vtk: 9.2.6 -> 9.4.2 by qbisi · Pull Request #407910 · NixOS/nixpkgs

qbisi · 2025-05-17T12:10:09Z

The vtk packages has been outdated for a while since upgrading the vtk packages may broke lots of package depends on it.
Also, the current vtk package recipe is not tested, we are not sure if updating vtk source to 9.4.2 also works fine at runtime.

This pr add vtk 9.4.2 that has been tested/fixed on x86-64-linux platform, it works fine with downstream pyvsita on both x86-64-linux and aarch64-darwin platform.

The check depends on the newly created hooks headlessDIsplayHook that can be reused by downstream pyvista* packages in nativeCheckInputs.

added 2025-05-19

the vtk-config.cmake requires nearly all its buildInputs as propagatedBuildInputs, for downstream package maintainers that use vtk as buildInputs, please check your buildInputs, some maybe required by the vtk-config.cmake and they are now propagated by vtk, so you should remove thouse deplicated buildInputs. e.g.

expat
libjpeg
utf8cpp
...

Things done

Add a 👍 reaction to pull requests you find important.

qbisi · 2025-05-25T12:25:40Z

`nixpkgs-review` result

Generated using nixpkgs-review-gha

Command: nixpkgs-review pr 407910

Logs: https://github.com/qbisi/nixpkgs-review-gha/actions/runs/15235919412

`aarch64-darwin` (sandbox = false)

⏩ 1 package marked as broken and skipped:

c3d

❌ 1 package failed to build:

therion

✅ 35 packages built:

ants
elmerfem
f3d
gdcm
itk (itk_5)
itk_5_2
octavePackages.dicom
pcl
python312Packages.f3d
python312Packages.gdcm
python312Packages.mayavi
python312Packages.mayavi.dist
python312Packages.pymatgen
python312Packages.pymatgen.dist
python312Packages.pyvista
python312Packages.pyvista.dist
python312Packages.sfepy
python312Packages.sfepy.dist
python312Packages.sumo
python312Packages.sumo.dist
python312Packages.vtk
python312Packages.wslink
python312Packages.wslink.dist
python313Packages.f3d
python313Packages.gdcm
python313Packages.mayavi
python313Packages.mayavi.dist
python313Packages.pyvista
python313Packages.pyvista.dist
python313Packages.vtk
python313Packages.wslink
python313Packages.wslink.dist
vtk (vtk_9)
vtkWithQt5 (vtk_9_withQt5)
vtkWithQt6 (vtk_9_withQt6)

qbisi · 2025-05-25T15:55:13Z

Build of Therion on aarch64-darwin is a known failure. https://hydra.nixos.org/build/298267154.
Some recent commits are downstream bug related and can be divided to individual pr.

Hi, @tfmoraes still active in maintaining these related packages?

qbisi · 2025-05-25T16:29:25Z

`nixpkgs-review` result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 407910

`x86_64-linux`

⏩ 4 packages marked as broken and skipped:

python312Packages.pydicom-seg
python312Packages.pydicom-seg.dist
python313Packages.pydicom-seg
python313Packages.pydicom-seg.dist

✅ 204 packages built:

ants
appcsxcad
blender
blender-hip
blendfarm
c3d
cloudcompare
csxcad
elastix
elmerfem
exhibit
expliot
expliot.dist
ezminc
f3d
f3d.man
freecad
freecad-qt6
freecad-wayland
gdcm
headlessDisplayHook
intensity-normalization (python312Packages.intensity-normalization)
intensity-normalization.dist (python312Packages.intensity-normalization.dist)
itk (itk_5)
itk_5_2
libsForQt5.qcsxcad (plasma5Packages.qcsxcad)
libsForQt5.qcsxcad.dev (plasma5Packages.qcsxcad.dev)
mirtk
mrtrix
octavePackages.dicom
openems
openusd
otb
pcl
python312Packages.dcmstack
python312Packages.dcmstack.dist
python312Packages.deid
python312Packages.deid.dist
python312Packages.dicom-numpy
python312Packages.dicom-numpy.dist
python312Packages.dicom2nifti
python312Packages.dicom2nifti.dist
python312Packages.dicomweb-client
python312Packages.dicomweb-client.dist
python312Packages.dipy
python312Packages.dipy.dist
python312Packages.f3d
python312Packages.f3d.man
python312Packages.fslpy
python312Packages.fslpy.dist
python312Packages.gdcm
python312Packages.heudiconv
python312Packages.heudiconv.dist
python312Packages.highdicom
python312Packages.highdicom.dist
python312Packages.itk
python312Packages.mayavi
python312Packages.mayavi.dist
python312Packages.medpy
python312Packages.medpy.dist
python312Packages.medvol
python312Packages.medvol.dist
python312Packages.napari-nifti
python312Packages.napari-nifti.dist
python312Packages.nibabel
python312Packages.nibabel.dist
python312Packages.nilearn
python312Packages.nilearn.dist
python312Packages.nipy
python312Packages.nipy.dist
python312Packages.nipype
python312Packages.nipype.dist
python312Packages.nitime
python312Packages.nitime.dist
python312Packages.nitransforms
python312Packages.nitransforms.dist
python312Packages.niworkflows
python312Packages.niworkflows.dist
python312Packages.openusd
python312Packages.pybids
python312Packages.pybids.dist
python312Packages.pydicom
python312Packages.pydicom.dist
python312Packages.pylibjpeg
python312Packages.pylibjpeg-openjpeg
python312Packages.pylibjpeg-openjpeg.dist
python312Packages.pylibjpeg.dist
python312Packages.pymatgen
python312Packages.pymatgen.dist
python312Packages.pymedio
python312Packages.pymedio.dist
python312Packages.pynetdicom
python312Packages.pynetdicom.dist
python312Packages.pyorthanc
python312Packages.pyorthanc.dist
python312Packages.pyotb
python312Packages.pyotb.dist
python312Packages.pyradiomics
python312Packages.pyradiomics.dist
python312Packages.python-csxcad
python312Packages.python-csxcad.dist
python312Packages.python-openems
python312Packages.python-openems.dist
python312Packages.pyvista
python312Packages.pyvista.dist
python312Packages.sfepy
python312Packages.sfepy.dist
python312Packages.simpleitk
python312Packages.simpleitk.dist
python312Packages.sumo
python312Packages.sumo.dist
python312Packages.templateflow
python312Packages.templateflow.dist
python312Packages.torchio
python312Packages.torchio.dist
python312Packages.trx-python
python312Packages.trx-python.dist
python312Packages.vtk
python312Packages.wslink
python312Packages.wslink.dist
python312Packages.xnatpy
python312Packages.xnatpy.dist
python313Packages.dcmstack
python313Packages.dcmstack.dist
python313Packages.deid
python313Packages.deid.dist
python313Packages.dicom-numpy
python313Packages.dicom-numpy.dist
python313Packages.dicom2nifti
python313Packages.dicom2nifti.dist
python313Packages.dicomweb-client
python313Packages.dicomweb-client.dist
python313Packages.dipy
python313Packages.dipy.dist
python313Packages.f3d
python313Packages.f3d.man
python313Packages.fslpy
python313Packages.fslpy.dist
python313Packages.gdcm
python313Packages.highdicom
python313Packages.highdicom.dist
python313Packages.intensity-normalization
python313Packages.intensity-normalization.dist
python313Packages.itk
python313Packages.mayavi
python313Packages.mayavi.dist
python313Packages.medpy
python313Packages.medpy.dist
python313Packages.medvol
python313Packages.medvol.dist
python313Packages.napari-nifti
python313Packages.napari-nifti.dist
python313Packages.nibabel
python313Packages.nibabel.dist
python313Packages.nilearn
python313Packages.nilearn.dist
python313Packages.nipy
python313Packages.nipy.dist
python313Packages.nitime
python313Packages.nitime.dist
python313Packages.nitransforms
python313Packages.nitransforms.dist
python313Packages.openusd
python313Packages.pybids
python313Packages.pybids.dist
python313Packages.pydicom
python313Packages.pydicom.dist
python313Packages.pylibjpeg
python313Packages.pylibjpeg-openjpeg
python313Packages.pylibjpeg-openjpeg.dist
python313Packages.pylibjpeg.dist
python313Packages.pymedio
python313Packages.pymedio.dist
python313Packages.pynetdicom
python313Packages.pynetdicom.dist
python313Packages.pyorthanc
python313Packages.pyorthanc.dist
python313Packages.pyotb
python313Packages.pyotb.dist
python313Packages.pyradiomics
python313Packages.pyradiomics.dist
python313Packages.python-csxcad
python313Packages.python-csxcad.dist
python313Packages.pyvista
python313Packages.pyvista.dist
python313Packages.simpleitk
python313Packages.simpleitk.dist
python313Packages.templateflow
python313Packages.templateflow.dist
python313Packages.torchio
python313Packages.torchio.dist
python313Packages.trx-python
python313Packages.trx-python.dist
python313Packages.vtk
python313Packages.wslink
python313Packages.wslink.dist
python313Packages.xnatpy
python313Packages.xnatpy.dist
rtabmap
simpleitk
therion
vtk (vtk_9)
vtkWithQt5 (vtk_9_withQt5)
vtkWithQt6 (vtk_9_withQt6)

qbisi · 2025-05-25T18:32:19Z

`nixpkgs-review` result

Generated using nixpkgs-review-gha

Command: nixpkgs-review pr 407910

Logs: https://github.com/qbisi/nixpkgs-review-gha/actions/runs/15239961501

`aarch64-darwin` (sandbox = true)

⏩ 1 package marked as broken and skipped:

c3d

❌ 33 packages failed to build:

ants
elmerfem
f3d
gdcm
itk (itk_5)
itk_5_2
octavePackages.dicom
pcl
python312Packages.f3d
python312Packages.gdcm
python312Packages.mayavi
python312Packages.mayavi.dist
python312Packages.pymatgen
python312Packages.pymatgen.dist
python312Packages.pyvista
python312Packages.pyvista.dist
python312Packages.sfepy
python312Packages.sfepy.dist
python312Packages.sumo
python312Packages.sumo.dist
python312Packages.vtk
python313Packages.f3d
python313Packages.gdcm
python313Packages.mayavi
python313Packages.mayavi.dist
python313Packages.openusd
python313Packages.pyvista
python313Packages.pyvista.dist
python313Packages.vtk
therion
vtk (vtk_9)
vtkWithQt5 (vtk_9_withQt5)
vtkWithQt6 (vtk_9_withQt6)

✅ 6 packages built:

openusd
python312Packages.openusd
python312Packages.wslink
python312Packages.wslink.dist
python313Packages.wslink
python313Packages.wslink.dist

Error logs: `aarch64-darwin`

python312Packages.vtk

/nix/store/rfng4494hxqxjgsamkcd01mzfdp2fwlh-libcxx-19.1.7-dev/include/c++/v1/strstream:233:7: note: 'istrstream' has been explicitly marked deprecated here
  233 | class _LIBCPP_DEPRECATED _LIBCPP_EXPORTED_FROM_ABI istrstream : public istream {
      |       ^
/nix/store/rfng4494hxqxjgsamkcd01mzfdp2fwlh-libcxx-19.1.7-dev/include/c++/v1/__config:688:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  688 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from /tmp/nix-build-vtk-9.4.2.drv-0/VTK-9.4.2/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfExprYacc.cxx:140:
In file included from /tmp/nix-build-vtk-9.4.2.drv-0/VTK-9.4.2/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfArray.h:28:
In file included from /tmp/nix-build-vtk-9.4.2.drv-0/VTK-9.4.2/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfDataDesc.h:28:
/tmp/nix-build-vtk-9.4.2.drv-0/VTK-9.4.2/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfObject.h:517:20: warning: 'istrstream' is deprecated [-Wdeprecated-declarations]
  517 | extern XDMF_EXPORT istrstream& XDMF_READ_STREAM64(istrstream& istr, XDMF_64_INT& i);
      |                    ^
/nix/store/rfng4494hxqxjgsamkcd01mzfdp2fwlh-libcxx-19.1.7-dev/include/c++/v1/strstream:233:7: note: 'istrstream' has been explicitly marked deprecated here
  233 | class _LIBCPP_DEPRECATED _LIBCPP_EXPORTED_FROM_ABI istrstream : public istream {
      |       ^
/nix/store/rfng4494hxqxjgsamkcd01mzfdp2fwlh-libcxx-19.1.7-dev/include/c++/v1/__config:688:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  688 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
2 warnings generated.
[  1%] Building CXX object ThirdParty/xdmf3/vtkxdmf3/core/CMakeFiles/vtkxdmfcore.dir/XdmfArray.cpp.o

python313Packages.openusd

[2532/4314] Building CXX object pxr/usd/usdUtils/CMakeFiles/usdUtils.dir/stageCache.cpp.o
[2533/4314] Building CXX object pxr/usd/usdUtils/CMakeFiles/usdUtils.dir/sparseValueWriter.cpp.o
[2534/4314] Building CXX object pxr/usd/usdUtils/CMakeFiles/usdUtils.dir/timeCodeRange.cpp.o
[2535/4314] Building CXX object pxr/usd/usdUtils/CMakeFiles/usdUtils.dir/stitch.cpp.o
[2536/4314] Generating moduleDeps.cpp
[2537/4314] Generating moduleDeps.cpp
[2538/4314] Generating moduleDeps.cpp
[2539/4314] Generating moduleDeps.cpp
[2540/4314] Building CXX object pxr/usd/usdUtils/CMakeFiles/usdUtils.dir/stitchClips.cpp.o
[2541/4314] Building CXX object pxr/usd/usdUtils/CMakeFiles/usdUtils.dir/usdzPackage.cpp.o
[2542/4314] Generating moduleDeps.cpp
[2543/4314] Building CXX object pxr/usd/usdVol/CMakeFiles/usdVol.dir/moduleDeps.cpp.o
[2544/4314] Building CXX object pxr/usd/usdVol/CMakeFiles/usdVol.dir/field3DAsset.cpp.o
[2545/4314] Building CXX object pxr/usd/usdVol/CMakeFiles/usdVol.dir/fieldAsset.cpp.o
[2546/4314] Building CXX object pxr/usd/usdVol/CMakeFiles/usdVol.dir/fieldBase.cpp.o
[2547/4314] Building CXX object pxr/usd/usdVol/CMakeFiles/usdVol.dir/tokens.cpp.o
[2548/4314] Building CXX object pxr/usd/usdLux/CMakeFiles/usdLux.dir/moduleDeps.cpp.o
[2549/4314] Building CXX object pxr/usd/usdVol/CMakeFiles/usdVol.dir/openVDBAsset.cpp.o
[2550/4314] Building CXX object pxr/usd/usdVol/CMakeFiles/usdVol.dir/volume.cpp.o
[2551/4314] Building CXX object pxr/usd/usdLux/CMakeFiles/usdLux.dir/blackbody.cpp.o

qbisi · 2025-07-10T23:43:46Z

Closed in favor of #417613

github-actions bot added the 6.topic: python Python is a high-level, general-purpose programming language. label May 17, 2025

nix-owners bot requested a review from natsukium May 17, 2025 12:11

qbisi force-pushed the vtk branch from 9ede68d to 20cd1ca Compare May 17, 2025 12:13

github-actions bot added 10.rebuild-darwin: 11-100 This PR causes between 11 and 100 packages to rebuild on Darwin. 10.rebuild-linux: 11-100 This PR causes between 11 and 100 packages to rebuild on Linux. labels May 17, 2025

qbisi force-pushed the vtk branch 4 times, most recently from 0030cde to bc4bc47 Compare May 17, 2025 12:40

qbisi changed the title ~~vtk_9_4: init at 9.4.2~~ vtk: 9.2.6 -> 9.4.2 May 17, 2025

github-actions bot added 10.rebuild-linux: 101-500 This PR causes between 101 and 500 packages to rebuild on Linux. and removed 10.rebuild-linux: 11-100 This PR causes between 11 and 100 packages to rebuild on Linux. labels May 17, 2025

qbisi force-pushed the vtk branch 3 times, most recently from d06b392 to 18f71f6 Compare May 17, 2025 17:46

nix-owners bot requested a review from tfmoraes May 17, 2025 17:49

qbisi force-pushed the vtk branch 2 times, most recently from 68f005b to 0997c73 Compare May 19, 2025 02:30

github-actions bot added the 8.has: maintainer-list (update) This PR changes `maintainers/maintainer-list.nix` label May 19, 2025

qbisi force-pushed the vtk branch 5 times, most recently from daa5271 to 9a8447f Compare May 19, 2025 10:47

github-actions bot removed the 8.has: maintainer-list (update) This PR changes `maintainers/maintainer-list.nix` label May 19, 2025

nix-owners bot requested a review from wegank May 19, 2025 10:52

qbisi force-pushed the vtk branch 3 times, most recently from 261b4c1 to 996b13b Compare May 19, 2025 21:24

nix-owners bot requested a review from Wulfsta May 19, 2025 21:31

qbisi added 12 commits May 25, 2025 09:36

vtk: move generic.nix to default.nix

d56dedd

headlessDisplayHook: init

f1c7e34

python3Packages.wslink: init at 2.3.3

b281736

vtk: 9.2.6 -> 9.4.2

20659ca

python313Packages.pyvista: unmark broken

b9b9dc8

elmerfem: unstable-2023-09-18 -> unstable-2025-05-19

b1bf72e

python3Packages.mayavi: 4.8.2 -> 4.8.3

4af82b7

f3d: build with EGL enabled vtk-9.4.2

a159b51

f3d: install default configuration files

a67b766

otb: include legacy vcl header file

ab61106

gdcm: 3.0.24 -> 3.0.25

74d5822

gdcm: use ctestCheckHook

5738219

qbisi force-pushed the vtk branch from c031908 to 5738219 Compare May 25, 2025 01:37

openusd: propagate dependencies OpenGL and X11

b6cfc64

qbisi force-pushed the vtk branch from 93ff868 to b6cfc64 Compare May 25, 2025 13:18

nix-owners bot requested review from ShaddyDC and gador May 25, 2025 13:25

This was referenced May 25, 2025

gdcm: 3.0.24 -> 3.0.25 #410841

Merged

python3Packages.mayavi: 4.8.2 -> 4.8.3 #410843

Merged

otb: include legacy vcl header file #410844

Merged

elmerfem: unstable-2023-09-18 -> 9.0-unstable-2025-05-25 #410847

Merged

qbisi mentioned this pull request Jun 7, 2025

openusd: propagate dependencies OpenGL #414827

Merged

13 tasks

wegank added the 2.status: merge conflict This PR has merge conflicts with the target branch label Jun 9, 2025

LordGrimmauld mentioned this pull request Jun 30, 2025

Freecad: fix build with vtk 9.5 #421276

Merged

13 tasks

qbisi closed this Jul 10, 2025

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