<div dir="ltr">I had a similar problem while installing PyMVPA on Mac OS (10.10.4). I think the problem is related to this line:<div><a href="https://github.com/PyMVPA/PyMVPA/blob/master/mvpa2/clfs/libsvmc/_svm.py#L22">https://github.com/PyMVPA/PyMVPA/blob/master/mvpa2/clfs/libsvmc/_svm.py#L22</a></div><div><br></div><div>When I tried to run this line in ipython</div><div><div>from mvpa2.clfs.libsvmc._svmc import C_SVC, NU_SVC, ONE_CLASS, EPSILON_SVR</div><div>What I got is:</div><div>ImportError: cannot import name C_SVC</div><div><br></div><div>I guess the problem might be related to compiling LibSVM. I vaguely remember there was some error messages with CLANG blah blah.</div><div><br></div><div>I installed python and some other packages using Homebrew, in case it's related to this issue.</div><div><br></div><div>Best,</div><div>Feilong </div><br><div class="gmail_quote"><div dir="ltr">On Wed, Jul 15, 2015 at 10:13 AM <<a href="mailto:pkg-exppsy-pymvpa-request@lists.alioth.debian.org">pkg-exppsy-pymvpa-request@lists.alioth.debian.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Pkg-ExpPsy-PyMVPA mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Re: LinearCSVMC not found in PyMVPA-upstream-2.4.0 release<br>
(Melanie Boly)<br>
2. Re: LinearCSVMC not found in PyMVPA-upstream-2.4.0 release<br>
(Yaroslav Halchenko)<br>
3. Re: LinearCSVMC not found in PyMVPA-upstream-2.4.0 release<br>
(Melanie Boly)<br>
4. Re: LinearCSVMC not found in PyMVPA-upstream-2.4.0 release<br>
(Yaroslav Halchenko)<br>
5. Re: LinearCSVMC not found in PyMVPA-upstream-2.4.0 release<br>
(Melanie Boly)<br>
<br><br><br>---------- Forwarded message ----------<br>From: Melanie Boly <<a href="mailto:boly.melanie@gmail.com" target="_blank">boly.melanie@gmail.com</a>><br>To: Development and support of PyMVPA <<a href="mailto:pkg-exppsy-pymvpa@lists.alioth.debian.org" target="_blank">pkg-exppsy-pymvpa@lists.alioth.debian.org</a>><br>Cc: <br>Date: Wed, 15 Jul 2015 08:37:21 -0500<br>Subject: Re: [pymvpa] LinearCSVMC not found in PyMVPA-upstream-2.4.0 release<br>Dear Yaroslav,<br>
I use a MacOsX Yosemite 10.10.4<br>
I downloaded the release from <a href="https://github.com/PyMVPA/PyMVPA/tags" rel="noreferrer" target="_blank">https://github.com/PyMVPA/PyMVPA/tags</a><br>
I did try once again the alternative procedure installation just now;<br>
everything works until I try to call the LinearCSVMC function; the<br>
only ones that are available in my python workspace are LinearKernel &<br>
LinearLSKernel.<br>
And when I try to call the module sum to import libsvm or sg it does<br>
not recognize these names..<br>
Thanks so much for your help,<br>
Melanie<br>
<br>
On Tue, Jul 14, 2015 at 10:46 PM, Yaroslav Halchenko<br>
<<a href="mailto:debian@onerussian.com" target="_blank">debian@onerussian.com</a>> wrote:<br>
><br>
> On Tue, 14 Jul 2015, Melanie Boly wrote:<br>
><br>
>> Dear,<br>
><br>
>> I just downloaded the PyMVPA-upstream-2.4.0 release and was trying out<br>
>> the tutorial but cannot find anywhere the LinearCSVMC module. I saw in<br>
>> the online documentation it should be in:<br>
><br>
>> mvpa2.clfs.svm.LinearCSVMC<br>
><br>
>> but I cannot find this structure in the python modules.<br>
>> Could you please help me on how to use the SVM classifier in this<br>
>> release and what should be the equivalent module to call/import then?<br>
>> Thank you so much in advance,<br>
><br>
> Hi Melanie,<br>
><br>
> give us more detail<br>
><br>
> - what is your OS<br>
> - how did you "Download" PyMVPA-upstream-2.4.0 release?<br>
> if "sources" only, did you see/follow smth like<br>
> <a href="http://www.pymvpa.org/installation.html#alternative-build-procedure" rel="noreferrer" target="_blank">http://www.pymvpa.org/installation.html#alternative-build-procedure</a><br>
><br>
> ?<br>
><br>
> --<br>
> Yaroslav O. Halchenko, Ph.D.<br>
> <a href="http://neuro.debian.net" rel="noreferrer" target="_blank">http://neuro.debian.net</a> <a href="http://www.pymvpa.org" rel="noreferrer" target="_blank">http://www.pymvpa.org</a> <a href="http://www.fail2ban.org" rel="noreferrer" target="_blank">http://www.fail2ban.org</a><br>
> Research Scientist, Psychological and Brain Sciences Dept.<br>
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755<br>
> Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419<br>
> WWW: <a href="http://www.linkedin.com/in/yarik" rel="noreferrer" target="_blank">http://www.linkedin.com/in/yarik</a><br>
><br>
> _______________________________________________<br>
> Pkg-ExpPsy-PyMVPA mailing list<br>
> <a href="mailto:Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org" target="_blank">Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org</a><br>
> <a href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa" rel="noreferrer" target="_blank">http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa</a><br>
<br>
<br>
<br><br><br>---------- Forwarded message ----------<br>From: Yaroslav Halchenko <<a href="mailto:debian@onerussian.com" target="_blank">debian@onerussian.com</a>><br>To: <a href="mailto:pkg-exppsy-pymvpa@lists.alioth.debian.org" target="_blank">pkg-exppsy-pymvpa@lists.alioth.debian.org</a><br>Cc: <br>Date: Wed, 15 Jul 2015 09:48:02 -0400<br>Subject: Re: [pymvpa] LinearCSVMC not found in PyMVPA-upstream-2.4.0 release<br><br>
On Wed, 15 Jul 2015, Melanie Boly wrote:<br>
<br>
> Dear Yaroslav,<br>
> I use a MacOsX Yosemite 10.10.4<br>
> I downloaded the release from <a href="https://github.com/PyMVPA/PyMVPA/tags" rel="noreferrer" target="_blank">https://github.com/PyMVPA/PyMVPA/tags</a><br>
> I did try once again the alternative procedure installation just now;<br>
<br>
so you did:<br>
<br>
cd PyMVPA<br>
make<br>
<br>
and that one completed without errors? if not -- cut/paste output<br>
<br>
if completed without errors you must have got LinearCSVMC ;) just paste<br>
output from above commands<br>
<br>
> everything works until I try to call the LinearCSVMC function; the<br>
> only ones that are available in my python workspace are LinearKernel &<br>
> LinearLSKernel.<br>
> And when I try to call the module sum to import libsvm or sg it does<br>
> not recognize these names..<br>
<br>
for sg -- you would need shogun installed... probably easiest would be<br>
first to resolve this issue with libsvm<br>
--<br>
Yaroslav O. Halchenko, Ph.D.<br>
<a href="http://neuro.debian.net" rel="noreferrer" target="_blank">http://neuro.debian.net</a> <a href="http://www.pymvpa.org" rel="noreferrer" target="_blank">http://www.pymvpa.org</a> <a href="http://www.fail2ban.org" rel="noreferrer" target="_blank">http://www.fail2ban.org</a><br>
Research Scientist, Psychological and Brain Sciences Dept.<br>
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755<br>
Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419<br>
WWW: <a href="http://www.linkedin.com/in/yarik" rel="noreferrer" target="_blank">http://www.linkedin.com/in/yarik</a><br>
<br>
<br>
<br><br><br>---------- Forwarded message ----------<br>From: Melanie Boly <<a href="mailto:boly.melanie@gmail.com" target="_blank">boly.melanie@gmail.com</a>><br>To: Development and support of PyMVPA <<a href="mailto:pkg-exppsy-pymvpa@lists.alioth.debian.org" target="_blank">pkg-exppsy-pymvpa@lists.alioth.debian.org</a>><br>Cc: <br>Date: Wed, 15 Jul 2015 08:54:34 -0500<br>Subject: Re: [pymvpa] LinearCSVMC not found in PyMVPA-upstream-2.4.0 release<br>Dear Yaroslav,<br>
the make script completed but I had a long error indeed<br>
Here it is:<br>
<br>
-----------------------------------------------------------------------------------------------------------------------------------------------------------<br>
<br>
$ sudo make<br>
<br>
fatal: Not a git repository (or any of the parent directories): .git<br>
<br>
python setup.py config --noisy<br>
<br>
running config<br>
<br>
python setup.py build_ext --inplace<br>
<br>
running build_ext<br>
<br>
running build_src<br>
<br>
build_src<br>
<br>
building extension "mvpa2.clfs.libsmlrc.smlrc" sources<br>
<br>
building extension "mvpa2.clfs.libsvmc._svmc" sources<br>
<br>
building data_files sources<br>
<br>
build_src: building npy-pkg config files<br>
<br>
customize UnixCCompiler<br>
<br>
customize UnixCCompiler using build_ext<br>
<br>
customize UnixCCompiler<br>
<br>
customize UnixCCompiler using build_ext<br>
<br>
building 'mvpa2.clfs.libsmlrc.smlrc' extension<br>
<br>
compiling C sources<br>
<br>
C compiler: cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64<br>
-arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv<br>
-DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes<br>
-Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes<br>
-DENABLE_DTRACE -arch x86_64 -arch i386 -pipe<br>
<br>
<br>
compile options:<br>
'-I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include<br>
-I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7<br>
-c'<br>
<br>
cc: mvpa2/clfs/libsmlrc/smlr.c<br>
<br>
mvpa2/clfs/libsmlrc/smlr.c:172:10: warning: implicit conversion loses<br>
integer precision: 'long long' to 'unsigned int' [-Wshorten-64-to-32]<br>
<br>
srand (seed);<br>
<br>
~~~~~ ^~~~<br>
<br>
mvpa2/clfs/libsmlrc/smlr.c:342:10: warning: implicit conversion loses<br>
integer precision: 'long' to 'int' [-Wshorten-64-to-32]<br>
<br>
return cycle;<br>
<br>
~~~~~~ ^~~~~<br>
<br>
2 warnings generated.<br>
<br>
mvpa2/clfs/libsmlrc/smlr.c:172:10: warning: implicit conversion loses<br>
integer precision: 'long long' to 'unsigned int' [-Wshorten-64-to-32]<br>
<br>
srand (seed);<br>
<br>
~~~~~ ^~~~<br>
<br>
1 warning generated.<br>
<br>
cc -bundle -undefined dynamic_lookup -arch x86_64 -arch i386 -Wl,-F.<br>
build/temp.macosx-10.10-intel-2.7/mvpa2/clfs/libsmlrc/smlr.o -lm -o<br>
mvpa2/clfs/libsmlrc/smlrc.so -bundle<br>
<br>
building 'mvpa2.clfs.libsvmc._svmc' extension<br>
<br>
compiling C++ sources<br>
<br>
C compiler: c++ -fno-strict-aliasing -fno-common -dynamic -arch x86_64<br>
-arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv<br>
-DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wshorten-64-to-32 -DNDEBUG -g<br>
-fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch x86_64<br>
-arch i386 -pipe<br>
<br>
<br>
creating build/temp.macosx-10.10-intel-2.7/mvpa2/clfs/libsvmc<br>
<br>
compile options: '-I3rd/libsvm<br>
-I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include<br>
-I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7<br>
-c'<br>
<br>
c++: 3rd/libsvm/svm.cpp<br>
<br>
c++: mvpa2/clfs/libsvmc/svmc_wrap.cpp<br>
<br>
In file included from mvpa2/clfs/libsvmc/svmc_wrap.cpp:3087:<br>
<br>
In file included from<br>
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/arrayobject.h:4:<br>
<br>
In file included from<br>
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarrayobject.h:17:<br>
<br>
In file included from<br>
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarraytypes.h:1760:<br>
<br>
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:<br>
warning: "Using deprecated NumPy API, disable it by "<br>
"#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]<br>
<br>
#warning "Using deprecated NumPy API, disable it by " \<br>
<br>
^<br>
<br>
mvpa2/clfs/libsvmc/svmc_wrap.cpp:3615:15: warning: implicit conversion<br>
loses integer precision: 'Py_ssize_t' (aka 'long') to 'int'<br>
[-Wshorten-64-to-32]<br>
<br>
int length = PyList_Size(indices);<br>
<br>
~~~~~~ ^~~~~~~~~~~~~~~~~~~~<br>
<br>
2 warnings generated.<br>
<br>
In file included from mvpa2/clfs/libsvmc/svmc_wrap.cpp:3087:<br>
<br>
In file included from<br>
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/arrayobject.h:4:<br>
<br>
In file included from<br>
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarrayobject.h:17:<br>
<br>
In file included from<br>
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarraytypes.h:1760:<br>
<br>
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:<br>
warning: "Using deprecated NumPy API, disable it by "<br>
"#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]<br>
<br>
#warning "Using deprecated NumPy API, disable it by " \<br>
<br>
^<br>
<br>
1 warning generated.<br>
<br>
c++ -bundle -undefined dynamic_lookup -arch x86_64 -arch i386 -Wl,-F.<br>
build/temp.macosx-10.10-intel-2.7/3rd/libsvm/svm.o<br>
build/temp.macosx-10.10-intel-2.7/mvpa2/clfs/libsvmc/svmc_wrap.o -o<br>
mvpa2/clfs/libsvmc/_svmc.so -bundle<br>
<br>
touch build-stamp<br>
<br>
<br>
<br>
<br>
<br>
<br>
----------------------------------------------------------------------------------------------------<br>
<br>
Any feedback appreciated. I do have Git installed as well as SWIG and<br>
Makeports on my Mac though<br>
Thanks a lot!<br>
Melanie<br>
<br>
On Wed, Jul 15, 2015 at 8:48 AM, Yaroslav Halchenko<br>
<<a href="mailto:debian@onerussian.com" target="_blank">debian@onerussian.com</a>> wrote:<br>
><br>
> On Wed, 15 Jul 2015, Melanie Boly wrote:<br>
><br>
>> Dear Yaroslav,<br>
>> I use a MacOsX Yosemite 10.10.4<br>
>> I downloaded the release from <a href="https://github.com/PyMVPA/PyMVPA/tags" rel="noreferrer" target="_blank">https://github.com/PyMVPA/PyMVPA/tags</a><br>
>> I did try once again the alternative procedure installation just now;<br>
><br>
> so you did:<br>
><br>
> cd PyMVPA<br>
> make<br>
><br>
> and that one completed without errors? if not -- cut/paste output<br>
><br>
> if completed without errors you must have got LinearCSVMC ;) just paste<br>
> output from above commands<br>
><br>
>> everything works until I try to call the LinearCSVMC function; the<br>
>> only ones that are available in my python workspace are LinearKernel &<br>
>> LinearLSKernel.<br>
>> And when I try to call the module sum to import libsvm or sg it does<br>
>> not recognize these names..<br>
><br>
> for sg -- you would need shogun installed... probably easiest would be<br>
> first to resolve this issue with libsvm<br>
> --<br>
> Yaroslav O. Halchenko, Ph.D.<br>
> <a href="http://neuro.debian.net" rel="noreferrer" target="_blank">http://neuro.debian.net</a> <a href="http://www.pymvpa.org" rel="noreferrer" target="_blank">http://www.pymvpa.org</a> <a href="http://www.fail2ban.org" rel="noreferrer" target="_blank">http://www.fail2ban.org</a><br>
> Research Scientist, Psychological and Brain Sciences Dept.<br>
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755<br>
> Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419<br>
> WWW: <a href="http://www.linkedin.com/in/yarik" rel="noreferrer" target="_blank">http://www.linkedin.com/in/yarik</a><br>
><br>
> _______________________________________________<br>
> Pkg-ExpPsy-PyMVPA mailing list<br>
> <a href="mailto:Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org" target="_blank">Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org</a><br>
> <a href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa" rel="noreferrer" target="_blank">http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa</a><br>
<br>
<br>
<br><br><br>---------- Forwarded message ----------<br>From: Yaroslav Halchenko <<a href="mailto:debian@onerussian.com" target="_blank">debian@onerussian.com</a>><br>To: <a href="mailto:pkg-exppsy-pymvpa@lists.alioth.debian.org" target="_blank">pkg-exppsy-pymvpa@lists.alioth.debian.org</a><br>Cc: <br>Date: Wed, 15 Jul 2015 10:05:25 -0400<br>Subject: Re: [pymvpa] LinearCSVMC not found in PyMVPA-upstream-2.4.0 release<br><br>
On Wed, 15 Jul 2015, Melanie Boly wrote:<br>
<br>
> Dear Yaroslav,<br>
> the make script completed but I had a long error indeed<br>
<br>
> Here it is:<br>
<br>
> -----------------------------------------------------------------------------------------------------------------------------------------------------------<br>
<br>
> $ sudo make<br>
<br>
> fatal: Not a git repository (or any of the parent directories): .git<br>
<br>
> python setup.py config --noisy<br>
<br>
> running config<br>
<br>
> python setup.py build_ext --inplace<br>
<br>
> running build_ext<br>
<br>
> running build_src<br>
<br>
> build_src<br>
<br>
> building extension "mvpa2.clfs.libsmlrc.smlrc" sources<br>
<br>
> building extension "mvpa2.clfs.libsvmc._svmc" sources<br>
<br>
> building data_files sources<br>
<br>
> build_src: building npy-pkg config files<br>
<br>
> customize UnixCCompiler<br>
<br>
> customize UnixCCompiler using build_ext<br>
<br>
> customize UnixCCompiler<br>
<br>
> customize UnixCCompiler using build_ext<br>
<br>
> building 'mvpa2.clfs.libsmlrc.smlrc' extension<br>
<br>
> compiling C sources<br>
<br>
> C compiler: cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64<br>
> -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv<br>
> -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes<br>
> -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes<br>
> -DENABLE_DTRACE -arch x86_64 -arch i386 -pipe<br>
<br>
<br>
> compile options:<br>
> '-I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include<br>
> -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7<br>
> -c'<br>
<br>
> cc: mvpa2/clfs/libsmlrc/smlr.c<br>
<br>
> mvpa2/clfs/libsmlrc/smlr.c:172:10: warning: implicit conversion loses<br>
> integer precision: 'long long' to 'unsigned int' [-Wshorten-64-to-32]<br>
<br>
> srand (seed);<br>
<br>
> ~~~~~ ^~~~<br>
<br>
> mvpa2/clfs/libsmlrc/smlr.c:342:10: warning: implicit conversion loses<br>
> integer precision: 'long' to 'int' [-Wshorten-64-to-32]<br>
<br>
> return cycle;<br>
<br>
> ~~~~~~ ^~~~~<br>
<br>
> 2 warnings generated.<br>
<br>
> mvpa2/clfs/libsmlrc/smlr.c:172:10: warning: implicit conversion loses<br>
> integer precision: 'long long' to 'unsigned int' [-Wshorten-64-to-32]<br>
<br>
> srand (seed);<br>
<br>
> ~~~~~ ^~~~<br>
<br>
> 1 warning generated.<br>
<br>
> cc -bundle -undefined dynamic_lookup -arch x86_64 -arch i386 -Wl,-F.<br>
> build/temp.macosx-10.10-intel-2.7/mvpa2/clfs/libsmlrc/smlr.o -lm -o<br>
> mvpa2/clfs/libsmlrc/smlrc.so -bundle<br>
<br>
> building 'mvpa2.clfs.libsvmc._svmc' extension<br>
<br>
> compiling C++ sources<br>
<br>
> C compiler: c++ -fno-strict-aliasing -fno-common -dynamic -arch x86_64<br>
> -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv<br>
> -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wshorten-64-to-32 -DNDEBUG -g<br>
> -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch x86_64<br>
> -arch i386 -pipe<br>
<br>
<br>
> creating build/temp.macosx-10.10-intel-2.7/mvpa2/clfs/libsvmc<br>
<br>
> compile options: '-I3rd/libsvm<br>
> -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include<br>
> -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7<br>
> -c'<br>
<br>
> c++: 3rd/libsvm/svm.cpp<br>
<br>
> c++: mvpa2/clfs/libsvmc/svmc_wrap.cpp<br>
<br>
> In file included from mvpa2/clfs/libsvmc/svmc_wrap.cpp:3087:<br>
<br>
> In file included from<br>
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/arrayobject.h:4:<br>
<br>
> In file included from<br>
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarrayobject.h:17:<br>
<br>
> In file included from<br>
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarraytypes.h:1760:<br>
<br>
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:<br>
> warning: "Using deprecated NumPy API, disable it by "<br>
> "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]<br>
<br>
> #warning "Using deprecated NumPy API, disable it by " \<br>
<br>
> ^<br>
<br>
> mvpa2/clfs/libsvmc/svmc_wrap.cpp:3615:15: warning: implicit conversion<br>
> loses integer precision: 'Py_ssize_t' (aka 'long') to 'int'<br>
> [-Wshorten-64-to-32]<br>
<br>
> int length = PyList_Size(indices);<br>
<br>
> ~~~~~~ ^~~~~~~~~~~~~~~~~~~~<br>
<br>
> 2 warnings generated.<br>
<br>
> In file included from mvpa2/clfs/libsvmc/svmc_wrap.cpp:3087:<br>
<br>
> In file included from<br>
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/arrayobject.h:4:<br>
<br>
> In file included from<br>
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarrayobject.h:17:<br>
<br>
> In file included from<br>
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarraytypes.h:1760:<br>
<br>
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:<br>
> warning: "Using deprecated NumPy API, disable it by "<br>
> "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]<br>
<br>
> #warning "Using deprecated NumPy API, disable it by " \<br>
<br>
> ^<br>
<br>
> 1 warning generated.<br>
<br>
> c++ -bundle -undefined dynamic_lookup -arch x86_64 -arch i386 -Wl,-F.<br>
> build/temp.macosx-10.10-intel-2.7/3rd/libsvm/svm.o<br>
> build/temp.macosx-10.10-intel-2.7/mvpa2/clfs/libsvmc/svmc_wrap.o -o<br>
> mvpa2/clfs/libsvmc/_svmc.so -bundle<br>
<br>
> touch build-stamp<br>
<br>
actually those are all just warnings and it generated bindings just<br>
fine.<br>
<br>
<br>
So what happens if you run in that directory:<br>
<br>
MVPA_DEBUG=EXT.* PYTHONPATH=$PWD python -c 'from mvpa2.clfs.svm import LinearCSVMC; print(LinearCSVMC)'<br>
<br>
--<br>
Yaroslav O. Halchenko, Ph.D.<br>
<a href="http://neuro.debian.net" rel="noreferrer" target="_blank">http://neuro.debian.net</a> <a href="http://www.pymvpa.org" rel="noreferrer" target="_blank">http://www.pymvpa.org</a> <a href="http://www.fail2ban.org" rel="noreferrer" target="_blank">http://www.fail2ban.org</a><br>
Research Scientist, Psychological and Brain Sciences Dept.<br>
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755<br>
Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419<br>
WWW: <a href="http://www.linkedin.com/in/yarik" rel="noreferrer" target="_blank">http://www.linkedin.com/in/yarik</a><br>
<br>
<br>
<br><br><br>---------- Forwarded message ----------<br>From: Melanie Boly <<a href="mailto:boly.melanie@gmail.com" target="_blank">boly.melanie@gmail.com</a>><br>To: Development and support of PyMVPA <<a href="mailto:pkg-exppsy-pymvpa@lists.alioth.debian.org" target="_blank">pkg-exppsy-pymvpa@lists.alioth.debian.org</a>><br>Cc: <br>Date: Wed, 15 Jul 2015 09:13:19 -0500<br>Subject: Re: [pymvpa] LinearCSVMC not found in PyMVPA-upstream-2.4.0 release<br>Dear Yaroslav, I just did it, and here is the message:<br>
<br>
-----------------------------------------<br>
<br>
$ MVPA_DEBUG=EXT.* PYTHONPATH=$PWD python -c 'from mvpa2.clfs.svm<br>
import LinearCSVMC; print(LinearCSVMC)'<br>
<br>
[EXT ] DBG: Checking for the presence of running ipython env<br>
<br>
[EXT ] DBG: Presence of running ipython env is NOT verified. Caught<br>
exception was: Not running in IPython session<br>
<br>
[EXT ] DBG: Checking for the presence of numpy<br>
<br>
[EXT ] DBG: Presence of numpy is verified<br>
<br>
[EXT ] DBG: Checking for the presence of scipy<br>
<br>
[EXT ] DBG: Skip retesting for 'numpy'.<br>
<br>
[EXT ] DBG: Presence of scipy is verified<br>
<br>
[EXT ] DBG: Checking for the presence of running ipython env<br>
<br>
[EXT ] DBG: Presence of running ipython env is NOT verified. Caught<br>
exception was: Not running in IPython session<br>
<br>
[EXT ] DBG: Checking for the presence of matplotlib<br>
<br>
[EXT ] DBG: Presence of matplotlib is verified<br>
<br>
[EXT ] DBG: Skip retesting for 'running ipython env'.<br>
<br>
[EXT ] DBG: Skip retesting for 'scipy'.<br>
<br>
[EXT ] DBG: Skip retesting for 'scipy'.<br>
<br>
[EXT ] DBG: Skip retesting for 'scipy'.<br>
<br>
[EXT ] DBG: Skip retesting for 'scipy'.<br>
<br>
[EXT ] DBG: Checking for the presence of good scipy.stats.rdist<br>
<br>
[EXT ] DBG: Presence of good scipy.stats.rdist is NOT verified.<br>
Caught exception was: scipy.stats carries misbehaving rdist<br>
distribution<br>
<br>
[EXT ] DBG: Fixing up scipy.stats.rdist<br>
<br>
[EXT ] DBG: Checking for the presence of good scipy.stats.rdist<br>
<br>
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy/integrate/quadpack.py:293:<br>
UserWarning: Extremely bad integrand behavior occurs at some points of<br>
the<br>
<br>
integration interval.<br>
<br>
warnings.warn(msg)<br>
<br>
[EXT ] DBG: Presence of good scipy.stats.rdist is verified<br>
<br>
[EXT ] DBG: Checking for the presence of good scipy.stats.rv_discrete.ppf<br>
<br>
[EXT ] DBG: Presence of good scipy.stats.rv_discrete.ppf is verified<br>
<br>
[EXT ] DBG: Checking for the presence of good<br>
scipy.stats.rv_continuous._reduce_func(floc,fscale)<br>
<br>
[EXT ] DBG: Presence of good<br>
scipy.stats.rv_continuous._reduce_func(floc,fscale) is verified<br>
<br>
[EXT ] DBG: Checking for the presence of pylab<br>
<br>
[EXT ] DBG: Skip retesting for 'matplotlib'.<br>
<br>
[EXT ] DBG: Presence of pylab is verified<br>
<br>
[EXT ] DBG: Skip retesting for 'scipy'.<br>
<br>
[EXT ] DBG: Skip retesting for 'scipy'.<br>
<br>
[EXT ] DBG: Checking for the presence of shogun<br>
<br>
[EXT ] DBG: Presence of shogun is NOT verified. Caught exception was:<br>
No module named shogun.Classifier<br>
<br>
[EXT ] DBG: Checking for the presence of libsvm<br>
<br>
[EXT ] DBG: Presence of libsvm is NOT verified. Caught exception was:<br>
cannot import name C_SVC<br>
<br>
WARNING: None of SVM implementation libraries was found<br>
<br>
* Please note: warnings are printed only once, but underlying problem<br>
might occur many times *<br>
<br>
Traceback (most recent call last):<br>
<br>
File "<string>", line 1, in <module><br>
<br>
ImportError: cannot import name LinearCSVMC<br>
<br>
<br>
<br>
-----------------<br>
I am very grateful for your help.<br>
Very best wishes,<br>
Melanie<br>
<br>
<br>
On Wed, Jul 15, 2015 at 9:05 AM, Yaroslav Halchenko<br>
<<a href="mailto:debian@onerussian.com" target="_blank">debian@onerussian.com</a>> wrote:<br>
><br>
> On Wed, 15 Jul 2015, Melanie Boly wrote:<br>
><br>
>> Dear Yaroslav,<br>
>> the make script completed but I had a long error indeed<br>
><br>
>> Here it is:<br>
><br>
>> -----------------------------------------------------------------------------------------------------------------------------------------------------------<br>
><br>
>> $ sudo make<br>
><br>
>> fatal: Not a git repository (or any of the parent directories): .git<br>
><br>
>> python setup.py config --noisy<br>
><br>
>> running config<br>
><br>
>> python setup.py build_ext --inplace<br>
><br>
>> running build_ext<br>
><br>
>> running build_src<br>
><br>
>> build_src<br>
><br>
>> building extension "mvpa2.clfs.libsmlrc.smlrc" sources<br>
><br>
>> building extension "mvpa2.clfs.libsvmc._svmc" sources<br>
><br>
>> building data_files sources<br>
><br>
>> build_src: building npy-pkg config files<br>
><br>
>> customize UnixCCompiler<br>
><br>
>> customize UnixCCompiler using build_ext<br>
><br>
>> customize UnixCCompiler<br>
><br>
>> customize UnixCCompiler using build_ext<br>
><br>
>> building 'mvpa2.clfs.libsmlrc.smlrc' extension<br>
><br>
>> compiling C sources<br>
><br>
>> C compiler: cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64<br>
>> -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv<br>
>> -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes<br>
>> -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes<br>
>> -DENABLE_DTRACE -arch x86_64 -arch i386 -pipe<br>
><br>
><br>
>> compile options:<br>
>> '-I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include<br>
>> -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7<br>
>> -c'<br>
><br>
>> cc: mvpa2/clfs/libsmlrc/smlr.c<br>
><br>
>> mvpa2/clfs/libsmlrc/smlr.c:172:10: warning: implicit conversion loses<br>
>> integer precision: 'long long' to 'unsigned int' [-Wshorten-64-to-32]<br>
><br>
>> srand (seed);<br>
><br>
>> ~~~~~ ^~~~<br>
><br>
>> mvpa2/clfs/libsmlrc/smlr.c:342:10: warning: implicit conversion loses<br>
>> integer precision: 'long' to 'int' [-Wshorten-64-to-32]<br>
><br>
>> return cycle;<br>
><br>
>> ~~~~~~ ^~~~~<br>
><br>
>> 2 warnings generated.<br>
><br>
>> mvpa2/clfs/libsmlrc/smlr.c:172:10: warning: implicit conversion loses<br>
>> integer precision: 'long long' to 'unsigned int' [-Wshorten-64-to-32]<br>
><br>
>> srand (seed);<br>
><br>
>> ~~~~~ ^~~~<br>
><br>
>> 1 warning generated.<br>
><br>
>> cc -bundle -undefined dynamic_lookup -arch x86_64 -arch i386 -Wl,-F.<br>
>> build/temp.macosx-10.10-intel-2.7/mvpa2/clfs/libsmlrc/smlr.o -lm -o<br>
>> mvpa2/clfs/libsmlrc/smlrc.so -bundle<br>
><br>
>> building 'mvpa2.clfs.libsvmc._svmc' extension<br>
><br>
>> compiling C++ sources<br>
><br>
>> C compiler: c++ -fno-strict-aliasing -fno-common -dynamic -arch x86_64<br>
>> -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv<br>
>> -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wshorten-64-to-32 -DNDEBUG -g<br>
>> -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch x86_64<br>
>> -arch i386 -pipe<br>
><br>
><br>
>> creating build/temp.macosx-10.10-intel-2.7/mvpa2/clfs/libsvmc<br>
><br>
>> compile options: '-I3rd/libsvm<br>
>> -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include<br>
>> -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7<br>
>> -c'<br>
><br>
>> c++: 3rd/libsvm/svm.cpp<br>
><br>
>> c++: mvpa2/clfs/libsvmc/svmc_wrap.cpp<br>
><br>
>> In file included from mvpa2/clfs/libsvmc/svmc_wrap.cpp:3087:<br>
><br>
>> In file included from<br>
>> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/arrayobject.h:4:<br>
><br>
>> In file included from<br>
>> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarrayobject.h:17:<br>
><br>
>> In file included from<br>
>> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarraytypes.h:1760:<br>
><br>
>> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:<br>
>> warning: "Using deprecated NumPy API, disable it by "<br>
>> "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]<br>
><br>
>> #warning "Using deprecated NumPy API, disable it by " \<br>
><br>
>> ^<br>
><br>
>> mvpa2/clfs/libsvmc/svmc_wrap.cpp:3615:15: warning: implicit conversion<br>
>> loses integer precision: 'Py_ssize_t' (aka 'long') to 'int'<br>
>> [-Wshorten-64-to-32]<br>
><br>
>> int length = PyList_Size(indices);<br>
><br>
>> ~~~~~~ ^~~~~~~~~~~~~~~~~~~~<br>
><br>
>> 2 warnings generated.<br>
><br>
>> In file included from mvpa2/clfs/libsvmc/svmc_wrap.cpp:3087:<br>
><br>
>> In file included from<br>
>> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/arrayobject.h:4:<br>
><br>
>> In file included from<br>
>> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarrayobject.h:17:<br>
><br>
>> In file included from<br>
>> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarraytypes.h:1760:<br>
><br>
>> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:<br>
>> warning: "Using deprecated NumPy API, disable it by "<br>
>> "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]<br>
><br>
>> #warning "Using deprecated NumPy API, disable it by " \<br>
><br>
>> ^<br>
><br>
>> 1 warning generated.<br>
><br>
>> c++ -bundle -undefined dynamic_lookup -arch x86_64 -arch i386 -Wl,-F.<br>
>> build/temp.macosx-10.10-intel-2.7/3rd/libsvm/svm.o<br>
>> build/temp.macosx-10.10-intel-2.7/mvpa2/clfs/libsvmc/svmc_wrap.o -o<br>
>> mvpa2/clfs/libsvmc/_svmc.so -bundle<br>
><br>
>> touch build-stamp<br>
><br>
> actually those are all just warnings and it generated bindings just<br>
> fine.<br>
><br>
><br>
> So what happens if you run in that directory:<br>
><br>
> MVPA_DEBUG=EXT.* PYTHONPATH=$PWD python -c 'from mvpa2.clfs.svm import LinearCSVMC; print(LinearCSVMC)'<br>
><br>
> --<br>
> Yaroslav O. Halchenko, Ph.D.<br>
> <a href="http://neuro.debian.net" rel="noreferrer" target="_blank">http://neuro.debian.net</a> <a href="http://www.pymvpa.org" rel="noreferrer" target="_blank">http://www.pymvpa.org</a> <a href="http://www.fail2ban.org" rel="noreferrer" target="_blank">http://www.fail2ban.org</a><br>
> Research Scientist, Psychological and Brain Sciences Dept.<br>
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755<br>
> Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419<br>
> WWW: <a href="http://www.linkedin.com/in/yarik" rel="noreferrer" target="_blank">http://www.linkedin.com/in/yarik</a><br>
><br>
> _______________________________________________<br>
> Pkg-ExpPsy-PyMVPA mailing list<br>
> <a href="mailto:Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org" target="_blank">Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org</a><br>
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<br>
<br>
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