HDF5 error about including private headers H5Tpkg.h

[phcerdan]

Raised by @lorensen in discourse https://discourse.itk.org/t/gcc-8-2/1601/2
and reproduced locally with gcc8.2.

build log: https://open.cdash.org/viewBuildError.php?buildid=5754102

Might be related to latest hdf5 update?

Building C object Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-shared.dir/__/shared/H5Tinit.c.o
FAILED: Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-shared.dir/__/shared/H5Tinit.c.o
/usr/lib/colorgcc/bin/cc -DH5_BUILT_AS_DYNAMIC_LIB -DH5_BUILT_AS_DYNAMIC_LIB=1 -DNDEBUG -D_GNU_SOURCE -Dhdf5_shared_EXPORTS -IModules/ThirdParty/ZLIB/src -IModules/ThirdParty/ZLIB/src -IModules/ThirdParty/HDF5/src -IModules/ThirdParty/HDF5/src -IModules/ThirdParty/HDF5/src/itkhdf5/src -IModules/ThirdParty/HDF5/src/itkhdf5 -Wno-uninitialized -Wno-unused-parameter -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  -w -std=c99 -fstdarg-opt -pedantic -Wall -Wextra -fmessage-length=0 -O2 -g -DNDEBUG -fPIC -MD -MT Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-shared.dir/__/shared/H5Tinit.c.o -MF Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-shared.dir/__/shared/H5Tinit.c.o.d -o Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-shared.dir/__/shared/H5Tinit.c.o   -c Modules/ThirdParty/HDF5/src/itkhdf5/shared/H5Tinit.c
In file included from Modules/ThirdParty/HDF5/src/itkhdf5/shared/H5Tinit.c:82:
Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Tpkg.h:23:2: error: #error "Do not include this file outside the H5T package!"
 #error "Do not include this file outside the H5T package!"

[thewtex]

This is likely related to the recent HDF5 update:

#397

It now showing up on the dashboard thanks to @lorensen 's build:

https://open.cdash.org/viewBuildError.php?buildid=5756101

I will take a look.

[thewtex]

@phcerdan @lorensen I addressed these issues with the gcc:8 Docker image compiler: #510

but I did not experience that error. What CMake version are you using? Are there any other CMake options passed?

[phcerdan]

I am using latest CMake, and I am sure both of us have the ITKVtkGlue module enabled.
I will be able to have a look next week if the docker image doesn't reproduce it.

[phcerdan]

I have tested it with ITKVtkGlue OFF and ON, BUILD_SHARED_LIBS OFF or ON, and same results.

The error is the same than the one reported in vcpkg: microsoft/vcpkg#3867
and might be related with the hdf5 CMakeFiles.txt problem related to find_package. Pinging @dzenanz, as he references the same issue in other PR in vcpkg. Even though there reported that was solved not using SYSTEM_HDF5, but here it fails compiling HDF5 internally.

[phcerdan]

My CMake version is 3.13.4-1

[phcerdan]

Ok, clean build with default CMake options (disabling tests) works good!
This is, no ITKVtkGlue, no CMAKE_BUILD_SHARED.

I will try to isolate the error enabling those options. I don't think this is related to gcc8

[phcerdan]

Enabling ITKVtkGlue with system VTK (this is system vtk-8.2.0-1 with system hdf5-1.10.4-1) fails with error:
Note that targets are cleaned before rebuilding with:
ninja -t clean hdf5-static hdf5_cpp-static

Error:

[352/354] Building C object Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-static.dir/__/H5Tinit.c.o
FAILED: Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-static.dir/__/H5Tinit.c.o
/usr/lib/colorgcc/bin/cc -DNDEBUG -D_GNU_SOURCE -IModules/ThirdParty/ZLIB/src -I/Modules/ThirdParty/ZLIB/src -I/Modules/ThirdParty/HDF5/src -IModules/ThirdParty/HDF5/src -I/Modules/ThirdParty/HDF5/src/itkhdf5/src -IModules/ThirdParty/HDF5/src/itkhdf5 -Wno-uninitialized -Wno-unused-parameter -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  -w -std=c99 -fstdarg-opt -pedantic -Wall -Wextra -fmessage-length=0 -O3 -DNDEBUG -fPIC -MD -MT Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-static.dir/__/H5Tinit.c.o -MF Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-static.dir/__/H5Tinit.c.o.d -o Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-static.dir/__/H5Tinit.c.o   -c Modules/ThirdParty/HDF5/src/itkhdf5/H5Tinit.c
cc: error: Modules/ThirdParty/HDF5/src/itkhdf5/H5Tinit.c: No such file or directory
cc: fatal error: no input files
compilation terminated.
ninja: build stopped: subcommand failed.

[phcerdan]

Using non-system VTK but VTK_DIR=/path-VTK 8.1.1/build works.

I guess there must be some clashing between HDF5 in ITK and the one used in VTK, at least when VTK uses system HDF5...

The thing I should double check is what happens when instead of system VTK-8.2.0-1 using system HDF5 (the one failing), I build the same version of VTK using their internal HDF5.

[phcerdan]

Tested with my compiled vtk-8.2.0 using their internal hdf5 and no problems. I guess it can be narrowed down to problems using system hdf5 in VTK and non-system hdf5 in ITK...

[thewtex]

Great deduction @phcerdan 👁️

system hdf5 in VTK and non-system hdf5 in ITK

This may be difficult to support versus 'system / system' and 'non-system / non-system'. Does VTKConfig.cmake provide information on whether VTK was built with a system HDF5? We could at least, then, throw an error when it is know to cause an issue.

[revolvet]

Is this issue fixed? I still having this problem, and can't build any project dependent on this library. Thanks!

[thewtex]

@revolvet are you also building with VTK? Is HDF5 system in both cases or non-system in both cases?

[revolvet]

@revolvet are you also building with VTK? Is HDF5 system in both cases or non-system in both cases?

I didn't enable itkvtkglue. Now it works when itkvtkglue is enabled, although itkvtkglue itself fails because of something wrong with vtkOStreamWrapper.h. Thanks!

[chenray844]

When I build Slicer https://github.com/Slicer/Slicer that is dependent on VTK and ITK, I meet this bug too.

In file included from /home/chenrf/Projects/medical/slicer/build/ITK-build/Modules/ThirdParty/HDF5/src/itkhdf5/shared/H5Tinit.c:82:0:
/home/chenrf/Projects/medical/slicer/build/ITK/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Tpkg.h:23:2: error: #error "Do not include this file outside the H5T package!"
 #error "Do not include this file outside the H5T package!"
  ^~~~~
Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-shared.dir/build.make:3944: recipe for target 'Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-shared.dir/__/shared/H5Tinit.c.o' failed
make[5]: *** [Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-shared.dir/__/shared/H5Tinit.c.o] Error 1
CMakeFiles/Makefile2:6965: recipe for target 'Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-shared.dir/all' failed
make[4]: *** [Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-shared.dir/all] Error 2
make[4]: *** Waiting for unfinished jobs....

How can I fix this bug?

Thanks.