[pymvpa] Cannot build LIBSVM files on Mac OS

[Michael Bannert]

Thanks Christopher and sorry for the late reply. It turned out that the
problem does not occur with Xcode 7. I tested this solution again on a
different Mac yesterday.

Best,
Michael

On 18/02/16 20:02, Christopher J Markiewicz wrote:
> On 02/14/2016 10:15 AM, Michael Bannert wrote:
>> Dear PyMVPA community,
>>
>> I have a problem installing PyMVPA on Mac OS X 10.10.5 (Yosemite). Since
>> my Homebrew does not get along well with MacPorts, I figured it would be
>> best to try to build it from source.
>>
>> "python setup.py build_ext" fails with the following error (just the
>> error bit):
>>
>> /Users/MYUSERNAME/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
>> warning: "Using deprecated NumPy API, disable it by "
>> "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
>> #warning "Using deprecated NumPy API, disable it by " \
>>  ^
>> 1 warning generated.
>> creating build/lib.macosx-10.5-x86_64-2.7/mvpa2/clfs/libsvmc
>> g++ -bundle -undefined dynamic_lookup -L/Users/MYUSERNAME/anaconda/lib
>> -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.5.sdk -arch x86_64
>> build/temp.macosx-10.5-x86_64-2.7/3rd/libsvm/svm.o
>> build/temp.macosx-10.5-x86_64-2.7/build/src.macosx-10.5-x86_64-2.7/mvpa2/clfs/libsvmc/svmc_wrap.o
>> -L/Users/MYUSERNAME/anaconda/lib -o
>> build/lib.macosx-10.5-x86_64-2.7/mvpa2/clfs/libsvmc/_svmc.so -bundle
>> ld: library not found for -lc++
>> clang: error: linker command failed with exit code 1 (use -v to see
>> invocation)
>> ld: library not found for -lc++
>> clang: error: linker command failed with exit code 1 (use -v to see
>> invocation)
>> error: Command "g++ -bundle -undefined dynamic_lookup
>> -L/Users/MYUSERNAME/anaconda/lib -arch x86_64 -isysroot
>> /Developer/SDKs/MacOSX10.5.sdk -arch x86_64
>> build/temp.macosx-10.5-x86_64-2.7/3rd/libsvm/svm.o
>> build/temp.macosx-10.5-x86_64-2.7/build/src.macosx-10.5-x86_64-2.7/mvpa2/clfs/libsvmc/svmc_wrap.o
>> -L/Users/MYUSERNAME/anaconda/lib -o
>> build/lib.macosx-10.5-x86_64-2.7/mvpa2/clfs/libsvmc/_svmc.so -bundle"
>> failed with exit status 1
>>
>> It seems that there is a problem with building the libsvm functions.
>> (After all, the installation works fine with the "--no-libsvm" option.)
>> I discovered a previous email reporting problems with that. The
>> suggested solution was to use an earlier version of swig (3.0.0 instead
>> of 3.0.8). This didn't work for me. (
>> http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2015q3/003176.html
>> )
>>
>> However, I did find the library "ld" on my system. How can I tell
>> PyMVPA's setup.py to use it? I played around with the config settings in
>> setup.py but to no avail so far ...
> 
> ld isn't a library, it's the linker. It was saying that it couldn't find
> libc++. These might be useful to you:
> 
> https://stackoverflow.com/questions/15981424/where-is-libc-on-os-x
> https://stackoverflow.com/questions/17302349/what-is-lc
> 
> I have very limited experience with Macs, so I can't really help much
> otherwise.
>