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vtk: 9.2.6 -> 9.4.2#385080

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bcdarwin wants to merge 8 commits intoNixOS:masterfrom
bcdarwin:vtk-9.4
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vtk: 9.2.6 -> 9.4.2#385080
bcdarwin wants to merge 8 commits intoNixOS:masterfrom
bcdarwin:vtk-9.4

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@bcdarwin bcdarwin commented Feb 25, 2025

A previous attempt at upgrading to VTK 9.3.x (#354855) seems stalled, so we may as well try updating to latest and pinning breaking packages to the previous nixpkgs version (9.2.6). Also replaces #370734 which is also stalled (and does not pin 9.2.6).

Note python3Packages.vtk is unfortunately one of the pinned packages due to e.g. pyvista although I did not try very hard to lift this.

@MatthewCroughan @wegank @emilazy

Things done

  • Built on platform(s)
    • x86_64-linux
    • aarch64-linux
    • x86_64-darwin
    • aarch64-darwin
  • For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)
    • sandbox = relaxed
    • sandbox = true
  • Tested, as applicable:
  • Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
  • Tested basic functionality of all binary files (usually in ./result/bin/)
  • 25.05 Release Notes (or backporting 24.11 and 25.05 Release notes)
    • (Package updates) Added a release notes entry if the change is major or breaking
    • (Module updates) Added a release notes entry if the change is significant
    • (Module addition) Added a release notes entry if adding a new NixOS module
  • Fits CONTRIBUTING.md.

Add a 👍 reaction to pull requests you find important.

@github-actions github-actions bot added 6.topic: python Python is a high-level, general-purpose programming language. 10.rebuild-darwin: 11-100 This PR causes between 11 and 100 packages to rebuild on Darwin. 10.rebuild-linux: 101-500 This PR causes between 101 and 500 packages to rebuild on Linux. labels Feb 25, 2025
@wegank wegank mentioned this pull request Mar 21, 2025
13 tasks
@wegank wegank added the 2.status: merge conflict This PR has merge conflicts with the target branch label Apr 2, 2025
@ofborg ofborg bot removed the 2.status: merge conflict This PR has merge conflicts with the target branch label Apr 25, 2025
@bcdarwin bcdarwin changed the title vtk: 9.2.6 -> 9.4.1 vtk: 9.2.6 -> 9.4.2 Apr 25, 2025
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nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 385080


x86_64-linux

⏩ 7 packages marked as broken and skipped:
  • python312Packages.pydicom-seg
  • python312Packages.pydicom-seg.dist
  • python313Packages.pydicom-seg
  • python313Packages.pydicom-seg.dist
  • python313Packages.pyvista
  • python313Packages.pyvista.dist
  • rtabmap
❌ 7 packages failed to build:
  • elmerfem
  • mirtk
  • otb
  • python312Packages.pyotb
  • python312Packages.pyotb.dist
  • python313Packages.pyotb
  • python313Packages.pyotb.dist
✅ 185 packages built:
  • ants
  • appcsxcad
  • c3d
  • cloudcompare
  • csxcad
  • elastix
  • exhibit
  • expliot
  • expliot.dist
  • ezminc
  • f3d
  • f3d.man
  • f3d_egl
  • f3d_egl.man
  • gdcm
  • 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)
  • mrtrix
  • octavePackages.dicom
  • openems
  • 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.f3d_egl
  • python312Packages.f3d_egl.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.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.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.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.f3d_egl
  • python313Packages.f3d_egl.man
  • python313Packages.fslpy
  • python313Packages.fslpy.dist
  • python313Packages.gdcm
  • python313Packages.highdicom
  • python313Packages.highdicom.dist
  • python313Packages.intensity-normalization
  • python313Packages.intensity-normalization.dist
  • python313Packages.itk
  • 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.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.pyradiomics
  • python313Packages.pyradiomics.dist
  • python313Packages.python-csxcad
  • python313Packages.python-csxcad.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.xnatpy
  • python313Packages.xnatpy.dist
  • simpleitk
  • therion
  • vtk (vtk_9)
  • vtkWithQt5 (vtk_9_withQt5)
  • vtk_9_2
  • vtk_9_egl

@bcdarwin bcdarwin marked this pull request as ready for review April 27, 2025 18:13
@nix-owners nix-owners bot requested review from Wulfsta, natsukium and tfmoraes April 27, 2025 18:14
@bcdarwin
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nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 385080


x86_64-linux

⏩ 7 packages marked as broken and skipped:
  • python312Packages.pydicom-seg
  • python312Packages.pydicom-seg.dist
  • python313Packages.pydicom-seg
  • python313Packages.pydicom-seg.dist
  • python313Packages.pyvista
  • python313Packages.pyvista.dist
  • rtabmap
❌ 5 packages failed to build:
  • otb
  • python312Packages.pyotb
  • python312Packages.pyotb.dist
  • python313Packages.pyotb
  • python313Packages.pyotb.dist
✅ 187 packages built:
  • ants
  • appcsxcad
  • c3d
  • cloudcompare
  • csxcad
  • elastix
  • elmerfem
  • exhibit
  • expliot
  • expliot.dist
  • ezminc
  • f3d
  • f3d.man
  • f3d_egl
  • f3d_egl.man
  • gdcm
  • 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
  • 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.f3d_egl
  • python312Packages.f3d_egl.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.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.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.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.f3d_egl
  • python313Packages.f3d_egl.man
  • python313Packages.fslpy
  • python313Packages.fslpy.dist
  • python313Packages.gdcm
  • python313Packages.highdicom
  • python313Packages.highdicom.dist
  • python313Packages.intensity-normalization
  • python313Packages.intensity-normalization.dist
  • python313Packages.itk
  • 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.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.pyradiomics
  • python313Packages.pyradiomics.dist
  • python313Packages.python-csxcad
  • python313Packages.python-csxcad.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.xnatpy
  • python313Packages.xnatpy.dist
  • simpleitk
  • therion
  • vtk (vtk_9)
  • vtkWithQt5 (vtk_9_withQt5)
  • vtk_9_2
  • vtk_9_egl

@bcdarwin
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Ready to go on Linux (Darwin may be another story).

@nix-owners nix-owners bot requested a review from daspk04 April 28, 2025 14:32
@bcdarwin bcdarwin mentioned this pull request Apr 28, 2025
13 tasks
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daspk04 commented Apr 28, 2025

Hi @bcdarwin !

Thanks for the update.

I think the otb package is failing possibly because it still replies on a modified version of ITK i.e 5.3.0. However I would assume VTK version 9.4.2 isn't compatible with it.

Can we add vtk_9_2 to the override as well ? here

@bcdarwin
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Hi @bcdarwin !

Thanks for the update.

I think the otb package is failing possibly because it still replies on a modified version of ITK i.e 5.3.0. However I would assume VTK version 9.4.2 isn't compatible with it.

Can we add vtk_9_2 to the override as well ? here

It should be fixed by the latest commit which adds -fpermissive - I'll re-run nixpkgs-review now.

@bcdarwin
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nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 385080


x86_64-linux

⏩ 7 packages marked as broken and skipped:
  • python312Packages.pydicom-seg
  • python312Packages.pydicom-seg.dist
  • python313Packages.pydicom-seg
  • python313Packages.pydicom-seg.dist
  • python313Packages.pyvista
  • python313Packages.pyvista.dist
  • rtabmap
✅ 192 packages built:
  • ants
  • appcsxcad
  • c3d
  • cloudcompare
  • csxcad
  • elastix
  • elmerfem
  • exhibit
  • expliot
  • expliot.dist
  • ezminc
  • f3d
  • f3d.man
  • f3d_egl
  • f3d_egl.man
  • gdcm
  • 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
  • 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.f3d_egl
  • python312Packages.f3d_egl.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.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.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.f3d_egl
  • python313Packages.f3d_egl.man
  • python313Packages.fslpy
  • python313Packages.fslpy.dist
  • python313Packages.gdcm
  • python313Packages.highdicom
  • python313Packages.highdicom.dist
  • python313Packages.intensity-normalization
  • python313Packages.intensity-normalization.dist
  • python313Packages.itk
  • 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.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.simpleitk
  • python313Packages.simpleitk.dist
  • python313Packages.templateflow
  • python313Packages.templateflow.dist
  • python313Packages.torchio
  • python313Packages.torchio.dist
  • python313Packages.trx-python
  • python313Packages.trx-python.dist
  • python313Packages.vtk
  • python313Packages.xnatpy
  • python313Packages.xnatpy.dist
  • simpleitk
  • therion
  • vtk (vtk_9)
  • vtkWithQt5 (vtk_9_withQt5)
  • vtk_9_2
  • vtk_9_egl

@pbsds
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pbsds commented May 2, 2025

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 385080


aarch64-darwin

⏩ 5 packages marked as broken and skipped:
  • c3d
  • python312Packages.mayavi
  • python312Packages.mayavi.dist
  • python313Packages.pyvista
  • python313Packages.pyvista.dist
❌ 25 packages failed to build:
  • ants
  • elmerfem
  • f3d
  • gdcm
  • itk (itk_5)
  • itk_5_2
  • octavePackages.dicom
  • pcl
  • python312Packages.f3d
  • python312Packages.gdcm
  • 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.vtk
  • therion
  • vtk (vtk_9)
  • vtkWithQt5 (vtk_9_withQt5)
✅ 1 package built:
  • vtk_9_2
vtk-qvtk-aarch64-darwin> /tmp/nix-build-vtk-qvtk-9.4.2.drv-0/VTK-9.4.2/ThirdParty/libxml2/vtklibxml2/dict.c:970:17: error: call to undeclared function 'getentropy'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
vtk-qvtk-aarch64-darwin>   970 |             if (getentropy(globalRngState, sizeof(globalRngState)) == 0)
vtk-qvtk-aarch64-darwin>       |                 ^

@bcdarwin
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bcdarwin commented May 5, 2025

So, the error on Darwin comes from the vendored copy of libxml2 using getentropy without including <sys/random.h>. However, trying to unvendor libxml2 seemingly doesn't have any effect even though -DVTK_MODULE_USE_EXTERNAL_vtklibxml2 is accepted by cmake without producing an unused variable warning.

@qbisi
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qbisi commented May 10, 2025

generated binary vtkProbeOpenGLVersion in vtk 9.4.2 will fail to find libGL.so unless export LD_LIBRARY_PATH=${lib.getLib ligGL}/lib
we need to patchelf on some .so file.

@qbisi
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qbisi commented May 11, 2025

This patch will work

diff --git a/pkgs/development/libraries/vtk/generic.nix b/pkgs/development/libraries/vtk/generic.nix
index 60b7ae238b83..c9a8f7911a2a 100644
--- a/pkgs/development/libraries/vtk/generic.nix
+++ b/pkgs/development/libraries/vtk/generic.nix
@@ -135,6 +135,10 @@ stdenv.mkDerivation {
       --subst-var-by VTK_VER "${version}"
   '';
 
+  postFixup = optionalString stdenv.hostPlatform.isLinux ''
+    patchelf --add-rpath ${lib.getLib libGL}/lib $out/lib/libvtkglad.so
+  '';
+
   meta = with lib; {
     description = "Open source libraries for 3D computer graphics, image processing and visualization";
     homepage = "https://www.vtk.org/";

@wegank wegank added the 2.status: merge conflict This PR has merge conflicts with the target branch label Jun 9, 2025
@wegank
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wegank commented Jul 29, 2025

Superseded by #417613.

@wegank wegank closed this Jul 29, 2025
@bcdarwin bcdarwin deleted the vtk-9.4 branch November 10, 2025 20:56
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2.status: merge conflict This PR has merge conflicts with the target branch 6.topic: python Python is a high-level, general-purpose programming language. 10.rebuild-darwin: 11-100 This PR causes between 11 and 100 packages to rebuild on Darwin. 10.rebuild-linux: 101-500 This PR causes between 101 and 500 packages to rebuild on Linux.

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6 participants