Your message dated Sat, 12 Sep 2026 17:18:49 +0000
with message-id <[email protected]>
and subject line Bug#1147167: fixed in vtk9 9.6.2+dfsg1-6
has caused the Debian Bug report #1147167,
regarding vtk9: CMake project using VTK and ITK fails configure: both want HDF5
but VTK uses older FindHDF5.cmake
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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1147167: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1147167
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: vtk9
Version: 9.6.2+dfsg1-5
Severity: normal
X-Debbugs-Cc: [email protected]
Dear Maintainer,
our package CamiTK does not build since the update to ITK 5.4.7. While
troubleshooting the issue, we noticed that this is caused by VTK and ITK
requesting the same library: HDF5.
VTK uses a custom, older FindHDF5.cmake, while ITK uses the system one.
The CMake variables defined by the two FindHDF5.cmake are different,
which leads to an error at the configure step about not finding HDF5.
Our package does not require HDF5 except through VTK and ITK.
The curent workaround we are considering is to require it before asking
for VTK and ITK in our CMake files.
Here is a minimal example of a CMakeLists.txt file that shows the issue:
cmake_minimum_required(VERSION 3.28)
project(HDF5Issue)
# FIX: find_package(HDF5 COMPONENTS C HL)
find_package(VTK REQUIRED COMPONENTS CommonCore)
find_package(ITK REQUIRED)
Configuring the project ("cmake -S . --build build") in the directory
with this CMakeLists.txt generates an error identical to the one in our package:
-- Found HDF5: /usr/lib/x86_64-linux-gnu/libhdf5_serial.so (found version
"2.2.0") found components: C
CMake Error at /usr/share/cmake-4.3/Modules/FindHDF5.cmake:1257 (message):
HDF5 was found, but a different variable was set which contains the
location of the `hdf5::hdf5` library.
Call Stack (most recent call first):
/usr/share/cmake-4.3/Modules/CMakeFindDependencyMacro.cmake:93 (find_package)
/usr/share/cmake-4.3/Modules/CMakeFindDependencyMacro.cmake:125
(__find_dependency_common)
/usr/lib/x86_64-linux-gnu/cmake/LIBMINC/LIBMINCConfig.cmake:54
(find_dependency)
/usr/lib/x86_64-linux-gnu/cmake/ITK-5.4/Modules/ITKMINC.cmake:15
(find_package)
/usr/lib/x86_64-linux-gnu/cmake/ITK-5.4/ITKModuleAPI.cmake:86 (include)
/usr/lib/x86_64-linux-gnu/cmake/ITK-5.4/ITKModuleAPI.cmake:31
(itk_module_load)
/usr/lib/x86_64-linux-gnu/cmake/ITK-5.4/ITKModuleAPI.cmake:143
(_itk_module_config_recurse)
/usr/lib/x86_64-linux-gnu/cmake/ITK-5.4/ITKConfig.cmake:89 (itk_module_config)
sdk/cmake/modules/macros/camitk/CamiTKLibrary.cmake:205 (find_package)
imaging/libraries/itktemplates/CMakeLists.txt:76 (camitk_library)
-- Found NetCDF headers: /usr/include
-- Found NetCDF library: /usr/lib/x86_64-linux-gnu/libnetcdf.so
-- Found Python3: /usr/bin/python3 (found suitable version "3.14.7", minimum
required is "3.14") found components: Interpreter Development.Module
Development.Embed
-- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.15.3")
-- Found HDF5: /usr/lib/x86_64-linux-gnu/libhdf5_serial.so (found version
"2.2.0") found components: C HL
CMake Error at
/usr/lib/x86_64-linux-gnu/cmake/vtk-9.6/patches/99/FindHDF5.cmake:1123
(message):
HDF5 was found, but a different variable was set which contains the
location of the `hdf5::hdf5_hl` library.
The reason I am posting this to the VTK9 package is that it is using a
specific FindHDF5.cmake
I am not sure why VTK may need a specific patch version of
FindHDF5.cmake, but the current one is based on an older version
than the one on the standard path in my sid image:
/usr/lib/x86_64-linux-gnu/cmake/vtk-9.6/patches/99/FindHDF5.cmake
/usr/share/cmake-4.3/Modules/FindHDF5.cmake
Is there a way to fix this in the VTK9 package ?
Best regards,
Manik Bhattacharjee.
-- System Information:
Debian Release: forky/sid
APT prefers unstable
APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)
Kernel: Linux 6.8.0-136-generic (SMP w/20 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE,
TAINT_UNSIGNED_MODULE
Locale: LANG=C, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: unable to detect
Versions of packages vtk9 depends on:
ii libc6 2.43-5
ii libgcc-s1 16.2.0-2
ii libstdc++6 16.2.0-2
ii libvtk9.6 9.6.2+dfsg1-5
vtk9 recommends no packages.
Versions of packages vtk9 suggests:
pn vtk9-doc <none>
pn vtk9-examples <none>
-- no debconf information
--- End Message ---
--- Begin Message ---
Source: vtk9
Source-Version: 9.6.2+dfsg1-6
Done: Dominique Belhachemi <[email protected]>
We believe that the bug you reported is fixed in the latest version of
vtk9, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Dominique Belhachemi <[email protected]> (supplier of updated vtk9 package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sat, 12 Sep 2026 09:35:02 -0400
Source: vtk9
Architecture: source
Version: 9.6.2+dfsg1-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers
<[email protected]>
Changed-By: Dominique Belhachemi <[email protected]>
Closes: 1147167
Changes:
vtk9 (9.6.2+dfsg1-6) unstable; urgency=medium
.
* Team upload.
* Drop unused 121_add_support_for_loong64.patch
* Do not install VTK's bundled FindHDF5.cmake (Closes: #1147167)
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