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gdcm: 3.0.24 -> 3.0.25#410841

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pbsds merged 2 commits intoNixOS:masterfrom
qbisi:gdcm
Jun 8, 2025
Merged

gdcm: 3.0.24 -> 3.0.25#410841
pbsds merged 2 commits intoNixOS:masterfrom
qbisi:gdcm

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@qbisi qbisi commented May 25, 2025

part of pr 407910

required for updating vtk.

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/)
  • Nixpkgs 25.11 Release Notes (or backporting 24.11 and 25.05 Nixpkgs Release notes)
    • (Package updates) Added a release notes entry if the change is major or breaking
  • NixOS 25.11 Release Notes (or backporting 24.11 and 25.05 NixOS Release notes)
    • (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.

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@github-actions github-actions bot added 10.rebuild-darwin: 1-10 This PR causes between 1 and 10 packages to rebuild on Darwin. 10.rebuild-linux: 11-100 This PR causes between 11 and 100 packages to rebuild on Linux. labels May 25, 2025
@nix-owners nix-owners bot requested a review from tfmoraes May 25, 2025 16:38
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qbisi commented Jun 5, 2025

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 410841
Commit: 6cffba31f094136e82d6923a50eb846134ec7562

x86_64-linux

❌ 5 packages failed to build:
  • otb
  • python312Packages.pyotb
  • python312Packages.pyotb.dist
  • python313Packages.pyotb
  • python313Packages.pyotb.dist
✅ 143 packages built:
  • ants
  • c3d
  • elastix
  • expliot
  • expliot.dist
  • ezminc
  • gdcm
  • intensity-normalization (python312Packages.intensity-normalization)
  • intensity-normalization.dist (python312Packages.intensity-normalization.dist)
  • itk (itk_5)
  • itk_5_2
  • mirtk
  • mrtrix
  • octavePackages.dicom
  • 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.fslpy
  • python312Packages.fslpy.dist
  • python312Packages.gdcm
  • python312Packages.heudiconv
  • python312Packages.heudiconv.dist
  • python312Packages.highdicom
  • python312Packages.highdicom.dist
  • python312Packages.itk
  • 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.pymedio
  • python312Packages.pymedio.dist
  • python312Packages.pynetdicom
  • python312Packages.pynetdicom.dist
  • python312Packages.pyorthanc
  • python312Packages.pyorthanc.dist
  • python312Packages.pyradiomics
  • python312Packages.pyradiomics.dist
  • python312Packages.simpleitk
  • python312Packages.simpleitk.dist
  • python312Packages.templateflow
  • python312Packages.templateflow.dist
  • python312Packages.torchio
  • python312Packages.torchio.dist
  • python312Packages.trx-python
  • python312Packages.trx-python.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.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.simpleitk
  • python313Packages.simpleitk.dist
  • python313Packages.templateflow
  • python313Packages.templateflow.dist
  • python313Packages.torchio
  • python313Packages.torchio.dist
  • python313Packages.trx-python
  • python313Packages.trx-python.dist
  • python313Packages.xnatpy
  • python313Packages.xnatpy.dist
  • simpleitk
Error logs: `x86_64-linux`
otb 
[ 34%] Linking CXX executable ../../../bin/OTBDEMHeaderTest1
[ 34%] Built target OTBSARCalibrationHeaderTest1
[ 34%] Built target OTBImageManipulationHeaderTest2
[ 34%] Built target OTBLabelMapHeaderTest1
[ 34%] Linking CXX executable ../../../bin/OTBDempsterShaferHeaderTest1
[ 34%] Built target OTBDEMHeaderTest1
[ 34%] Linking CXX executable ../../../bin/OTBConversionHeaderTest1
[ 34%] Linking CXX executable ../../../../bin/OTBCornerHeaderTest1
[ 34%] Linking CXX shared library ../../../../lib/libOTBOpticalCalibration.so
[ 34%] Built target OTBDempsterShaferHeaderTest1
[ 34%] Built target OTBOpticalCalibration
[ 34%] Built target OTBConversionHeaderTest1
[ 34%] Linking CXX executable ../../../bin/OTBVectorDataManipulationHeaderTest1
[ 34%] Built target OTBCornerHeaderTest1
[ 34%] Built target OTBVectorDataManipulationHeaderTest1
[ 34%] Linking CXX shared library ../../../../lib/libOTBProjection.so
[ 34%] Built target OTBProjection
[ 35%] Linking CXX shared library ../../../../../lib/libOTBImageIO.so
[ 35%] Built target OTBImageIO
make: *** [Makefile:166: all] Error 2

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pbsbot commented Jun 8, 2025

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 410841

x86_64-linux

✅ 148 packages built:
  • ants
  • c3d
  • elastix
  • expliot
  • expliot.dist
  • ezminc
  • gdcm
  • intensity-normalization (python312Packages.intensity-normalization)
  • intensity-normalization.dist (python312Packages.intensity-normalization.dist)
  • itk (itk_5)
  • itk_5_2
  • mirtk
  • mrtrix
  • octavePackages.dicom
  • otb
  • 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.fslpy
  • python312Packages.fslpy.dist
  • python312Packages.gdcm
  • python312Packages.heudiconv
  • python312Packages.heudiconv.dist
  • python312Packages.highdicom
  • python312Packages.highdicom.dist
  • python312Packages.itk
  • 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.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.simpleitk
  • python312Packages.simpleitk.dist
  • python312Packages.templateflow
  • python312Packages.templateflow.dist
  • python312Packages.torchio
  • python312Packages.torchio.dist
  • python312Packages.trx-python
  • python312Packages.trx-python.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.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.simpleitk
  • python313Packages.simpleitk.dist
  • python313Packages.templateflow
  • python313Packages.templateflow.dist
  • python313Packages.torchio
  • python313Packages.torchio.dist
  • python313Packages.trx-python
  • python313Packages.trx-python.dist
  • python313Packages.xnatpy
  • python313Packages.xnatpy.dist
  • simpleitk

@pbsds pbsds merged commit a81800c into NixOS:master Jun 8, 2025
17 of 18 checks passed
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10.rebuild-darwin: 1-10 This PR causes between 1 and 10 packages to rebuild on Darwin. 10.rebuild-linux: 11-100 This PR causes between 11 and 100 packages to rebuild on Linux.

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