[pymvpa] LinearCSVMC not found in PyMVPA-upstream-2.4.0 release

[Yaroslav Halchenko]

On Wed, 15 Jul 2015, Melanie Boly wrote:

> Dear Yaroslav,
> the make script completed but I had a long error indeed

> Here it is:

> -----------------------------------------------------------------------------------------------------------------------------------------------------------

> $ sudo make

> fatal: Not a git repository (or any of the parent directories): .git

> python setup.py config --noisy

> running config

> python setup.py build_ext --inplace

> running build_ext

> running build_src

> build_src

> building extension "mvpa2.clfs.libsmlrc.smlrc" sources

> building extension "mvpa2.clfs.libsvmc._svmc" sources

> building data_files sources

> build_src: building npy-pkg config files

> customize UnixCCompiler

> customize UnixCCompiler using build_ext

> customize UnixCCompiler

> customize UnixCCompiler using build_ext

> building 'mvpa2.clfs.libsmlrc.smlrc' extension

> compiling C sources

> C compiler: cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64
> -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv
> -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes
> -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes
> -DENABLE_DTRACE -arch x86_64 -arch i386 -pipe


> compile options:
> '-I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include
> -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
> -c'

> cc: mvpa2/clfs/libsmlrc/smlr.c

> mvpa2/clfs/libsmlrc/smlr.c:172:10: warning: implicit conversion loses
> integer precision: 'long long' to 'unsigned int' [-Wshorten-64-to-32]

>   srand (seed);

>   ~~~~~  ^~~~

> mvpa2/clfs/libsmlrc/smlr.c:342:10: warning: implicit conversion loses
> integer precision: 'long' to 'int' [-Wshorten-64-to-32]

>   return cycle;

>   ~~~~~~ ^~~~~

> 2 warnings generated.

> mvpa2/clfs/libsmlrc/smlr.c:172:10: warning: implicit conversion loses
> integer precision: 'long long' to 'unsigned int' [-Wshorten-64-to-32]

>   srand (seed);

>   ~~~~~  ^~~~

> 1 warning generated.

> cc -bundle -undefined dynamic_lookup -arch x86_64 -arch i386 -Wl,-F.
> build/temp.macosx-10.10-intel-2.7/mvpa2/clfs/libsmlrc/smlr.o -lm -o
> mvpa2/clfs/libsmlrc/smlrc.so -bundle

> building 'mvpa2.clfs.libsvmc._svmc' extension

> compiling C++ sources

> C compiler: c++ -fno-strict-aliasing -fno-common -dynamic -arch x86_64
> -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv
> -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wshorten-64-to-32 -DNDEBUG -g
> -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch x86_64
> -arch i386 -pipe


> creating build/temp.macosx-10.10-intel-2.7/mvpa2/clfs/libsvmc

> compile options: '-I3rd/libsvm
> -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include
> -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
> -c'

> c++: 3rd/libsvm/svm.cpp

> c++: mvpa2/clfs/libsvmc/svmc_wrap.cpp

> In file included from mvpa2/clfs/libsvmc/svmc_wrap.cpp:3087:

> In file included from
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/arrayobject.h:4:

> In file included from
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarrayobject.h:17:

> In file included from
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarraytypes.h:1760:

> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/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 " \

>  ^

> mvpa2/clfs/libsvmc/svmc_wrap.cpp:3615:15: warning: implicit conversion
> loses integer precision: 'Py_ssize_t' (aka 'long') to 'int'
> [-Wshorten-64-to-32]

>         int length = PyList_Size(indices);

>             ~~~~~~   ^~~~~~~~~~~~~~~~~~~~

> 2 warnings generated.

> In file included from mvpa2/clfs/libsvmc/svmc_wrap.cpp:3087:

> In file included from
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/arrayobject.h:4:

> In file included from
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarrayobject.h:17:

> In file included from
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarraytypes.h:1760:

> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/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.

> c++ -bundle -undefined dynamic_lookup -arch x86_64 -arch i386 -Wl,-F.
> build/temp.macosx-10.10-intel-2.7/3rd/libsvm/svm.o
> build/temp.macosx-10.10-intel-2.7/mvpa2/clfs/libsvmc/svmc_wrap.o -o
> mvpa2/clfs/libsvmc/_svmc.so -bundle

> touch build-stamp

actually those are all just warnings and it generated bindings just
fine.


So what happens if you run in that directory:

MVPA_DEBUG=EXT.* PYTHONPATH=$PWD python -c 'from mvpa2.clfs.svm import LinearCSVMC; print(LinearCSVMC)'

-- 
Yaroslav O. Halchenko, Ph.D.
http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
Research Scientist,            Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik