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Update hdf5 1.12.1 to 1.12.3 #4653

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Update hdf5 1.12.1 to 1.12.3 #4653

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seanm
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@seanm seanm commented May 8, 2024

This smaller update seems easier to deal with than going to 1.14...

seanm and others added 3 commits May 5, 2024 21:17
Code extracted from:

    https://github.com/HDFGroup/hdf5.git

at commit 106fb56936d1d785ca96147601a3608e433ddc3b (hdf5-1_12_3).
# By HDF5 Maintainers
* upstream-HDF5:
  HDF5 2023-11-06 (106fb569)

# Conflicts:
#	Modules/ThirdParty/HDF5/src/itkhdf5/CMakeFilters.cmake
#	Modules/ThirdParty/HDF5/src/itkhdf5/CMakeLists.txt
#	Modules/ThirdParty/HDF5/src/itkhdf5/config/cmake/ConfigureChecks.cmake
#	Modules/ThirdParty/HDF5/src/itkhdf5/config/cmake/HDFCompilerFlags.cmake
#	Modules/ThirdParty/HDF5/src/itkhdf5/config/cmake/HDFMacros.cmake
#	Modules/ThirdParty/HDF5/src/itkhdf5/config/cmake_ext_mod/ConfigureChecks.cmake
#	Modules/ThirdParty/HDF5/src/itkhdf5/config/cmake_ext_mod/HDFUseCXX.cmake
#	Modules/ThirdParty/HDF5/src/itkhdf5/hl/CMakeLists.txt
#	Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeLists.txt
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Looks good on a glance.

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dzenanz commented May 8, 2024

It looks like pleasing the CI will take some doing.

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dzenanz commented May 9, 2024

CMake Warning at Modules/ThirdParty/HDF5/src/itkhdf5/CMakeFilters.cmake:132 (message):
   ZLib support in HDF5 was enabled but not found
Call Stack (most recent call first):
  Modules/ThirdParty/HDF5/src/itkhdf5/CMakeLists.txt:886 (include)

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seanm commented May 9, 2024

CMake Warning at Modules/ThirdParty/HDF5/src/itkhdf5/CMakeFilters.cmake:132 (message):
   ZLib support in HDF5 was enabled but not found
Call Stack (most recent call first):
  Modules/ThirdParty/HDF5/src/itkhdf5/CMakeLists.txt:886 (include)

3012756 should fix that. It was OFF in ITK 5.3, I must have accidentally turned it on.

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dzenanz commented May 9, 2024

[4087/5894] Building C object Modules\ThirdParty\HDF5\src\itkhdf5\src\CMakeFiles\hdf5-shared.dir\H5Ztrans.c.obj
[4088/5894] Building C object Modules\ThirdParty\HDF5\src\itkhdf5\hl\src\CMakeFiles\hdf5_hl-shared.dir\H5DO.c.obj
[4089/5894] Building C object Modules\ThirdParty\HDF5\src\itkhdf5\hl\src\CMakeFiles\hdf5_hl-shared.dir\H5DS.c.obj
[4090/5894] Building C object Modules\ThirdParty\HDF5\src\itkhdf5\hl\src\CMakeFiles\hdf5_hl-shared.dir\H5IM.c.obj
[4091/5894] Linking C shared library bin\itkhdf5-shared-5.4.dll
FAILED: bin/itkhdf5-shared-5.4.dll lib/itkhdf5-shared-5.4.lib 
C:\Windows\system32\cmd.exe /C "cd . && "C:\Program Files\CMake\bin\cmake.exe" -E vs_link_dll --intdir=Modules\ThirdParty\HDF5\src\itkhdf5\src\CMakeFiles\hdf5-shared.dir --rc=C:\PROGRA~2\WI3CF2~1\10\bin\100226~1.0\x64\rc.exe --mt=C:\PROGRA~2\WI3CF2~1\10\bin\100226~1.0\x64\mt.exe --manifests  -- C:\PROGRA~2\MICROS~2\2019\ENTERP~1\VC\Tools\MSVC\1429~1.301\bin\Hostx64\x64\link.exe /nologo @CMakeFiles\hdf5-shared.rsp  /out:bin\itkhdf5-shared-5.4.dll /implib:lib\itkhdf5-shared-5.4.lib /pdb:bin\itkhdf5-shared-5.4.pdb /dll /version:1.0 /machine:x64  /INCREMENTAL:NO && cd ."
LINK: command "C:\PROGRA~2\MICROS~2\2019\ENTERP~1\VC\Tools\MSVC\1429~1.301\bin\Hostx64\x64\link.exe /nologo @CMakeFiles\hdf5-shared.rsp /out:bin\itkhdf5-shared-5.4.dll /implib:lib\itkhdf5-shared-5.4.lib /pdb:bin\itkhdf5-shared-5.4.pdb /dll /version:1.0 /machine:x64 /INCREMENTAL:NO /MANIFEST:EMBED,ID=2" failed (exit code 1120) with the following output:
   Creating library lib\itkhdf5-shared-5.4.lib and object lib\itkhdf5-shared-5.4.exp
H5Zdeflate.c.obj : error LNK2019: unresolved external symbol itkzlib_inflate referenced in function H5Z__filter_deflate
H5Zdeflate.c.obj : error LNK2019: unresolved external symbol itkzlib_inflateEnd referenced in function H5Z__filter_deflate
H5Zdeflate.c.obj : error LNK2019: unresolved external symbol itkzlib_compress2 referenced in function H5Z__filter_deflate

H5Zdeflate.c.obj : error LNK2019: unresolved external symbol itkzlib_inflateInit_ referenced in function H5Z__filter_deflate

bin\itkhdf5-shared-5.4.dll : fatal error LNK1120: 4 unresolved externals

[4092/5894] Building C object Modules\ThirdParty\HDF5\src\itkhdf5\hl\src\CMakeFiles\hdf5_hl-shared.dir\H5LT.c.obj
[4093/5894] Building C object Modules\ThirdParty\HDF5\src\itkhdf5\hl\src\CMakeFiles\hdf5_hl-shared.dir\H5LTanalyze.c.obj
ninja: build stopped: subcommand failed.
Command exited with the value: 1
MakeCommand:"C:\Program Files\CMake\bin\cmake.exe" --build . --config "MinSizeRel"
   5 Compiler errors
   1 Compiler warnings

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thewtex commented May 20, 2024

@seanm please rebase on master

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thewtex commented May 21, 2024

@seanm please also create PR's from forks -- we do not want to clutter the main repo with topic branches.

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seanm commented May 23, 2024

@seanm please also create PR's from forks -- we do not want to clutter the main repo with topic branches.

Mmmm, not sure what you mean here? I'm pretty sure I created this PR the same way I always do...

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thewtex commented May 29, 2024

The branch was pushed to the main InsightSoftwareConsortium/ITK repository:

image

We want to create the pull request from a forked repository, e.g.:

image

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3 participants