[pymvpa] Cannot build LIBSVM files on Mac OS

[Christopher J Markiewicz]

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.

-- 
Christopher J Markiewicz
Ph.D. Candidate, Quantitative Neuroscience Laboratory
Boston University