Compilation Error on Linux #354
Comments
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Thanks @raphaellenain for the report. |
I fixed the Eigen problems in ITK (hopefully!). Eigen Related phcerdan PR's Search in ITK You are going to get the same results using your system Eigen for ITK. Try compile ITK with However, this seems a valid DGtalTool error. The matrix in ITK computation might have changed from the "Dynamic" vnl matrix to a fixed EigenMatrix for that case. That's not an ITK bug. |
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Thanks @phcerdan. If it works with the suggested commandline I would be in favor of having this flag activated by default. |
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+1 thanks @phcerdan. @dcoeurjo for the command line it looks difficult since it is the option to compile ITK itself. If I well understand perhaps a solution in DGtal could be force to use eigen from ITK when ITK is present ? @phcerdan let me know If I am wrong (perhaps not easy to do it in cmake but if it can fix the issue that could be nice). |
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Oh I see.. |
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I think this is because some internals (the matrices) changed in ITK, but it is not related to CMake, or what Eigen to use, using -DITK_USE_SYSTEM_EIGEN won't solve it, neither if DGtal uses the internal ITKEigen3. So, I think dealing with the right matrix (changed from vnl_matrix to EigenMatrix) is something DGtalTools has to fix. And that's what the error shows.
We could do that, but this particular problem will stay. |
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I confirm that compiling ITK with -DITK_USE_SYSTEM_EIGEN cmake option don't solve the problem. In a first time, I will compile DGtal without ITK. |
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Digging a little bit here, the problem is that an Eigen3::matrrix does not have a This is triggered when using volSurfaceRegularization in DGtalTools. |
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thanks @phcerdan! perhaps @dcoeurjo @JacquesOlivierLachaud or @elcerdo can have a look to a workaround to the clear() miss. |
I started a new compilation / install of DGtal and DGtalTools on a new install of Ubuntu, from the 1.0 version of DGtal.
Here are my commands :
cd ~ ; mkdir DGtal_src ; cd DGtal_src ; mkdir dgtal_deps ; cd dgtal_depssudo apt install git mercurial cmake python autoconf automake bison flex texinfo qt5-default qtcreator qttools5-devsudo apt install zlib1g-devsudo apt install libboost-all-devhg clone https://gmplib.org/repo/gmp-6.1/ gmp ; cd gmp ; ./.bootstrap ; ./configure ; make ; make check ; sudo make install ; cd ..wget http://www.libqglviewer.com/src/libQGLViewer-2.7.1.tar.gz ; tar xfz libQGLViewer-2.7.1.tar.gz ; cd libQGLViewer-2.7.1 ; qmake ; make ; sudo make install ; cd ..sudo apt install libcgal-dev libcgal-demogit clone https://github.com/InsightSoftwareConsortium/ITK ; cd ITK ; mkdir build ; cd build ; cmake .. ; make ; sudo make install ; cd ../..sudo apt install doxygensudo apt install fftw3 fftw3-devsudo apt install libcairo2-devsudo apt install libeigen3-devgit clone https://gitlab.inria.fr/patate/patate.git ; cd patate ; mkdir build ; cd build ; cmake .. ; make ; sudo make install ; cd ../..sudo apt install graphicsmagick graphicsmagick-libmagick-dev-compatwget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5.tar.gz ; tar xfz hdf5-1.10.5.tar.gz ; cd hdf5-1.10.5 ; mkdir build ; cd build ; cmake .. ; make ; sudo make install ; cd ../..cd ..git clone git://github.com/DGtal-team/DGtal.git ; cd DGtal ; mkdir build ; cd buildcmake -DWITH_OPENMP:string=true -DWITH_GMP:string=true -DWITH_CGAL:string=true -DWITH_ITK:string=true -DWITH_CAIRO:string=true -DWITH_HDF5:string=true -DHDF5_ROOT:string="/usr/local/HDF_Group/HDF5/1.10.5/" -DWITH_EIGEN:string=true -DWITH_PATATE:string=true -DWITH_QGLVIEWER:string=true -DWITH_QT5:string=true -DWITH_FFTW3:string=true -DWITH_MAGICK:string=true ..make ; sudo make installcd ../..git clone https://github.com/DGtal-team/DGtalTools.git ; cd DGtalTools ; mkdir build ; cd build ; cmake ..# After the next line, there is a compile errormakeAnd the errors are :
In file included from /usr/local/include/DGtal/math/linalg/CMatrix.h:45:0,from /usr/local/include/DGtal/math/linalg/CDynamicMatrix.h:45,from /usr/local/include/DGtal/dec/DiscreteExteriorCalculus.h:61,from /home/dgtal_user/DGtal_install/DGtalTools/estimators/volSurfaceRegularization-details/surface_approx.h:7,from /home/dgtal_user/DGtal_install/DGtalTools/estimators/volSurfaceRegularization.cpp:96:/usr/local/include/DGtal/math/linalg/CVectorSpace.h: In instantiation of ‘DGtal::concepts::CVectorSpace<T>::~CVectorSpace() [with T = itkeigen::Matrix<double, -1, 1>]’:/usr/include/boost/concept/usage.hpp:16:29: required from ‘boost::concepts::usage_requirements<Model>::~usage_requirements() [with Model = DGtal::concepts::CVectorSpace<itkeigen::Matrix<double, -1, 1> >]’/usr/include/boost/concept/detail/general.hpp:39:28: required from ‘static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::usage_requirements<DGtal::concepts::CVectorSpace<itkeigen::Matrix<double, -1, 1> > >]’/usr/local/include/DGtal/math/linalg/CVectorSpace.h:101:7: required from ‘struct DGtal::concepts::CVectorSpace<itkeigen::Matrix<double, -1, 1> >’/usr/local/include/DGtal/math/linalg/CVector.h:90:8: required from ‘struct DGtal::concepts::CVector<itkeigen::Matrix<double, -1, 1> >’/usr/local/include/DGtal/math/linalg/CDynamicVector.h:88:8: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]/usr/include/boost/concept/detail/has_constraints.hpp:42:5: required from ‘const bool boost::concepts::not_satisfied<DGtal::concepts::CDynamicVector<itkeigen::Matrix<double, -1, 1> > >::value’/usr/include/boost/concept/detail/has_constraints.hpp:45:31: required from ‘struct boost::concepts::not_satisfied<DGtal::concepts::CDynamicVector<itkeigen::Matrix<double, -1, 1> > >’/usr/include/boost/mpl/if.hpp:63:11: required from ‘struct boost::mpl::if_<boost::concepts::not_satisfied<DGtal::concepts::CDynamicVector<itkeigen::Matrix<double, -1, 1> > >, boost::concepts::constraint<DGtal::concepts::CDynamicVector<itkeigen::Matrix<double, -1, 1> > >, boost::concepts::requirement<boost::concepts::failed************ DGtal::concepts::CDynamicVector<itkeigen::Matrix<double, -1, 1> >::************> >’/usr/include/boost/concept/detail/general.hpp:51:8: required from ‘struct boost::concepts::requirement_<void (*)(DGtal::concepts::CDynamicVector<itkeigen::Matrix<double, -1, 1> >)>’/usr/local/include/DGtal/dec/DiscreteExteriorCalculus.h:115:5: required from ‘class DGtal::DiscreteExteriorCalculus<2, 3, DGtal::EigenLinearAlgebraBackend>’/home/dgtal_user/DGtal_install/DGtalTools/estimators/volSurfaceRegularization-details/surface_approx.h:13:17: required from here/usr/local/include/DGtal/math/linalg/CVectorSpace.h:103:11: error: ‘class itkeigen::Matrix<double, -1, 1>’ has no member named ‘clear’; did you mean ‘Scalar’?z.clear();~~^~~~~Scalar/usr/local/include/DGtal/math/linalg/CVectorSpace.h: In instantiation of ‘DGtal::concepts::CVectorSpace<T>::~CVectorSpace() [with T = itkeigen::Matrix<double, -1, -1>]’:/usr/include/boost/concept/usage.hpp:16:29: required from ‘boost::concepts::usage_requirements<Model>::~usage_requirements() [with Model = DGtal::concepts::CVectorSpace<itkeigen::Matrix<double, -1, -1> >]’/usr/include/boost/concept/detail/general.hpp:39:28: required from ‘static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::usage_requirements<DGtal::concepts::CVectorSpace<itkeigen::Matrix<double, -1, -1> > >]’/usr/local/include/DGtal/math/linalg/CVectorSpace.h:101:7: required from ‘struct DGtal::concepts::CVectorSpace<itkeigen::Matrix<double, -1, -1> >’/usr/local/include/DGtal/math/linalg/CMatrix.h:90:8: required from ‘struct DGtal::concepts::CMatrix<itkeigen::Matrix<double, -1, -1> >’/usr/local/include/DGtal/math/linalg/CDynamicMatrix.h:88:8: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]/usr/include/boost/concept/detail/has_constraints.hpp:42:5: required from ‘const bool boost::concepts::not_satisfied<DGtal::concepts::CDynamicMatrix<itkeigen::Matrix<double, -1, -1> > >::value’/usr/include/boost/concept/detail/has_constraints.hpp:45:31: required from ‘struct boost::concepts::not_satisfied<DGtal::concepts::CDynamicMatrix<itkeigen::Matrix<double, -1, -1> > >’/usr/include/boost/mpl/if.hpp:63:11: required from ‘struct boost::mpl::if_<boost::concepts::not_satisfied<DGtal::concepts::CDynamicMatrix<itkeigen::Matrix<double, -1, -1> > >, boost::concepts::constraint<DGtal::concepts::CDynamicMatrix<itkeigen::Matrix<double, -1, -1> > >, boost::concepts::requirement<boost::concepts::failed************ DGtal::concepts::CDynamicMatrix<itkeigen::Matrix<double, -1, -1> >::************> >’/usr/include/boost/concept/detail/general.hpp:51:8: required from ‘struct boost::concepts::requirement_<void (*)(DGtal::concepts::CDynamicMatrix<itkeigen::Matrix<double, -1, -1> >)>’/usr/local/include/DGtal/dec/DiscreteExteriorCalculus.h:116:5: required from ‘class DGtal::DiscreteExteriorCalculus<2, 3, DGtal::EigenLinearAlgebraBackend>’/home/dgtal_user/DGtal_install/DGtalTools/estimators/volSurfaceRegularization-details/surface_approx.h:13:17: required from here/usr/local/include/DGtal/math/linalg/CVectorSpace.h:103:11: error: ‘class itkeigen::Matrix<double, -1, -1>’ has no member named ‘clear’; did you mean ‘Scalar’?z.clear();~~^~~~~ScalarIn file included from /usr/local/include/DGtal/dec/KForm.h:244:0,from /usr/local/include/DGtal/dec/DiscreteExteriorCalculus.h:54,from /home/dgtal_user/DGtal_install/DGtalTools/estimators/volSurfaceRegularization-details/surface_approx.h:7,from /home/dgtal_user/DGtal_install/DGtalTools/estimators/volSurfaceRegularization.cpp:96:/usr/local/include/DGtal/dec/KForm.ih: In instantiation of ‘void DGtal::KForm<TCalculus, order, duality>::clear() [with TCalculus = DGtal::DiscreteExteriorCalculus<2, 3, DGtal::EigenLinearAlgebraBackend>; unsigned int order = 0; DGtal::Duality duality = (DGtal::Duality)1]’:/usr/local/include/DGtal/dec/KForm.ih:66:10: required from ‘DGtal::KForm<TCalculus, order, duality>::KForm(DGtal::ConstAlias<TPointPredicate>) [with TCalculus = DGtal::DiscreteExteriorCalculus<2, 3, DGtal::EigenLinearAlgebraBackend>; unsigned int order = 0; DGtal::Duality duality = (DGtal::Duality)1]’/usr/local/include/DGtal/dec/KForm.ih:40:37: required from ‘static DGtal::KForm<Calculus, order, duality> DGtal::KForm<TCalculus, order, duality>::ones(DGtal::ConstAlias<TPointPredicate>) [with TCalculus = DGtal::DiscreteExteriorCalculus<2, 3, DGtal::EigenLinearAlgebraBackend>; unsigned int order = 0; DGtal::Duality duality = (DGtal::Duality)1]’/home/dgtal_user/DGtal_install/DGtalTools/estimators/volSurfaceRegularization-details/surface_extract.ih:53:103: required from ‘Calculus createCalculusFromShapeBorder(const KSpace&, const Shape&) [with Shape = ImageShape<DGtal::ImageContainerBySTLVector<DGtal::HyperRectDomain<DGtal::SpaceND<3, int> >, unsigned char> >; Calculus = DGtal::DiscreteExteriorCalculus<2, 3, DGtal::EigenLinearAlgebraBackend>; KSpace = DGtal::KhalimskySpaceND<3, int>]’/home/dgtal_user/DGtal_install/DGtalTools/estimators/volSurfaceRegularization-details/surface_extract.ih:192:54: required from ‘std::tuple<DGtal::DiscreteExteriorCalculus<2, 3, DGtal::EigenLinearAlgebraBackend, int>, itkeigen::Matrix<double, -1, 1, 0, -1, 1> > initCalculusAndNormals(const KSpace&, const Shape&, double) [with Shape = ImageShape<DGtal::ImageContainerBySTLVector<DGtal::HyperRectDomain<DGtal::SpaceND<3, int> >, unsigned char> >; KSpace = DGtal::KhalimskySpaceND<3, int>]’/home/dgtal_user/DGtal_install/DGtalTools/estimators/volSurfaceRegularization-details/surface_extract.ih:170:50: required from ‘std::tuple<DGtal::DiscreteExteriorCalculus<2, 3, DGtal::EigenLinearAlgebraBackend, int>, itkeigen::Matrix<double, -1, 1, 0, -1, 1> > initCalculusAndNormalsWithNoise(const KSpace&, const Shape&, double, double) [with Shape = ImageShape<DGtal::ImageContainerBySTLVector<DGtal::HyperRectDomain<DGtal::SpaceND<3, int> >, unsigned char> >; KSpace = DGtal::KhalimskySpaceND<3, int>]’/home/dgtal_user/DGtal_install/DGtalTools/estimators/volSurfaceRegularization.cpp:211:102: required from here/usr/local/include/DGtal/dec/KForm.ih:120:17: error: ‘DGtal::KForm<DGtal::DiscreteExteriorCalculus<2, 3, DGtal::EigenLinearAlgebraBackend>, 0, (DGtal::Duality)1>::Container {aka class itkeigen::Matrix<double, -1, 1>}’ has no member named ‘clear’; did you mean ‘Scalar’?myContainer.clear();~~~~~~~~~~~~^~~~~Scalar/usr/local/include/DGtal/dec/KForm.ih: In instantiation of ‘void DGtal::KForm<TCalculus, order, duality>::clear() [with TCalculus = DGtal::DiscreteExteriorCalculus<2, 3, DGtal::EigenLinearAlgebraBackend>; unsigned int order = 0; DGtal::Duality duality = (DGtal::Duality)0]’:/usr/local/include/DGtal/dec/KForm.ih:66:10: required from ‘DGtal::KForm<TCalculus, order, duality>::KForm(DGtal::ConstAlias<TPointPredicate>) [with TCalculus = DGtal::DiscreteExteriorCalculus<2, 3, DGtal::EigenLinearAlgebraBackend>; unsigned int order = 0; DGtal::Duality duality = (DGtal::Duality)0]’/usr/local/include/DGtal/dec/KForm.ih:40:37: required from ‘static DGtal::KForm<Calculus, order, duality> DGtal::KForm<TCalculus, order, duality>::ones(DGtal::ConstAlias<TPointPredicate>) [with TCalculus = DGtal::DiscreteExteriorCalculus<2, 3, DGtal::EigenLinearAlgebraBackend>; unsigned int order = 0; DGtal::Duality duality = (DGtal::Duality)0]’/home/dgtal_user/DGtal_install/DGtalTools/estimators/volSurfaceRegularization-details/surface_extract.ih:54:103: required from ‘Calculus createCalculusFromShapeBorder(const KSpace&, const Shape&) [with Shape = ImageShape<DGtal::ImageContainerBySTLVector<DGtal::HyperRectDomain<DGtal::SpaceND<3, int> >, unsigned char> >; Calculus = DGtal::DiscreteExteriorCalculus<2, 3, DGtal::EigenLinearAlgebraBackend>; KSpace = DGtal::KhalimskySpaceND<3, int>]’/home/dgtal_user/DGtal_install/DGtalTools/estimators/volSurfaceRegularization-details/surface_extract.ih:192:54: required from ‘std::tuple<DGtal::DiscreteExteriorCalculus<2, 3, DGtal::EigenLinearAlgebraBackend, int>, itkeigen::Matrix<double, -1, 1, 0, -1, 1> > initCalculusAndNormals(const KSpace&, const Shape&, double) [with Shape = ImageShape<DGtal::ImageContainerBySTLVector<DGtal::HyperRectDomain<DGtal::SpaceND<3, int> >, unsigned char> >; KSpace = DGtal::KhalimskySpaceND<3, int>]’/home/dgtal_user/DGtal_install/DGtalTools/estimators/volSurfaceRegularization-details/surface_extract.ih:170:50: required from ‘std::tuple<DGtal::DiscreteExteriorCalculus<2, 3, DGtal::EigenLinearAlgebraBackend, int>, itkeigen::Matrix<double, -1, 1, 0, -1, 1> > initCalculusAndNormalsWithNoise(const KSpace&, const Shape&, double, double) [with Shape = ImageShape<DGtal::ImageContainerBySTLVector<DGtal::HyperRectDomain<DGtal::SpaceND<3, int> >, unsigned char> >; KSpace = DGtal::KhalimskySpaceND<3, int>]’/home/dgtal_user/DGtal_install/DGtalTools/estimators/volSurfaceRegularization.cpp:211:102: required from here/usr/local/include/DGtal/dec/KForm.ih:120:17: error: ‘DGtal::KForm<DGtal::DiscreteExteriorCalculus<2, 3, DGtal::EigenLinearAlgebraBackend>, 0, (DGtal::Duality)0>::Container {aka class itkeigen::Matrix<double, -1, 1>}’ has no member named ‘clear’; did you mean ‘Scalar’?myContainer.clear();~~~~~~~~~~~~^~~~~Scalarestimators/CMakeFiles/volSurfaceRegularization.dir/build.make:62: recipe for target 'estimators/CMakeFiles/volSurfaceRegularization.dir/volSurfaceRegularization.cpp.o' failedmake[2]: *** [estimators/CMakeFiles/volSurfaceRegularization.dir/volSurfaceRegularization.cpp.o] Error 1CMakeFiles/Makefile2:1060: recipe for target 'estimators/CMakeFiles/volSurfaceRegularization.dir/all' failedmake[1]: *** [estimators/CMakeFiles/volSurfaceRegularization.dir/all] Error 2Makefile:129: recipe for target 'all' failedmake: *** [all] Error 2The text was updated successfully, but these errors were encountered: