Re: [Open-ms-general] Deprecated NumPy API

[Hannes R. <han...@gm...>]

Hi Antonio

are you compiling pyOpenMS using a system libsvm? To me it seems to be
an issue with libsvm, not numpy. You might have run into issue 643,
see https://github.com/OpenMS/OpenMS/issues/643

You can try to fix it using this patch:
https://github.com/OpenMS/OpenMS/commit/7e85e1ed12601e852eb0dc25e285a889304cf08e

Can you try this?

I hope that works

Hannes


On 31 May 2014 15:22, Antonio Trande <ant...@gm...> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
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> Is there an incompatibility with newer Numpy version?
>
> OpenMS 1.11.1
> Numpy 1.8.0
> I'm still compiling OpenMS like reported in this mail
> http://sourceforge.net/p/open-ms/mailman/message/32398927/
>
> Regards.
>
> [ 96%] Building CXX object
> CMakeFiles/SpectraFilterScaler.dir/source/APPLICATIONS/TOPP/SpectraFilterScaler.C.o
> /usr/lib64/ccache/c++   -DBOOST_ALL_NO_LIB -DQT_NETWORK_LIB
> - -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_SQL_LIB -DQT_SVG_LIB -DQT_TEST_LIB
> - -DQT_WEBKIT_LIB -DQT_XML_LIB -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
> - -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4
> - -grecord-gcc-switches  -m64 -mtune=generic  -fopenmp -DNDEBUG
> - -I/usr/include/gsl -I/usr/include/libsvm
> - -I/home/sagitter/rpmbuild/BUILD/OpenMS-Release1.11.1/include
> - -I/home/sagitter/rpmbuild/BUILD/OpenMS-Release1.11.1/contrib/include
> - -isystem /usr/include/QtOpenGL -isystem /usr/include/QtSvg -isystem
> /usr/include/QtWebKit -isystem /usr/include/QtTest -isystem
> /usr/include/QtXml -isystem /usr/include/QtSql -isystem
> /usr/include/QtNetwork -I/usr/include/QtDesigner
> - -I/usr/include/QtDeclarative -I/usr/include/QtScriptTools
> - -I/usr/include/QtDBus -I/usr/include/QtMultimedia
> - -I/usr/include/QtXmlPatterns -I/usr/include/QtHelp
> - -I/usr/include/QtUiTools -I/usr/include/QtScript
> - -I/usr/include/Qt3Support -I/usr/include/QtGui -I/usr/include/QtCore
> - -I/usr/lib64/qt4/mkspecs/default    -Wall -Wextra -Wno-non-virtual-dtor
> - -Wno-long-long -Wno-variadic-macros --pedantic -fPIC -o
> CMakeFiles/SpectraFilterScaler.dir/source/APPLICATIONS/TOPP/SpectraFilterScaler.C.o
> - -c
> /home/sagitter/rpmbuild/BUILD/OpenMS-Release1.11.1/source/APPLICATIONS/TOPP/SpectraFilterScaler.C
> In file included from
> /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1760:0,
>                  from
> /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
>                  from
> /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
>                  from pyopenms/pyopenms.cpp:351:
> /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
> warning: #warning "Using deprecated NumPy API, disable it by "
> "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
>  #warning "Using deprecated NumPy API, disable it by " \
>   ^
> In file included from pyopenms/pyopenms.cpp:465:0:
> /home/sagitter/rpmbuild/BUILD/OpenMS-Release1.11.1/include/OpenMS/ANALYSIS/SVM/SVMWrapper.h:38:17:
> fatal error: svm.h: No such file or directory
>  #include <svm.h>
>                  ^
>
>
> - --
> Antonio Trande
>
> mailto: sagitterATfedoraproject.org
> http://www.fedoraos.worpress.com
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