blasdot/_dotblas.o -faltivec -I/System/Library/Frameworks/vecLib.framework/Headers" failed with exit status 1

I believe the problem is that the bumpy version that comes with the OS (/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy) interferes.

How can we prevent this from happening (preferably without deleting what came with the OS, as the user may have other software that depends on it)?

thouis commented 12 years ago

The CPhomebrew shouldn't refer to the system python at all, it should only use the python.org installed one.

I think this might have been addressed in the devel branch of numpy, already.