[pymvpa] LinearCSVMC not found in PyMVPA-upstream-2.4.0 release
Melanie Boly
boly.melanie at gmail.com
Wed Jul 15 13:54:34 UTC 2015
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
----------------------------------------------------------------------------------------------------
Any feedback appreciated. I do have Git installed as well as SWIG and
Makeports on my Mac though
Thanks a lot!
Melanie
On Wed, Jul 15, 2015 at 8:48 AM, Yaroslav Halchenko
<debian at onerussian.com> wrote:
>
> On Wed, 15 Jul 2015, Melanie Boly wrote:
>
>> Dear Yaroslav,
>> I use a MacOsX Yosemite 10.10.4
>> I downloaded the release from https://github.com/PyMVPA/PyMVPA/tags
>> I did try once again the alternative procedure installation just now;
>
> so you did:
>
> cd PyMVPA
> make
>
> and that one completed without errors? if not -- cut/paste output
>
> if completed without errors you must have got LinearCSVMC ;) just paste
> output from above commands
>
>> everything works until I try to call the LinearCSVMC function; the
>> only ones that are available in my python workspace are LinearKernel &
>> LinearLSKernel.
>> And when I try to call the module sum to import libsvm or sg it does
>> not recognize these names..
>
> for sg -- you would need shogun installed... probably easiest would be
> first to resolve this issue with libsvm
> --
> 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
>
> _______________________________________________
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