[Debian-med-packaging] Bug#1037697: insighttoolkit5: ftbfs with GCC-13
Matthias Klose
doko at debian.org
Wed Jun 14 10:25:48 BST 2023
Package: src:insighttoolkit5
Version: 5.2.1-5
Severity: normal
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-13
[This bug is targeted to the upcoming trixie release]
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-13/g++-13, but succeeds to build with gcc-12/g++-12. The
severity of this report will be raised before the trixie release.
The full build log can be found at:
http://qa-logs.debian.net/2023/05/22/logs/insighttoolkit5_5.2.1-5_unstable_gccexp.log
The last lines of the build log are at the end of this report.
To build with GCC 13, either set CC=gcc-13 CXX=g++-13 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-13/porting_to.html
[...]
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[ 50%] Built target ITKLabelMap
[ 50%] Building CXX object Modules/IO/XML/src/CMakeFiles/ITKIOXML.dir/itkFancyString.cxx.o
cd /<<PKGBUILDDIR>>/BUILD/Modules/IO/XML/src && /usr/bin/c++ -DITKIOXML_EXPORTS -I/usr/include/gdcm-3.0 -I/<<PKGBUILDDIR>>/BUILD/Modules/ThirdParty/Expat/src -I/<<PKGBUILDDIR>>/BUILD/Modules/ThirdParty/Eigen3/src -I/<<PKGBUILDDIR>>/BUILD/Modules/ThirdParty/KWIML/src -I/<<PKGBUILDDIR>>/Modules/ThirdParty/KWIML/src -I/<<PKGBUILDDIR>>/BUILD/Modules/ThirdParty/KWSys/src -I/<<PKGBUILDDIR>>/Modules/ThirdParty/VNL/src/vxl/v3p/netlib -I/<<PKGBUILDDIR>>/Modules/ThirdParty/VNL/src/vxl/vcl -I/<<PKGBUILDDIR>>/Modules/ThirdParty/VNL/src/vxl/core -I/<<PKGBUILDDIR>>/BUILD/Modules/ThirdParty/VNL/src/vxl/v3p/netlib -I/<<PKGBUILDDIR>>/BUILD/Modules/ThirdParty/VNL/src/vxl/vcl -I/<<PKGBUILDDIR>>/BUILD/Modules/ThirdParty/VNL/src/vxl/core -I/<<PKGBUILDDIR>>/BUILD/Modules/Core/Common -I/<<PKGBUILDDIR>>/Modules/Core/Common/include -I/<<PKGBUILDDIR>>/BUILD/Modules/IO/ImageBase -I/<<PKGBUILDDIR>>/Modules/IO/ImageBase/include -I/<<PKGBUILDDIR>>/Modules/IO/XML/include -I/<<PKGBUILDDIR>>/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo -I/<<PKGBUILDDIR>>/Modules/ThirdParty/VNL/src/vxl/core/vnl -I/<<PKGBUILDDIR>>/BUILD/Modules/ThirdParty/VNL/src/vxl/core/vnl -isystem /<<PKGBUILDDIR>>/Modules/ThirdParty/Eigen3/src/itkeigen/.. -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/nifti -g1 -mtune=generic -march=corei7 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel -fPIC -std=c++11 -MD -MT Modules/IO/XML/src/CMakeFiles/ITKIOXML.dir/itkFancyString.cxx.o -MF CMakeFiles/ITKIOXML.dir/itkFancyString.cxx.o.d -o CMakeFiles/ITKIOXML.dir/itkFancyString.cxx.o -c /<<PKGBUILDDIR>>/Modules/IO/XML/src/itkFancyString.cxx
[ 50%] Linking CXX shared library ../../../../lib/libITKIOTIFF-5.2.so
cd /<<PKGBUILDDIR>>/BUILD/Modules/IO/TIFF/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ITKIOTIFF.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/nifti -g1 -mtune=generic -march=corei7 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel -Wl,-z,relro -shared -Wl,-soname,libITKIOTIFF-5.2.so.1 -o ../../../../lib/libITKIOTIFF-5.2.so.1 CMakeFiles/ITKIOTIFF.dir/itkTIFFImageIO.cxx.o CMakeFiles/ITKIOTIFF.dir/itkTIFFReaderInternal.cxx.o CMakeFiles/ITKIOTIFF.dir/itkTIFFImageIOFactory.cxx.o -Wl,-rpath,/<<PKGBUILDDIR>>/BUILD/lib: ../../../../lib/libITKIOImageBase-5.2.so.1 ../../../../lib/libitktiff-5.2.so.1 ../../../../lib/libITKCommon-5.2.so.1 ../../../../lib/libitksys-5.2.so.1 ../../../../lib/libITKVNLInstantiation-5.2.so.1 ../../../../lib/libitkvnl_algo-5.2.so.1 ../../../../lib/libitkvnl-5.2.so.1 ../../../../lib/libitkv3p_netlib-5.2.so.1 ../../../../lib/libitkvcl-5.2.so.1 -lm -ldl /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libjpeg.so -lm -Wl,-rpath-link,/<<PKGBUILDDIR>>/BUILD/lib
cd /<<PKGBUILDDIR>>/BUILD/Modules/IO/TIFF/src && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libITKIOTIFF-5.2.so.1 ../../../../lib/libITKIOTIFF-5.2.so.1 ../../../../lib/libITKIOTIFF-5.2.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/BUILD'
[ 50%] Built target ITKIOTIFF
[ 50%] Linking CXX shared library ../../../../lib/libITKIOXML-5.2.so
cd /<<PKGBUILDDIR>>/BUILD/Modules/IO/XML/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ITKIOXML.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/nifti -g1 -mtune=generic -march=corei7 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel -Wl,-z,relro -shared -Wl,-soname,libITKIOXML-5.2.so.1 -o ../../../../lib/libITKIOXML-5.2.so.1 CMakeFiles/ITKIOXML.dir/itkXMLFile.cxx.o CMakeFiles/ITKIOXML.dir/itkDOMNode.cxx.o CMakeFiles/ITKIOXML.dir/itkDOMNodeXMLReader.cxx.o CMakeFiles/ITKIOXML.dir/itkDOMNodeXMLWriter.cxx.o CMakeFiles/ITKIOXML.dir/itkStringTools.cxx.o CMakeFiles/ITKIOXML.dir/itkFancyString.cxx.o -Wl,-rpath,/<<PKGBUILDDIR>>/BUILD/lib: ../../../../lib/libITKIOImageBase-5.2.so.1 /usr/lib/x86_64-linux-gnu/libexpat.so ../../../../lib/libITKCommon-5.2.so.1 ../../../../lib/libitksys-5.2.so.1 ../../../../lib/libITKVNLInstantiation-5.2.so.1 ../../../../lib/libitkvnl_algo-5.2.so.1 ../../../../lib/libitkvnl-5.2.so.1 ../../../../lib/libitkv3p_netlib-5.2.so.1 ../../../../lib/libitkvcl-5.2.so.1 -lm -lm -ldl -Wl,-rpath-link,/<<PKGBUILDDIR>>/BUILD/lib
cd /<<PKGBUILDDIR>>/BUILD/Modules/IO/XML/src && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libITKIOXML-5.2.so.1 ../../../../lib/libITKIOXML-5.2.so.1 ../../../../lib/libITKIOXML-5.2.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/BUILD'
[ 50%] Built target ITKIOXML
In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkImageRegion.h:33,
from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkImage.h:21,
from /<<PKGBUILDDIR>>/Modules/Core/Transform/include/itkBSplineBaseTransform.h:23,
from /<<PKGBUILDDIR>>/Modules/Core/Transform/include/itkBSplineTransform.h:21,
from /<<PKGBUILDDIR>>/Modules/IO/TransformFactory/src/itkTransformFactoryBaseRegister.hxx:44,
from /<<PKGBUILDDIR>>/Modules/IO/TransformFactory/src/itkTransformFactoryBaseRegisterDoubleParameters.cxx:18:
In member function ‘const itk::Size<VDimension>::value_type& itk::Size<VDimension>::operator[](size_type) const [with unsigned int VDimension = 2]’,
inlined from ‘itk::Neighborhood<TPixel, VDimension, TAllocator>::SizeValueType itk::Neighborhood<TPixel, VDimension, TAllocator>::GetSize(DimensionValueType) const [with TPixel = double; unsigned int VDimension = 2; TAllocator = itk::NeighborhoodAllocator<double>]’ at /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkNeighborhood.h:160:18,
inlined from ‘void itk::NeighborhoodOperator<TPixel, VDimension, TAllocator>::FillCenteredDirectional(const CoefficientVector&) [with TPixel = double; unsigned int VDimension = 2; TAllocator = itk::NeighborhoodAllocator<double>]’ at /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkNeighborhoodOperator.hxx:113:43:
/<<PKGBUILDDIR>>/Modules/Core/Common/include/itkSize.h:329:75: warning: array subscript 2 is above array bounds of ‘const itk::Size<2>::SizeValueType [2]’ {aka ‘const long unsigned int [2]’} [-Warray-bounds=]
329 | const_reference operator[](size_type pos) const { return m_InternalArray[pos]; }
| ~~~~~~~~~~~~~~~^
/<<PKGBUILDDIR>>/Modules/Core/Common/include/itkSize.h: In member function ‘void itk::NeighborhoodOperator<TPixel, VDimension, TAllocator>::FillCenteredDirectional(const CoefficientVector&) [with TPixel = double; unsigned int VDimension = 2; TAllocator = itk::NeighborhoodAllocator<double>]’:
/<<PKGBUILDDIR>>/Modules/Core/Common/include/itkSize.h:227:40: note: while referencing ‘itk::Size<2>::m_InternalArray’
227 | alignas(SizeValueType) SizeValueType m_InternalArray[VDimension];
| ^~~~~~~~~~~~~~~
[ 50%] Linking CXX shared library ../../../../lib/libITKTransformFactory-5.2.so
cd /<<PKGBUILDDIR>>/BUILD/Modules/IO/TransformFactory/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ITKTransformFactory.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/nifti -g1 -mtune=generic -march=corei7 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel -Wl,-z,relro -shared -Wl,-soname,libITKTransformFactory-5.2.so.1 -o ../../../../lib/libITKTransformFactory-5.2.so.1 CMakeFiles/ITKTransformFactory.dir/itkTransformFactoryBase.cxx.o CMakeFiles/ITKTransformFactory.dir/itkTransformFactoryBaseRegisterFloatParameters.cxx.o CMakeFiles/ITKTransformFactory.dir/itkTransformFactoryBaseRegisterDoubleParameters.cxx.o -Wl,-rpath,/<<PKGBUILDDIR>>/BUILD/lib: ../../../../lib/libITKTransform-5.2.so.1 ../../../../lib/libITKCommon-5.2.so.1 ../../../../lib/libitksys-5.2.so.1 ../../../../lib/libITKVNLInstantiation-5.2.so.1 ../../../../lib/libitkvnl_algo-5.2.so.1 ../../../../lib/libitkvnl-5.2.so.1 ../../../../lib/libitkv3p_netlib-5.2.so.1 ../../../../lib/libitkvcl-5.2.so.1 -lm -lm -ldl -Wl,-rpath-link,/<<PKGBUILDDIR>>/BUILD/lib
cd /<<PKGBUILDDIR>>/BUILD/Modules/IO/TransformFactory/src && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libITKTransformFactory-5.2.so.1 ../../../../lib/libITKTransformFactory-5.2.so.1 ../../../../lib/libITKTransformFactory-5.2.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/BUILD'
[ 50%] Built target ITKTransformFactory
make[2]: Leaving directory '/<<PKGBUILDDIR>>/BUILD'
make[1]: *** [Makefile:169: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/BUILD'
dh_auto_build: error: cd BUILD && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:77: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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