Hi Adrian, Adrian Bunk, on 2021-12-09: > On Tue, Nov 09, 2021 at 11:34:13PM +0100, Étienne Mollier wrote: > > Étienne Mollier, on 2021-11-08: > > > I haven't pushed investigations further for the moment. This > > > possibly appeared with tiff 4.3.0, and probably got fixed in > > > ITKv5 as well. > > > > Or not, the embedded copy is still libtiff 4.0.3 in ITKv5 > > instead of the version 4.3.0. Maybe something went wrong with > > our system tiff library, or the way it is called needs change; > > it's probably worth pinging upstream. > >... > > ITKv5 appears to build, how was it fixed there? If I append -DITK_USE_SYSTEM_TIFF:BOOL=ON, I see the same segmentation faults already witnessed in itk4, so guess the tiff 4.0.3 embedded works these issues around: 1129: Test command: /<<PKGBUILDDIR>>/BUILD/bin/ITKIOTIFFTestDriver "--compare-MD5" "/<<PKGBUILDDIR>>/BUILD/Testing/Temporary/itkTIFFImageIOPlannarConfig2.tif" "91975481ba66709c8f3ccb538af5cd2a" "itkTIFFImageIOTest" "/<<PKGBUILDDIR>>/BUILD/ExternalData/Modules/IO/TIFF/test/Input/ps-separated.tif" "/<<PKGBUILDDIR>>/BUILD/Testing/Temporary/itkTIFFImageIOPlannarConfig2.tif" "2" "1" 1129: Test timeout computed to be: 1500 1129: Trying reader->Update() 1129/2826 Testing: itkTIFFImageIOPlannarConfig2 1129/2826 Test: itkTIFFImageIOPlannarConfig2 1132: Test command: /<<PKGBUILDDIR>>/BUILD/bin/ITKIOTIFFTestDriver "itkTIFFImageIOInfoTest" "/<<PKGBUILDDIR>>/BUILD/ExternalData/Modules/IO/TIFF/test/Input/ps-separated.tif" 1132: Test timeout computed to be: 1500 1132/2826 Testing: itkTIFFImageIOInfoTest2 1132/2826 Test: itkTIFFImageIOInfoTest2 There are also additionnal failures. I suspect these are new checks from itk5 to properly support large tiff images, greater in size than 4GiB: 1148: Test command: /<<PKGBUILDDIR>>/BUILD/bin/ITKIOTIFFTestDriver "itkLargeTIFFImageWriteReadTest" "/<<PKGBUILDDIR>>/BUILD/Testing/Temporary/LargeImage02.tif" "40000L" 1148: Test timeout computed to be: 1500 1148: Trying to allocate an image of size 3051 MiB 1148: Initializing pixel values 1148: Trying to write the image to disk 1148: Trying writer->Update() 1148: 1148: itk::ExceptionObject (0x55906ce88950) 1148: Location: "void itk::TIFFImageIO::InternalWrite(const void*)" 1148: File: ./Modules/IO/TIFF/src/itkTIFFImageIO.cxx 1148: Line: 622 1148: Description: ITK ERROR: TIFFImageIO(0x55906ce89950): Size of image exceeds the limit of libtiff. 1148: 1148: 1148: In ./Modules/IO/TIFF/test/itkLargeTIFFImageWriteReadTest.cxx, line 104 2825/2826 Test #1148: itkLargeTIFFImageWriteReadTest2 ........................................................................***Failed 2.85 sec 1149: Test command: /<<PKGBUILDDIR>>/BUILD/bin/ITKIOTIFFTestDriver "itkLargeTIFFImageWriteReadTest" "/<<PKGBUILDDIR>>/BUILD/Testing/Temporary/LargeImage03.tif" "50000L" 1149: Test timeout computed to be: 1500 1149: Trying to allocate an image of size 4768 MiB 1149: Initializing pixel values 1149: Trying to write the image to disk 1149: Trying writer->Update() 1149: 1149: itk::ExceptionObject (0x56036aeef950) 1149: Location: "void itk::TIFFImageIO::InternalWrite(const void*)" 1149: File: ./Modules/IO/TIFF/src/itkTIFFImageIO.cxx 1149: Line: 622 1149: Description: ITK ERROR: TIFFImageIO(0x56036aef0950): Size of image exceeds the limit of libtiff. 1149: 1149: 1149: In ./Modules/IO/TIFF/test/itkLargeTIFFImageWriteReadTest.cxx, line 104 2826/2826 Test #1149: itkLargeTIFFImageWriteReadTest3 ........................................................................***Failed 4.93 sec 1150: Test command: /<<PKGBUILDDIR>>/BUILD/bin/ITKIOTIFFTestDriver "itkLargeTIFFImageWriteReadTest" "/<<PKGBUILDDIR>>/BUILD/Testing/Temporary/LargeImage04.tif" "70000L" 1150: Test timeout computed to be: 1500 1150: Trying to allocate an image of size 9346 MiB 1150: Initializing pixel values 1150: Trying to write the image to disk 1150: Trying writer->Update() 1150: 1150: itk::ExceptionObject (0x563af54b4950) 1150: Location: "void itk::TIFFImageIO::InternalWrite(const void*)" 1150: File: ./Modules/IO/TIFF/src/itkTIFFImageIO.cxx 1150: Line: 622 1150: Description: ITK ERROR: TIFFImageIO(0x563af54b5950): Size of image exceeds the limit of libtiff. 1150: 1150: 1150: In ./Modules/IO/TIFF/test/itkLargeTIFFImageWriteReadTest.cxx, line 104 2040/2826 Test #1150: itkLargeTIFFImageWriteReadTest4 ........................................................................***Failed 10.33 sec The embedded copy of libtiff is excluded from itk4 .dsc. I would prefer not putting it back, given the trail of security issues behind tiff. I considered pushing a change yesterday to disable those tests on insighttoolkit4, not to hide dust under the carpet, but to give a chance to reverse dependencies to make it to testing in a decent enough shape hopefuly. However I caught a build issue in the meantime: [ 3%] Generating /<<PKGBUILDDIR>>/BUILD/ExternalData/Modules/Filtering/Deconvolution/test/Baseline/itkWienerDeconvolutionImageFilterIrregularKernelTest.nrrd usr/bin/cmake -Drelative_top=/<<PKGBUILDDIR>>/BUILD -Dfile=/<<PKGBUILDDIR>>/BUILD/ExternalData/Modules/Filtering/Deconvolution/test/Baseline/itkWienerDeconvolutionImageFilterIrregularKernelTest.nrrd -Dname=/<<PKGBUILDDIR>>/Modules/Filtering/Deconvolution/test/Baseline/itkWienerDeconvolutionImageFilterIrregularKernelTest.nrrd -Dexts=.md5+.sha512 -DExternalData_ACTION=fetch -DExternalData_CONFIG=/<<PKGBUILDDIR>>/BUILD/ITKData_config.cmake -P /<<PKGBUILDDIR>>/CMake/ExternalData.cmake -- Found object: "/<<PKGBUILDDIR>>/data/.ExternalData/MD5/58a1c99268c5f29b8b1ad1ae68529205" In file included from /<<PKGBUILDDIR>>/BUILD/Wrapping/ITKCommonBase.cxx:12: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkImage.h:28: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkNeighborhoodAccessorFunctor.h:21: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkImageBoundaryCondition.h:22: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkNeighborhood.h:24: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkSliceIterator.h:23: /usr/include/c++/11/valarray:1215:5: error: exception specification in declaration does not match previous declaration begin(valarray<_Tp>& __va) noexcept ^ /usr/include/c++/11/bits/range_access.h:107:31: note: previous declaration is here template<typename _Tp> _Tp* begin(valarray<_Tp>&); ^ In file included from /<<PKGBUILDDIR>>/BUILD/Wrapping/ITKCommonBase.cxx:12: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkImage.h:28: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkNeighborhoodAccessorFunctor.h:21: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkImageBoundaryCondition.h:22: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkNeighborhood.h:24: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkSliceIterator.h:23: /usr/include/c++/11/valarray:1226:5: error: exception specification in declaration does not match previous declaration begin(const valarray<_Tp>& __va) noexcept ^ /usr/include/c++/11/bits/range_access.h:108:37: note: previous declaration is here template<typename _Tp> const _Tp* begin(const valarray<_Tp>&); ^ In file included from /<<PKGBUILDDIR>>/BUILD/Wrapping/ITKCommonBase.cxx:12: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkImage.h:28: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkNeighborhoodAccessorFunctor.h:21: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkImageBoundaryCondition.h:22: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkNeighborhood.h:24: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkSliceIterator.h:23: /usr/include/c++/11/valarray:1237:5: error: exception specification in declaration does not match previous declaration end(valarray<_Tp>& __va) noexcept ^ /usr/include/c++/11/bits/range_access.h:109:31: note: previous declaration is here template<typename _Tp> _Tp* end(valarray<_Tp>&); ^ In file included from /<<PKGBUILDDIR>>/BUILD/Wrapping/ITKCommonBase.cxx:12: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkImage.h:28: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkNeighborhoodAccessorFunctor.h:21: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkImageBoundaryCondition.h:22: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkNeighborhood.h:24: In file included from /<<PKGBUILDDIR>>/Modules/Core/Common/include/itkSliceIterator.h:23: /usr/include/c++/11/valarray:1253:5: error: exception specification in declaration does not match previous declaration end(const valarray<_Tp>& __va) noexcept ^ /usr/include/c++/11/bits/range_access.h:110:37: note: previous declaration is here template<typename _Tp> const _Tp* end(const valarray<_Tp>&); I'm a bit dry about the root cause right now. > The other problem is #984284, which seems to require a rename > of the libinsighttoolkit4.13 package. I attempted to build otb against itk5, but it's not ready for the version bump yet apparently. What rename did you have in mind for the libinsighttoolkit4.13 package exactly? Thanks for jumping in, :) -- Étienne Mollier <emollier@emlwks999.eu> Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/2, please excuse my verbosity.
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