[Debian-med-packaging] Bug#759945: elastix: FTBFS: make[3]: *** No rule to make target '/usr/lib/x86_64-linux-gnu/libhdf5.so', needed by 'bin/elastix'. Stop.

Sat Aug 30 21:29:35 UTC 2014

Source: elastix
Version: 4.7-2
Severity: serious
Tags: jessie sid
User: debian-qa at 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.