[Insight-developers] WrapITK build errors

Gaëtan Lehmann gaetan.lehmann at jouy.inra.fr
Wed Nov 17 09:06:16 EST 2010 

Le 17 nov. 10 à 15:00, Michal Suchanek a écrit :

> 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:
>

The two following changes should fix the last problems with wrapitk

   http://review.source.kitware.com/#change,376
   http://review.source.kitware.com/#change,377

Submitted to gerrit just a few minutes ago!

>
> 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
>>
>>

-- 
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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