[Insight-developers] WrapITK build errors

Michal Suchanek hramrach at centrum.cz
Wed Nov 17 09:00:39 EST 2010 

2010/11/16 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>:
>
> Hi Michal,
>
> I've proposed a fix for that problem
>
>  http://review.source.kitware.com/#change,369
>
> It would be nice if you can test it and report the result in the link above.
>
> Gaëtan

The patch posted there fixes this issue but there is another issue
which prevents WrapITK from building:


cd /scratch/itk/wrapitk-read-only/obj-x86_64-linux-gnu/Libraries/Review
&& /usr/bin/g++   -DReviewJava_EXPORTS -DSWIG_GLOBAL -g
 -O2 -g -Wall -O2  -Wno-deprecated  -ftemplate-depth-50 -Wall
-Wno-deprecated -fPIC -I/scratch/itk/wrapitk-read-only/Libraries/
Review -I/usr/include/InsightToolkit-4.0/Review
-I/usr/include/InsightToolkit-4.0/gdcm/Source/DataDictionary
-I/usr/include/Ins
ightToolkit-4.0/gdcm/Source/MediaStorageAndFileFormat
-I/usr/include/InsightToolkit-4.0/gdcm/Source/DataStructureAndEncodingDef
inition -I/usr/include/InsightToolkit-4.0/gdcm/Source/Common
-I/usr/include/InsightToolkit-4.0/Utilities/vxl/core -I/usr/includ
e/InsightToolkit-4.0/Utilities/vxl/vcl
-I/usr/include/InsightToolkit-4.0/Utilities/vxl/v3p/netlib
-I/usr/include/InsightToolkit
-4.0/Utilities -I/usr/include/InsightToolkit-4.0/Utilities/itkExtHdrs
-I/usr/include/InsightToolkit-4.0/Utilities/nifti/znzlib
-I/usr/include/InsightToolkit-4.0/Utilities/nifti/niftilib
-I/usr/include/InsightToolkit-4.0/Utilities/expat -I/usr/include/Ins
ightToolkit-4.0/Utilities/DICOMParser
-I/usr/include/InsightToolkit-4.0/Utilities/NrrdIO
-I/usr/include/InsightToolkit-4.0/Util
ities/MetaIO -I/usr/include/InsightToolkit-4.0/SpatialObject
-I/usr/include/InsightToolkit-4.0/Numerics/NeuralNetworks -I/usr/i
nclude/InsightToolkit-4.0/Numerics/FEM
-I/usr/include/InsightToolkit-4.0/IO
-I/usr/include/InsightToolkit-4.0/Numerics -I/usr/i
nclude/InsightToolkit-4.0/Common
-I/usr/include/InsightToolkit-4.0/BasicFilters
-I/usr/include/InsightToolkit-4.0/Algorithms -I
/usr/include/InsightToolkit-4.0/Numerics/Statistics
-I/usr/include/InsightToolkit-4.0 -I/usr/include/gdcm-2.0
-I/usr/include/vt
k-5.6 -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi
-I/usr/include/tcl8.5 -I/usr/include/python2.6 -I/usr/lib/j
vm/default-java/include -I/usr/include/libxml2
-I/usr/include/freetype2
-I/scratch/itk/wrapitk-read-only/obj-x86_64-linux-gnu/T
ypedefs -I/usr/lib/jvm/java-6-openjdk/include   -fno-strict-aliasing
-o CMakeFiles/ReviewJava.dir/wrap_itkMaskedRankImageFilter
Java.o -c /scratch/itk/wrapitk-read-only/obj-x86_64-linux-gnu/Libraries/Review/wrap_itkMaskedRankImageFilterJava.cpp
In file included from
/scratch/itk/wrapitk-read-only/obj-x86_64-linux-gnu/Typedefs/Review.includes:467,
                 from
/scratch/itk/wrapitk-read-only/obj-x86_64-linux-gnu/Libraries/Review/wrap_itkMaskedRankImageFilterPython.
cpp:3095:
/usr/include/InsightToolkit-4.0/Review/itkMaskedRankImageFilter.h: In
member function ‘bool itk::MaskedRankImageFilter<TInputIm
age, TMaskImage, TOutputImage, TKernel>::GetUseVectorBasedHistogram()
[with TInputImage = itk::Image<float, 2u>, TMaskImage = i
tk::Image<unsigned char, 2u>, TOutputImage = itk::Image<float, 2u>,
TKernel = itk::FlatStructuringElement<2u>]’:
/scratch/itk/wrapitk-read-only/obj-x86_64-linux-gnu/Libraries/Review/wrap_itkMaskedRankImageFilterPython.cpp:13886:
  instantia
ted from here
/usr/include/InsightToolkit-4.0/Review/itkMaskedRankImageFilter.h:109:
error: ‘UseVectorBasedHistogram’ is not a member of ‘itk
::RankHistogram<float>’
/usr/include/InsightToolkit-4.0/Review/itkMaskedRankImageFilter.h: In
member function ‘bool itk::MaskedRankImageFilter<TInputIm
age, TMaskImage, TOutputImage, TKernel>::GetUseVectorBasedHistogram()
[with TInputImage = itk::Image<float, 2u>, TMaskImage = i
tk::Image<short unsigned int, 2u>, TOutputImage = itk::Image<float,
2u>, TKernel = itk::FlatStructuringElement<2u>]’:
/scratch/itk/wrapitk-read-only/obj-x86_64-linux-gnu/Libraries/Review/wrap_itkMaskedRankImageFilterPython.cpp:14140:
  instantia
ted from here
/usr/include/InsightToolkit-4.0/Review/itkMaskedRankImageFilter.h:109:
error: ‘UseVectorBasedHistogram’ is not a member of ‘itk
::RankHistogram<float>’
/usr/include/InsightToolkit-4.0/Review/itkMaskedRankImageFilter.h: In
member function ‘bool itk::MaskedRankImageFilter<TInputIm
age, TMaskImage, TOutputImage, TKernel>::GetUseVectorBasedHistogram()
[with TInputImage = itk::Image<float, 3u>, TMaskImage = i
tk::Image<unsigned char, 3u>, TOutputImage = itk::Image<float, 3u>,
TKernel = itk::FlatStructuringElement<3u>]’:
/scratch/itk/wrapitk-read-only/obj-x86_64-linux-gnu/Libraries/Review/wrap_itkMaskedRankImageFilterPython.cpp:14394:
  instantia
ted from here
/usr/include/InsightToolkit-4.0/Review/itkMaskedRankImageFilter.h:109:
error: ‘UseVectorBasedHistogram’ is not a member of ‘itk
::RankHistogram<float>’
/usr/include/InsightToolkit-4.0/Review/itkMaskedRankImageFilter.h: In
member function ‘bool itk::MaskedRankImageFilter<TInputI

There are many more messages about missing UseVectorBasedHistogram.

Thanks

Michal
>
>
> Le 16 nov. 10 à 17:19, Michal Suchanek a écrit :
>
>> Hello
>>
>> Since ITK was fixed to build with libjpeg I tried to rebuild ITK and
>> WrapITK with it.
>>
>> While ITK builds fine WrapITK has some issues.
>>
>> First the ITK installation directory changed from
>> /usr/lib/InsightToolkit to /usr/lib/InsightToolkit-4.0 and it is not
>> found there by CMake.
>>
>> The error is reported from /usr/share/cmake-2.8/Modules/FindITK.cmake
>> so I see two issues here:
>>
>> 1) ITK is not found
>> 2) the file which is used to search for ITK and contains the ITK
>> installation path is installed by CMake, not ITK.
>>
>> The other issue is that WrapITK fails to compile:
>>
>> [ 30%] Building CXX object
>>
>> Libraries/Base/CMakeFiles/BasePython.dir/wrap_itkImageBoundaryConditionPython.o
>> cd /scratch/itk/wrapitk-read-only/obj-x86_64-linux-gnu/Libraries/Base
>> && /usr/bin/g++   -DBasePython_EXPORTS -DSWIG_GLOBAL -g -O2 -g -Wall
>> -O2  -Wno-deprecated  -ftemplate-depth-50 -Wall -Wno-deprecated -fPIC
>> -I/scratch/itk/wrapitk-read-only/Libraries/Base
>> -I/usr/include/InsightToolkit-4.0/Review
>> -I/usr/include/InsightToolkit-4.0/gdcm/Source/DataDictionary
>> -I/usr/include/InsightToolkit-4.0/gdcm/Source/MediaStorageAndFileFormat
>>
>> -I/usr/include/InsightToolkit-4.0/gdcm/Source/DataStructureAndEncodingDefinition
>> -I/usr/include/InsightToolkit-4.0/gdcm/Source/Common
>> -I/usr/include/InsightToolkit-4.0/Utilities/vxl/core
>> -I/usr/include/InsightToolkit-4.0/Utilities/vxl/vcl
>> -I/usr/include/InsightToolkit-4.0/Utilities/vxl/v3p/netlib
>> -I/usr/include/InsightToolkit-4.0/Utilities
>> -I/usr/include/InsightToolkit-4.0/Utilities/itkExtHdrs
>> -I/usr/include/InsightToolkit-4.0/Utilities/nifti/znzlib
>> -I/usr/include/InsightToolkit-4.0/Utilities/nifti/niftilib
>> -I/usr/include/InsightToolkit-4.0/Utilities/expat
>> -I/usr/include/InsightToolkit-4.0/Utilities/DICOMParser
>> -I/usr/include/InsightToolkit-4.0/Utilities/NrrdIO
>> -I/usr/include/InsightToolkit-4.0/Utilities/MetaIO
>> -I/usr/include/InsightToolkit-4.0/SpatialObject
>> -I/usr/include/InsightToolkit-4.0/Numerics/NeuralNetworks
>> -I/usr/include/InsightToolkit-4.0/Numerics/FEM
>> -I/usr/include/InsightToolkit-4.0/IO
>> -I/usr/include/InsightToolkit-4.0/Numerics
>> -I/usr/include/InsightToolkit-4.0/Common
>> -I/usr/include/InsightToolkit-4.0/BasicFilters
>> -I/usr/include/InsightToolkit-4.0/Algorithms
>> -I/usr/include/InsightToolkit-4.0/Numerics/Statistics
>> -I/usr/include/InsightToolkit-4.0 -I/usr/include/gdcm-2.0
>> -I/usr/include/vtk-5.6 -I/usr/lib/openmpi/include
>> -I/usr/lib/openmpi/include/openmpi -I/usr/include/tcl8.5
>> -I/usr/include/python2.6 -I/usr/lib/jvm/default-java/include
>> -I/usr/include/libxml2 -I/usr/include/freetype2
>> -I/scratch/itk/wrapitk-read-only/obj-x86_64-linux-gnu/Typedefs
>> -I/usr/lib/jvm/java-6-openjdk/include   -fno-strict-aliasing -o
>> CMakeFiles/BasePython.dir/wrap_itkImageBoundaryConditionPython.o -c
>>
>> /scratch/itk/wrapitk-read-only/obj-x86_64-linux-gnu/Libraries/Base/wrap_itkImageBoundaryConditionPython.cpp
>>
>> /scratch/itk/wrapitk-read-only/obj-x86_64-linux-gnu/Libraries/Base/wrap_itkFlatStructuringElementPython.cpp:4943:
>>  instantiated from here
>>
>> /usr/include/InsightToolkit-4.0/Algorithms/itkFlatStructuringElement.txx:601:
>> error: conversion from ‘itk::FlatStructuringElement<2u>’ to non-scalar
>> type ‘itk::FlatStructuringElement<3u>’ requested
>> /usr/include/InsightToolkit-4.0/Algorithms/itkFlatStructuringElement.txx:
>> In static member function ‘static itk::FlatStructuringElement<2u>
>> itk::FlatStructuringElement<VDimension>::Polygon(itk::Size<2u>,
>> unsigned int) [with unsigned int VDimension = 3u]’:
>>
>> /scratch/itk/wrapitk-read-only/obj-x86_64-linux-gnu/Libraries/Base/wrap_itkFlatStructuringElementPython.cpp:5677:
>>  instantiated from here
>>
>> /usr/include/InsightToolkit-4.0/Algorithms/itkFlatStructuringElement.txx:57:
>> error: no matching function for call to
>> ‘itk::FlatStructuringElement<3u>::SetRadius(itk::Size<2u>&)’
>> /usr/include/InsightToolkit-4.0/Common/itkNeighborhood.txx:92: note:
>> candidates are: void itk::Neighborhood<TPixel, VDimension,
>> TAllocator>::SetRadius(const itk::Size<VDimension>&) [with TPixel =
>> bool, unsigned int VDimension = 3u, TAllocator =
>> itk::NeighborhoodAllocator<bool>]
>> /usr/include/InsightToolkit-4.0/Common/itkNeighborhood.h:183: note:
>>            void itk::Neighborhood<TPixel, VDimension,
>> TAllocator>::SetRadius(const long unsigned int*) [with TPixel = bool,
>> unsigned int VDimension = 3u, TAllocator =
>> itk::NeighborhoodAllocator<bool>]
>> /usr/include/InsightToolkit-4.0/Common/itkNeighborhood.txx:78: note:
>>             void itk::Neighborhood<TPixel, VDimension,
>> TAllocator>::SetRadius(long unsigned int) [with TPixel = bool,
>> unsigned int VDimension = 3u, TAllocator =
>> itk::NeighborhoodAllocator<bool>]
>>
>> /scratch/itk/wrapitk-read-only/obj-x86_64-linux-gnu/Libraries/Base/wrap_itkFlatStructuringElementPython.cpp:5677:
>>  instantiated from here
>>
>> /usr/include/InsightToolkit-4.0/Algorithms/itkFlatStructuringElement.txx:109:
>> error: conversion from ‘itk::FlatStructuringElement<3u>’ to non-scalar
>> type ‘itk::FlatStructuringElement<2u>’ requested
>> make[3]: ***
>> [Libraries/Base/CMakeFiles/BasePython.dir/wrap_itkFlatStructuringElementPython.o]
>> Error 1
>>
>> Thanks
>>
>> Michal
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>
> --
> Gaëtan Lehmann
> Biologie du Développement et de la Reproduction
> INRA de Jouy-en-Josas (France)
> tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
> http://voxel.jouy.inra.fr  http://www.itk.org
> http://www.mandriva.org  http://www.bepo.fr
>
>

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