[pymvpa] LinearCSVMC not found in PyMVPA-upstream-2.4.0 release
Feilong Ma
mafeilong at gmail.com
Wed Jul 15 16:46:32 UTC 2015
I had a similar problem while installing PyMVPA on Mac OS (10.10.4). I
think the problem is related to this line:
https://github.com/PyMVPA/PyMVPA/blob/master/mvpa2/clfs/libsvmc/_svm.py#L22
When I tried to run this line in ipython
from mvpa2.clfs.libsvmc._svmc import C_SVC, NU_SVC, ONE_CLASS, EPSILON_SVR
What I got is:
ImportError: cannot import name C_SVC
I guess the problem might be related to compiling LibSVM. I vaguely
remember there was some error messages with CLANG blah blah.
I installed python and some other packages using Homebrew, in case it's
related to this issue.
Best,
Feilong
On Wed, Jul 15, 2015 at 10:13 AM <
pkg-exppsy-pymvpa-request at lists.alioth.debian.org> wrote:
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> Today's Topics:
>
> 1. Re: LinearCSVMC not found in PyMVPA-upstream-2.4.0 release
> (Melanie Boly)
> 2. Re: LinearCSVMC not found in PyMVPA-upstream-2.4.0 release
> (Yaroslav Halchenko)
> 3. Re: LinearCSVMC not found in PyMVPA-upstream-2.4.0 release
> (Melanie Boly)
> 4. Re: LinearCSVMC not found in PyMVPA-upstream-2.4.0 release
> (Yaroslav Halchenko)
> 5. Re: LinearCSVMC not found in PyMVPA-upstream-2.4.0 release
> (Melanie Boly)
>
>
>
> ---------- Forwarded message ----------
> From: Melanie Boly <boly.melanie at gmail.com>
> To: Development and support of PyMVPA <
> pkg-exppsy-pymvpa at lists.alioth.debian.org>
> Cc:
> Date: Wed, 15 Jul 2015 08:37:21 -0500
> Subject: Re: [pymvpa] LinearCSVMC not found in PyMVPA-upstream-2.4.0
> release
> 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;
> 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..
> Thanks so much for your help,
> Melanie
>
> On Tue, Jul 14, 2015 at 10:46 PM, Yaroslav Halchenko
> <debian at onerussian.com> wrote:
> >
> > On Tue, 14 Jul 2015, Melanie Boly wrote:
> >
> >> Dear,
> >
> >> I just downloaded the PyMVPA-upstream-2.4.0 release and was trying out
> >> the tutorial but cannot find anywhere the LinearCSVMC module. I saw in
> >> the online documentation it should be in:
> >
> >> mvpa2.clfs.svm.LinearCSVMC
> >
> >> but I cannot find this structure in the python modules.
> >> Could you please help me on how to use the SVM classifier in this
> >> release and what should be the equivalent module to call/import then?
> >> Thank you so much in advance,
> >
> > Hi Melanie,
> >
> > give us more detail
> >
> > - what is your OS
> > - how did you "Download" PyMVPA-upstream-2.4.0 release?
> > if "sources" only, did you see/follow smth like
> > http://www.pymvpa.org/installation.html#alternative-build-procedure
> >
> > ?
> >
> > --
> > 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
> >
> > _______________________________________________
> > Pkg-ExpPsy-PyMVPA mailing list
> > Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
> >
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
>
>
>
>
>
> ---------- Forwarded message ----------
> From: Yaroslav Halchenko <debian at onerussian.com>
> To: pkg-exppsy-pymvpa at lists.alioth.debian.org
> Cc:
> Date: Wed, 15 Jul 2015 09:48:02 -0400
> Subject: Re: [pymvpa] LinearCSVMC not found in PyMVPA-upstream-2.4.0
> release
>
> 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
>
>
>
>
>
> ---------- Forwarded message ----------
> From: Melanie Boly <boly.melanie at gmail.com>
> To: Development and support of PyMVPA <
> pkg-exppsy-pymvpa at lists.alioth.debian.org>
> Cc:
> Date: Wed, 15 Jul 2015 08:54:34 -0500
> Subject: Re: [pymvpa] LinearCSVMC not found in PyMVPA-upstream-2.4.0
> release
> 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
> >
> > _______________________________________________
> > Pkg-ExpPsy-PyMVPA mailing list
> > Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
> >
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
>
>
>
>
>
> ---------- Forwarded message ----------
> From: Yaroslav Halchenko <debian at onerussian.com>
> To: pkg-exppsy-pymvpa at lists.alioth.debian.org
> Cc:
> Date: Wed, 15 Jul 2015 10:05:25 -0400
> Subject: Re: [pymvpa] LinearCSVMC not found in PyMVPA-upstream-2.4.0
> release
>
> 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
>
>
>
>
>
> ---------- Forwarded message ----------
> From: Melanie Boly <boly.melanie at gmail.com>
> To: Development and support of PyMVPA <
> pkg-exppsy-pymvpa at lists.alioth.debian.org>
> Cc:
> Date: Wed, 15 Jul 2015 09:13:19 -0500
> Subject: Re: [pymvpa] LinearCSVMC not found in PyMVPA-upstream-2.4.0
> release
> 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
> >
> > _______________________________________________
> > Pkg-ExpPsy-PyMVPA mailing list
> > Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
> >
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
>
>
> _______________________________________________
> Pkg-ExpPsy-PyMVPA mailing list
> Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
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