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. -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
