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 < [email protected]> wrote: > Send Pkg-ExpPsy-PyMVPA mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa > > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pkg-ExpPsy-PyMVPA digest..." > 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 <[email protected]> > To: Development and support of PyMVPA < > [email protected]> > 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 > <[email protected]> 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 > > [email protected] > > > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa > > > > > > ---------- Forwarded message ---------- > From: Yaroslav Halchenko <[email protected]> > To: [email protected] > 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 <[email protected]> > To: Development and support of PyMVPA < > [email protected]> > 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 > <[email protected]> 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 > > [email protected] > > > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa > > > > > > ---------- Forwarded message ---------- > From: Yaroslav Halchenko <[email protected]> > To: [email protected] > 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 <[email protected]> > To: Development and support of PyMVPA < > [email protected]> > 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 > <[email protected]> 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 > > [email protected] > > > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa > > > _______________________________________________ > Pkg-ExpPsy-PyMVPA mailing list > [email protected] > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
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