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

Melanie Boly boly.melanie at gmail.com
Wed Jul 15 14:13:19 UTC 2015


Dear Yaroslav, I just did it, and here is the message:

-----------------------------------------

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

[EXT ] DBG:    Checking for the presence of running ipython env

[EXT ] DBG:    Presence of running ipython env is NOT verified. Caught
exception was: Not running in IPython session

[EXT ] DBG:  Checking for the presence of numpy

[EXT ] DBG:  Presence of numpy is verified

[EXT ] DBG:  Checking for the presence of scipy

[EXT ] DBG:     Skip retesting for 'numpy'.

[EXT ] DBG:  Presence of scipy is verified

[EXT ] DBG:  Checking for the presence of running ipython env

[EXT ] DBG:  Presence of running ipython env is NOT verified. Caught
exception was: Not running in IPython session

[EXT ] DBG:  Checking for the presence of matplotlib

[EXT ] DBG:  Presence of matplotlib is verified

[EXT ] DBG:      Skip retesting for 'running ipython env'.

[EXT ] DBG:      Skip retesting for 'scipy'.

[EXT ] DBG:      Skip retesting for 'scipy'.

[EXT ] DBG:      Skip retesting for 'scipy'.

[EXT ] DBG:       Skip retesting for 'scipy'.

[EXT ] DBG:       Checking for the presence of good scipy.stats.rdist

[EXT ] DBG:       Presence of good scipy.stats.rdist is NOT verified.
Caught exception was: scipy.stats carries misbehaving rdist
distribution

[EXT ] DBG:      Fixing up scipy.stats.rdist

[EXT ] DBG:       Checking for the presence of good scipy.stats.rdist

/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy/integrate/quadpack.py:293:
UserWarning: Extremely bad integrand behavior occurs at some points of
the

  integration interval.

  warnings.warn(msg)

[EXT ] DBG:       Presence of good scipy.stats.rdist is verified

[EXT ] DBG:       Checking for the presence of good scipy.stats.rv_discrete.ppf

[EXT ] DBG:       Presence of good scipy.stats.rv_discrete.ppf is verified

[EXT ] DBG:       Checking for the presence of good
scipy.stats.rv_continuous._reduce_func(floc,fscale)

[EXT ] DBG:       Presence of good
scipy.stats.rv_continuous._reduce_func(floc,fscale) is verified

[EXT ] DBG:      Checking for the presence of pylab

[EXT ] DBG:         Skip retesting for 'matplotlib'.

[EXT ] DBG:      Presence of pylab is verified

[EXT ] DBG:     Skip retesting for 'scipy'.

[EXT ] DBG:      Skip retesting for 'scipy'.

[EXT ] DBG:  Checking for the presence of shogun

[EXT ] DBG:  Presence of shogun is NOT verified. Caught exception was:
No module named shogun.Classifier

[EXT ] DBG:  Checking for the presence of libsvm

[EXT ] DBG:  Presence of libsvm is NOT verified. Caught exception was:
cannot import name C_SVC

WARNING: None of SVM implementation libraries was found

 * Please note: warnings are printed only once, but underlying problem
might occur many times *

Traceback (most recent call last):

  File "<string>", line 1, in <module>

ImportError: cannot import name LinearCSVMC



-----------------
I am very grateful for your help.
Very best wishes,
Melanie


On Wed, Jul 15, 2015 at 9:05 AM, Yaroslav Halchenko
<debian at onerussian.com> wrote:
>
> 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
>
> _______________________________________________
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