Affine Gap fails to compile in OSX Mountain Lion

[derekeder]

When running on Mountain Lion

python setup.py install

executes successfully, but when the dedupe library is called, the following error occurs:

Traceback (most recent call last):
File "examples/canonical_example.py", line 3, in
import exampleIO
File "/Users/derekeder/projects/open-city/deduplication/dedupe/examples/exampleIO.py", line 3, in
import dedupe.core
File "/Users/derekeder/projects/open-city/deduplication/dedupe/dedupe/init.py", line 14, in
import affinegap
ImportError: dlopen(/Users/derekeder/projects/open-city/deduplication/dedupe/dedupe/affinegap.so, 2): Symbol not found: _newarrayobject
Referenced from: /Users/derekeder/projects/open-city/deduplication/dedupe/dedupe/affinegap.so
Expected in: flat namespace
in /Users/derekeder/projects/open-city/deduplication/dedupe/dedupe/affinegap.so


[derekeder]

This appears to be an issue with clang, the default compiler for OSX from Lion (10.7) and on.

This can be solved in two ways:

• change the default compiler set in xCode by adding the following lines your .bash_profile

#Set LLVM GCC as the default compiler for the system
export CPP='llvm-gcc-4.2'
export CC='llvm-gcc-4.2'
export CXX='llvm-g++'

For more, see http://stackoverflow.com/questions/6796982/clang-and-the-default-compiler-in-os-x-lion

• Run setup.py by specifying the compiler in the command line

LDSHARED="gcc-4.2 -Wl,-F. -bundle -undefined dynamic_lookup" CC=gcc-4.2 python setup.py install

for more info, see http://stackoverflow.com/questions/5967065/python-distutils-not-using-correct-version-of-gcc

[derekeder]

Update: we updated cython and rebuilt the affinegap.so and it now compiles using clang