--- Begin Message ---
Source: elastix
Version: 4.7-2
Severity: serious
Tags: jessie sid
User: debian...@lists.debian.org
Usertags: qa-ftbfs-20140830 qa-ftbfs
Justification: FTBFS on amd64
Hi,
During a rebuild of all packages in sid, your package failed to build on
amd64.
Relevant part (hopefully):
> make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu'
> /usr/bin/cmake -E cmake_progress_report
> /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 68
> [ 93%] Building CXX object Core/CMakeFiles/elastix.dir/Main/elastix.cxx.o
> cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Core && /usr/bin/c++
> -DELASTIX_USE_OPENMP -DITK_IO_FACTORY_REGISTER_MANAGER -g -O2
> -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2
> -fopenmp -O3 -DNDEBUG
> -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/ITKIOFactoryRegistration
> -I/home/steve/Packages/debian-med/trunk/packages/insighttoolkit/build-area/insighttoolkit4-4.6.0/BUILD/Modules/ThirdParty/HDF5/src
> -I/usr/include/dcmtk -I/usr/include/dcmtk/oflog -I/usr/include/dcmtk/ofstd
> -I/usr/include/dcmtk/dcmtls -I/usr/include/dcmtk/dcmsr
> -I/usr/include/dcmtk/dcmsign -I/usr/include/dcmtk/dcmqrdb
> -I/usr/include/dcmtk/dcmpstat -I/usr/include/dcmtk/dcmnet
> -I/usr/include/dcmtk/dcmjpls -I/usr/include/dcmtk/dcmjpeg
> -I/usr/include/dcmtk/dcmimgle -I/usr/include/dcmtk/dcmimage
> -I/usr/include/dcmtk/dcmdata -I/usr/include/dcmtk/config
> -I/usr/include/x86_64-linux-gnu -I/usr/include/gdcm-2.4
> -I/usr/include/ITK-4.6 -I/«PKGBUILDDIR»/src/Common
> -I/«PKGBUILDDIR»/src/Common/CostFunctions -I/«PKGBUILDDIR»/src/Common/CUDA
> -I/«PKGBUILDDIR»/src/Common/ImageSamplers -I/«PKGBUILDDIR»/src/Common/KNN
> -I/«PKGBUILDDIR»/src/Common/KNN/ann_1.1/include
> -I/«PKGBUILDDIR»/src/Common/LineSearchOptimizers
> -I/«PKGBUILDDIR»/src/Common/ParameterFileParser
> -I/«PKGBUILDDIR»/src/Common/Transforms -I/«PKGBUILDDIR»/src/Common/xout
> -I/«PKGBUILDDIR»/src/Common/MevisDicomTiff -I/«PKGBUILDDIR»/src/Core
> -I/«PKGBUILDDIR»/src/Core/Install -I/«PKGBUILDDIR»/src/Core/Kernel
> -I/«PKGBUILDDIR»/src/Core/ComponentBaseClasses
> -I/«PKGBUILDDIR»/src/Core/Configuration -I/«PKGBUILDDIR»/src/Core/Main
> -I/«PKGBUILDDIR»/src/Components/FixedImagePyramids
> -I/«PKGBUILDDIR»/src/Components/ImageSamplers
> -I/«PKGBUILDDIR»/src/Components/Interpolators
> -I/«PKGBUILDDIR»/src/Components/Metrics
> -I/«PKGBUILDDIR»/src/Components/MovingImagePyramids
> -I/«PKGBUILDDIR»/src/Components/Optimizers
> -I/«PKGBUILDDIR»/src/Components/Registrations
> -I/«PKGBUILDDIR»/src/Components/ResampleInterpolators
> -I/«PKGBUILDDIR»/src/Components/Resamplers
> -I/«PKGBUILDDIR»/src/Components/Transforms
> -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu -o
> CMakeFiles/elastix.dir/Main/elastix.cxx.o -c
> /«PKGBUILDDIR»/src/Core/Main/elastix.cxx
> /usr/bin/cmake -E cmake_progress_report
> /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 69
> [ 94%] Building CXX object
> Core/CMakeFiles/elastix.dir/Kernel/elxElastixMain.cxx.o
> cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Core && /usr/bin/c++
> -DELASTIX_USE_OPENMP -DITK_IO_FACTORY_REGISTER_MANAGER -g -O2
> -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2
> -fopenmp -O3 -DNDEBUG
> -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/ITKIOFactoryRegistration
> -I/home/steve/Packages/debian-med/trunk/packages/insighttoolkit/build-area/insighttoolkit4-4.6.0/BUILD/Modules/ThirdParty/HDF5/src
> -I/usr/include/dcmtk -I/usr/include/dcmtk/oflog -I/usr/include/dcmtk/ofstd
> -I/usr/include/dcmtk/dcmtls -I/usr/include/dcmtk/dcmsr
> -I/usr/include/dcmtk/dcmsign -I/usr/include/dcmtk/dcmqrdb
> -I/usr/include/dcmtk/dcmpstat -I/usr/include/dcmtk/dcmnet
> -I/usr/include/dcmtk/dcmjpls -I/usr/include/dcmtk/dcmjpeg
> -I/usr/include/dcmtk/dcmimgle -I/usr/include/dcmtk/dcmimage
> -I/usr/include/dcmtk/dcmdata -I/usr/include/dcmtk/config
> -I/usr/include/x86_64-linux-gnu -I/usr/include/gdcm-2.4
> -I/usr/include/ITK-4.6 -I/«PKGBUILDDIR»/src/Common
> -I/«PKGBUILDDIR»/src/Common/CostFunctions -I/«PKGBUILDDIR»/src/Common/CUDA
> -I/«PKGBUILDDIR»/src/Common/ImageSamplers -I/«PKGBUILDDIR»/src/Common/KNN
> -I/«PKGBUILDDIR»/src/Common/KNN/ann_1.1/include
> -I/«PKGBUILDDIR»/src/Common/LineSearchOptimizers
> -I/«PKGBUILDDIR»/src/Common/ParameterFileParser
> -I/«PKGBUILDDIR»/src/Common/Transforms -I/«PKGBUILDDIR»/src/Common/xout
> -I/«PKGBUILDDIR»/src/Common/MevisDicomTiff -I/«PKGBUILDDIR»/src/Core
> -I/«PKGBUILDDIR»/src/Core/Install -I/«PKGBUILDDIR»/src/Core/Kernel
> -I/«PKGBUILDDIR»/src/Core/ComponentBaseClasses
> -I/«PKGBUILDDIR»/src/Core/Configuration -I/«PKGBUILDDIR»/src/Core/Main
> -I/«PKGBUILDDIR»/src/Components/FixedImagePyramids
> -I/«PKGBUILDDIR»/src/Components/ImageSamplers
> -I/«PKGBUILDDIR»/src/Components/Interpolators
> -I/«PKGBUILDDIR»/src/Components/Metrics
> -I/«PKGBUILDDIR»/src/Components/MovingImagePyramids
> -I/«PKGBUILDDIR»/src/Components/Optimizers
> -I/«PKGBUILDDIR»/src/Components/Registrations
> -I/«PKGBUILDDIR»/src/Components/ResampleInterpolators
> -I/«PKGBUILDDIR»/src/Components/Resamplers
> -I/«PKGBUILDDIR»/src/Components/Transforms
> -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu -o
> CMakeFiles/elastix.dir/Kernel/elxElastixMain.cxx.o -c
> /«PKGBUILDDIR»/src/Core/Kernel/elxElastixMain.cxx
> /usr/bin/cmake -E cmake_progress_report
> /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 70
> [ 95%] Building CXX object
> Core/CMakeFiles/elastix.dir/Install/elxComponentLoader.cxx.o
> cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Core && /usr/bin/c++
> -DELASTIX_USE_OPENMP -DITK_IO_FACTORY_REGISTER_MANAGER -g -O2
> -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2
> -fopenmp -O3 -DNDEBUG
> -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/ITKIOFactoryRegistration
> -I/home/steve/Packages/debian-med/trunk/packages/insighttoolkit/build-area/insighttoolkit4-4.6.0/BUILD/Modules/ThirdParty/HDF5/src
> -I/usr/include/dcmtk -I/usr/include/dcmtk/oflog -I/usr/include/dcmtk/ofstd
> -I/usr/include/dcmtk/dcmtls -I/usr/include/dcmtk/dcmsr
> -I/usr/include/dcmtk/dcmsign -I/usr/include/dcmtk/dcmqrdb
> -I/usr/include/dcmtk/dcmpstat -I/usr/include/dcmtk/dcmnet
> -I/usr/include/dcmtk/dcmjpls -I/usr/include/dcmtk/dcmjpeg
> -I/usr/include/dcmtk/dcmimgle -I/usr/include/dcmtk/dcmimage
> -I/usr/include/dcmtk/dcmdata -I/usr/include/dcmtk/config
> -I/usr/include/x86_64-linux-gnu -I/usr/include/gdcm-2.4
> -I/usr/include/ITK-4.6 -I/«PKGBUILDDIR»/src/Common
> -I/«PKGBUILDDIR»/src/Common/CostFunctions -I/«PKGBUILDDIR»/src/Common/CUDA
> -I/«PKGBUILDDIR»/src/Common/ImageSamplers -I/«PKGBUILDDIR»/src/Common/KNN
> -I/«PKGBUILDDIR»/src/Common/KNN/ann_1.1/include
> -I/«PKGBUILDDIR»/src/Common/LineSearchOptimizers
> -I/«PKGBUILDDIR»/src/Common/ParameterFileParser
> -I/«PKGBUILDDIR»/src/Common/Transforms -I/«PKGBUILDDIR»/src/Common/xout
> -I/«PKGBUILDDIR»/src/Common/MevisDicomTiff -I/«PKGBUILDDIR»/src/Core
> -I/«PKGBUILDDIR»/src/Core/Install -I/«PKGBUILDDIR»/src/Core/Kernel
> -I/«PKGBUILDDIR»/src/Core/ComponentBaseClasses
> -I/«PKGBUILDDIR»/src/Core/Configuration -I/«PKGBUILDDIR»/src/Core/Main
> -I/«PKGBUILDDIR»/src/Components/FixedImagePyramids
> -I/«PKGBUILDDIR»/src/Components/ImageSamplers
> -I/«PKGBUILDDIR»/src/Components/Interpolators
> -I/«PKGBUILDDIR»/src/Components/Metrics
> -I/«PKGBUILDDIR»/src/Components/MovingImagePyramids
> -I/«PKGBUILDDIR»/src/Components/Optimizers
> -I/«PKGBUILDDIR»/src/Components/Registrations
> -I/«PKGBUILDDIR»/src/Components/ResampleInterpolators
> -I/«PKGBUILDDIR»/src/Components/Resamplers
> -I/«PKGBUILDDIR»/src/Components/Transforms
> -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu -o
> CMakeFiles/elastix.dir/Install/elxComponentLoader.cxx.o -c
> /«PKGBUILDDIR»/src/Core/Install/elxComponentLoader.cxx
> In file included from
> /«PKGBUILDDIR»/src/Core/ComponentBaseClasses/elxFixedImagePyramidBase.hxx:18:0,
> from
> /«PKGBUILDDIR»/src/Core/ComponentBaseClasses/elxFixedImagePyramidBase.h:134,
> from /«PKGBUILDDIR»/src/Core/Kernel/elxElastixTemplate.h:27,
> from
> /«PKGBUILDDIR»/obj-x86_64-linux-gnu/elxSupportedImageTypes.h:23,
> from
> /«PKGBUILDDIR»/src/Core/Install/elxComponentLoader.cxx:19:
> /«PKGBUILDDIR»/src/Common/itkImageFileCastWriter.h: In instantiation of
> 'class itk::ImageFileCastWriter<itk::Image<short int, 4u> >':
> /«PKGBUILDDIR»/src/Core/ComponentBaseClasses/elxResamplerBase.hxx:381:55:
> required from 'void elastix::ResamplerBase<TElastix>::WriteResultImage(const
> char*, const bool&) [with TElastix =
> elastix::ElastixTemplate<itk::Image<short int, 4u>, itk::Image<short int, 4u>
> >]'
> /«PKGBUILDDIR»/src/Core/Kernel/elxElastixTemplate.hxx:463:5: required from
> 'int elastix::ElastixTemplate<TFixedImage, TMovingImage>::ApplyTransform()
> [with TFixedImage = itk::Image<short int, 4u>; TMovingImage =
> itk::Image<short int, 4u>]'
> /«PKGBUILDDIR»/src/Core/Install/elxComponentLoader.cxx:189:1: required from
> here
> /«PKGBUILDDIR»/src/Common/itkImageFileCastWriter.h:36:7: warning:
> 'itk::ImageFileCastWriter<itk::Image<short int, 4u> >' declared with greater
> visibility than the type of its field
> 'itk::ImageFileCastWriter<itk::Image<short int, 4u> >::<anonymous>'
> [-Wattributes]
> class ImageFileCastWriter : public ImageFileWriter< TInputImage >
> ^
> /«PKGBUILDDIR»/src/Common/itkImageFileCastWriter.h:36:7: warning:
> 'itk::ImageFileCastWriter<itk::Image<short int, 4u> >' declared with greater
> visibility than its base 'itk::ImageFileWriter<itk::Image<short int, 4u> >'
> [-Wattributes]
> /«PKGBUILDDIR»/src/Common/itkImageFileCastWriter.h: In instantiation of
> 'class itk::ImageFileCastWriter<itk::Image<float, 3u> >':
> /«PKGBUILDDIR»/src/Core/ComponentBaseClasses/elxResamplerBase.hxx:381:55:
> required from 'void elastix::ResamplerBase<TElastix>::WriteResultImage(const
> char*, const bool&) [with TElastix =
> elastix::ElastixTemplate<itk::Image<float, 3u>, itk::Image<float, 3u> >]'
> /«PKGBUILDDIR»/src/Core/Kernel/elxElastixTemplate.hxx:463:5: required from
> 'int elastix::ElastixTemplate<TFixedImage, TMovingImage>::ApplyTransform()
> [with TFixedImage = itk::Image<float, 3u>; TMovingImage = itk::Image<float,
> 3u>]'
> /«PKGBUILDDIR»/src/Core/Install/elxComponentLoader.cxx:189:1: required from
> here
> /«PKGBUILDDIR»/src/Common/itkImageFileCastWriter.h:36:7: warning:
> 'itk::ImageFileCastWriter<itk::Image<float, 3u> >' declared with greater
> visibility than the type of its field
> 'itk::ImageFileCastWriter<itk::Image<float, 3u> >::<anonymous>' [-Wattributes]
> /«PKGBUILDDIR»/src/Common/itkImageFileCastWriter.h:36:7: warning:
> 'itk::ImageFileCastWriter<itk::Image<float, 3u> >' declared with greater
> visibility than its base 'itk::ImageFileWriter<itk::Image<float, 3u> >'
> [-Wattributes]
> /«PKGBUILDDIR»/src/Common/itkImageFileCastWriter.h: In instantiation of
> 'class itk::ImageFileCastWriter<itk::Image<short int, 3u> >':
> /«PKGBUILDDIR»/src/Core/ComponentBaseClasses/elxResamplerBase.hxx:381:55:
> required from 'void elastix::ResamplerBase<TElastix>::WriteResultImage(const
> char*, const bool&) [with TElastix =
> elastix::ElastixTemplate<itk::Image<short int, 3u>, itk::Image<short int, 3u>
> >]'
> /«PKGBUILDDIR»/src/Core/Kernel/elxElastixTemplate.hxx:463:5: required from
> 'int elastix::ElastixTemplate<TFixedImage, TMovingImage>::ApplyTransform()
> [with TFixedImage = itk::Image<short int, 3u>; TMovingImage =
> itk::Image<short int, 3u>]'
> /«PKGBUILDDIR»/src/Core/Install/elxComponentLoader.cxx:189:1: required from
> here
> /«PKGBUILDDIR»/src/Common/itkImageFileCastWriter.h:36:7: warning:
> 'itk::ImageFileCastWriter<itk::Image<short int, 3u> >' declared with greater
> visibility than the type of its field
> 'itk::ImageFileCastWriter<itk::Image<short int, 3u> >::<anonymous>'
> [-Wattributes]
> /«PKGBUILDDIR»/src/Common/itkImageFileCastWriter.h:36:7: warning:
> 'itk::ImageFileCastWriter<itk::Image<short int, 3u> >' declared with greater
> visibility than its base 'itk::ImageFileWriter<itk::Image<short int, 3u> >'
> [-Wattributes]
> /«PKGBUILDDIR»/src/Common/itkImageFileCastWriter.h: In instantiation of
> 'class itk::ImageFileCastWriter<itk::Image<float, 2u> >':
> /«PKGBUILDDIR»/src/Core/ComponentBaseClasses/elxResamplerBase.hxx:381:55:
> required from 'void elastix::ResamplerBase<TElastix>::WriteResultImage(const
> char*, const bool&) [with TElastix =
> elastix::ElastixTemplate<itk::Image<float, 2u>, itk::Image<float, 2u> >]'
> /«PKGBUILDDIR»/src/Core/Kernel/elxElastixTemplate.hxx:463:5: required from
> 'int elastix::ElastixTemplate<TFixedImage, TMovingImage>::ApplyTransform()
> [with TFixedImage = itk::Image<float, 2u>; TMovingImage = itk::Image<float,
> 2u>]'
> /«PKGBUILDDIR»/src/Core/Install/elxComponentLoader.cxx:189:1: required from
> here
> /«PKGBUILDDIR»/src/Common/itkImageFileCastWriter.h:36:7: warning:
> 'itk::ImageFileCastWriter<itk::Image<float, 2u> >' declared with greater
> visibility than the type of its field
> 'itk::ImageFileCastWriter<itk::Image<float, 2u> >::<anonymous>' [-Wattributes]
> /«PKGBUILDDIR»/src/Common/itkImageFileCastWriter.h:36:7: warning:
> 'itk::ImageFileCastWriter<itk::Image<float, 2u> >' declared with greater
> visibility than its base 'itk::ImageFileWriter<itk::Image<float, 2u> >'
> [-Wattributes]
> In file included from /usr/include/ITK-4.6/itkHexahedronCell.h:147:0,
> from /usr/include/ITK-4.6/itkMeshFileReader.h:23,
> from /«PKGBUILDDIR»/src/Common/itkMeshFileReaderBase.h:19,
> from
> /«PKGBUILDDIR»/src/Common/itkTransformixInputPointFileReader.h:18,
> from
> /«PKGBUILDDIR»/src/Core/ComponentBaseClasses/elxTransformBase.hxx:21,
> from
> /«PKGBUILDDIR»/src/Core/ComponentBaseClasses/elxTransformBase.h:341,
> from /«PKGBUILDDIR»/src/Core/Kernel/elxElastixTemplate.h:35,
> from
> /«PKGBUILDDIR»/obj-x86_64-linux-gnu/elxSupportedImageTypes.h:23,
> from
> /«PKGBUILDDIR»/src/Core/Install/elxComponentLoader.cxx:19:
> /usr/include/ITK-4.6/itkHexahedronCell.hxx: In member function 'bool
> itk::HexahedronCell<TCellInterface>::EvaluatePosition(itk::HexahedronCell<TCellInterface>::CoordRepType*,
> itk::HexahedronCell<TCellInterface>::PointsContainer*,
> itk::HexahedronCell<TCellInterface>::CoordRepType*,
> itk::HexahedronCell<TCellInterface>::CoordRepType*, double*,
> itk::HexahedronCell<TCellInterface>::InterpolationWeightType*) [with
> TCellInterface = itk::CellInterface<float, itk::CellTraitsInfo<4, double,
> float, long unsigned int, long unsigned int, long unsigned int,
> itk::Point<double, 4u>, itk::VectorContainer<long unsigned int,
> itk::Point<double, 4u> >, std::set<long unsigned int> > >;
> itk::HexahedronCell<TCellInterface>::CoordRepType = double;
> itk::HexahedronCell<TCellInterface>::PointsContainer =
> itk::VectorContainer<long unsigned int, itk::Point<double, 4u> >;
> itk::HexahedronCell<TCellInterface>::InterpolationWeightType = float]':
> /usr/include/ITK-4.6/itkHexahedronCell.hxx:380:9: warning: iteration 3u
> invokes undefined behavior [-Waggressive-loop-optimizations]
> tcol[j] += pt[j] * derivs[i + 16];
> ^
> /usr/include/ITK-4.6/itkHexahedronCell.hxx:375:7: note: containing loop
> for ( unsigned int j = 0; j < PointDimension; j++ )
> ^
> make[3]: *** No rule to make target '/usr/lib/x86_64-linux-gnu/libhdf5.so',
> needed by 'bin/elastix'. Stop.
> make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu'
> make[2]: *** [Core/CMakeFiles/elastix.dir/all] Error 2
The full build log is available from:
http://aws-logs.debian.net/ftbfs-logs/2014/08/30/elastix_4.7-2_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures. The build
was done with DEB_BUILD_OPTIONS="parallel=4", so if your packaging tries
to support this, it might be a good idea to explore whether this might
be the cause of the failure.
--- End Message ---
