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----------- ENTRY ------------
----------- PHASE 2 ------------
Configuring CIP...
----------- DONE ------------
-- Configuring SEM CLI module: ConvertDicom
-- Configuring SEM CLI module: MergeParticleDataSets
-- Configuring SEM CLI module: RemoveParticlesFromParticlesDataSet
-- Configuring SEM CLI module: ExtractParticlesFromChestRegionChestType
-- Configuring SEM CLI module: GenerateOtsuLungCast
-- Configuring SEM CLI module: GenerateAtlasConvexHull
-- Configuring SEM CLI module: RegisterLungAtlas
-- Configuring SEM CLI module: ResampleLabelMap
-- Configuring SEM CLI module: RescaleLabelMap
-- Configuring CIP
-- Configuring SEM CLI module: ResampleCT2D
-- Configuring CIP
-- Configuring SEM CLI module: ResampleCT3D
-- Configuring CIP
-- Configuring SEM CLI module: ResampleCT
-- Configuring SEM CLI module: QualityControl
-- Configuring SEM CLI module: RemoveChestTypeFromLabelMapUsingParticles
-- Configuring SEM CLI module: SegmentLungLobes
-- Configuring SEM CLI module: ReadDicomWriteTags
-- Configuring SEM CLI module: SplitLeftLungRightLung
-- Configuring SEM CLI module: ExtractChestLabelMap
-- Configuring SEM CLI module: LabelParticlesByChestRegionChestType
-- Configuring SEM CLI module: GenerateStenciledLabelMapFromParticles
-- Configuring SEM CLI module: GenerateDistanceMapFromLabelMap
-- Configuring SEM CLI module: FilterVesselParticleData
-- Configuring SEM CLI module: FilterAirwayParticleData
-- Configuring SEM CLI module: ScourParticleData
-- Configuring SEM CLI module: ReadNRRDsWriteVTK
-- Configuring SEM CLI module: ComputeCrossSectionalArea
-- Configuring SEM CLI module: ComputeIntensityStatistics
-- Configuring SEM CLI module: FilterFissureParticleData
-- Configuring SEM CLI module: GenerateLobeSurfaceModels
-- Configuring SEM CLI module: ClassifyFissureParticles
-- Configuring SEM CLI module: CropLung
-- Configuring SEM CLI module: GenerateModel
-- Configuring SEM CLI module: GenerateImageSubVolumes
-- Configuring SEM CLI module: GenerateMedianFilteredImage
-- Configuring SEM CLI module: EvaluateLungLobeSegmentationResults
-- Configuring SEM CLI module: ConvertLabelMapValueToChestRegionChestType
-- Configuring SEM CLI module: GenerateRegionHistogramsAndParenchymaPhenotypes
-- Configuring SEM CLI module: ComputeDistanceMap
-- Configuring SEM CLI module: TransferFieldDataToFromPointData
-- Configuring SEM CLI module: PerturbParticles
-- Configuring SEM CLI module: ReadWriteRegionAndTypePoints
-- Configuring SEM CLI module: PerformMorphological
-- Configuring SEM CLI module: GenerateOverlayImages
-- Configuring SEM CLI module: GetTransformationSimilarityMetric3D
-- Configuring SEM CLI module: GetTransformationSimilarityMetric2D
-- Configuring SEM CLI module: GetTransformationSimilarityMetric
-- Configuring SEM CLI module: GetTransformationKappa2D
-- Configuring SEM CLI module: GetTransformationKappa
-- Configuring SEM CLI module: ReadWriteImageData
-- Configuring SEM CLI module: GetStructuresInLabelMap
-- Configuring SEM CLI module: GeneratePartialLungLabelMap
-- Configuring SEM CLI module: ReadVidaWriteCIP
-- Configuring SEM CLI module: RegisterLabelMaps
-- Configuring SEM CLI module: RegisterCT
-- Configuring SEM CLI module: RegisterCT2D
-- Configuring SEM CLI module: MergeChestLabelMaps
-- Configuring SEM CLI module: MaskOutLabelMapStructures
-- Configuring SEM CLI module: ComputeFeatureStrength
-- Configuring SEM CLI module: LabelMapFromRegionAndTypePoints
-- Configuring SEM CLI module: GenerateSimpleLungMask
-- Configuring SEM CLI module: GenerateBinaryThinning3D
-- Configuring SEM CLI module: ConvertChestRegionChestTypeToLabelMapValue
-- Configuring SEM CLI module: FilterConnectedComponents
-- Configuring SEM CLI module: EnhanceFissuresInImage
-- Configuring SEM CLI module: ComputeFissureFeatureVectors
-- Configuring SEM CLI module: FitLobeSurfaceModelsToParticleData
-- Configuring SEM CLI module: GenerateLesionSegmentation
-- Configuring SEM CLI module: RemapLabelMap
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ec2-user/Projects/CIP-master-build/CIP-build

Build Log line 1122

-- Configuring SEM CLI module: ComputeFissureFeatureVectors
-- Configuring SEM CLI module: FitLobeSurfaceModelsToParticleData
-- Configuring SEM CLI module: GenerateLesionSegmentation
-- Configuring SEM CLI module: RemapLabelMap
-- Configuring done
-- Generating done
-- Build files have been written to: /.../CIP-master-build/CIP-build
[ 87%] Performing forcebuild step for 'CIP'
[ 89%] Performing build step for 'CIP'
[  0%] Building CXX object Utilities/CMakeFiles/CIPUtilities.dir/VTK/vtkImageResliceWithPlane.cxx.o

/.../CIP-master/Utilities/VTK/vtkImageResliceWithPlane.cxx:31:27: fatal error: vtkNRRDReader.h: No such file or directory

 #include "vtkNRRDReader.h"
                           ^
compilation terminated.
Linking CXX static library /.../CIP-master-build/lib/libCIPUtilities.a

/usr/bin/ar: CMakeFiles/CIPUtilities.dir/VTK/vtkImageResliceWithPlane.cxx.o: No such file or directory

[  8%] Built target CIPUtilities
[ 14%] Built target CIPCommon
[ 15%] Built target ChestConventions
[ 16%] Built target CIPIO
running build_ext
skipping '/.../CIP-master/cip_python/wrap_ChestConventions.cpp' Cython extension (up-to-date)
[ 16%] Built target CIP_PYTHON

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `Common/Testing/cipHelperTEST'.  Stop.

[ 16%] Built target cipHelperTEST

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `Common/Testing/cipLobeSurfaceModelTEST'.  Stop.

[ 17%] Built target cipLobeSurfaceModelTEST

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `Common/Testing/cipNelderMeadSimplexOptimizerTEST'.  Stop.

[ 17%] Built target cipNelderMeadSimplexOptimizerTEST

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `Common/Testing/itkCIPExtractChestLabelMapImageFilterTEST'.  Stop.

[ 17%] Built target itkCIPExtractChestLabelMapImageFilterTEST

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `Common/Testing/itkCIPMergeChestLabelMapsImageFilterTEST'.  Stop.

[ 18%] Built target itkCIPMergeChestLabelMapsImageFilterTEST

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `IO/Testing/cipChestRegionChestTypeLocationsIOTEST'.  Stop.

[ 19%] Built target cipChestRegionChestTypeLocationsIOTEST

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `IO/Testing/cipLobeSurfaceModelIOTEST'.  Stop.

[ 19%] Built target cipLobeSurfaceModelIOTEST
[ 20%] Built target ConvertDicomLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/ConvertDicom'.  Stop.

[ 20%] Built target ConvertDicom

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/ConvertDicomTest'.  Stop.

[ 20%] Built target ConvertDicomTest
[ 20%] Built target MergeParticleDataSetsLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/MergeParticleDataSets'.  Stop.

[ 20%] Built target MergeParticleDataSets

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/MergeParticleDataSetsTest'.  Stop.

[ 21%] Built target MergeParticleDataSetsTest
[ 21%] Built target RemoveParticlesFromParticlesDataSetLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/RemoveParticlesFromParticlesDataSet'.  Stop.

[ 22%] Built target RemoveParticlesFromParticlesDataSet

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/RemoveParticlesFromParticlesDataSetTest'.  Stop.

[ 23%] Built target RemoveParticlesFromParticlesDataSetTest
[ 24%] Built target ExtractParticlesFromChestRegionChestTypeLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/ExtractParticlesFromChestRegionChestType'.  Stop.

[ 24%] Built target ExtractParticlesFromChestRegionChestType

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/ExtractParticlesFromChestRegionChestTypeTest'.  Stop.

[ 24%] Built target ExtractParticlesFromChestRegionChestTypeTest
[ 24%] Built target GenerateOtsuLungCastLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/GenerateOtsuLungCast'.  Stop.

[ 25%] Built target GenerateOtsuLungCast

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/GenerateOtsuLungCastTest'.  Stop.

[ 26%] Built target GenerateOtsuLungCastTest
[ 27%] Built target GenerateAtlasConvexHullLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/GenerateAtlasConvexHull'.  Stop.

[ 27%] Built target GenerateAtlasConvexHull

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/GenerateAtlasConvexHullTest'.  Stop.

[ 27%] Built target GenerateAtlasConvexHullTest
[ 28%] Built target RegisterLungAtlasLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/RegisterLungAtlas'.  Stop.

[ 28%] Built target RegisterLungAtlas

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/RegisterLungAtlasTest'.  Stop.

[ 28%] Built target RegisterLungAtlasTest
[ 28%] Built target ResampleLabelMapLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/ResampleLabelMap'.  Stop.

[ 29%] Built target ResampleLabelMap

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/ResampleLabelMapTest'.  Stop.

[ 29%] Built target ResampleLabelMapTest
[ 29%] Built target RescaleLabelMapLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/RescaleLabelMap'.  Stop.

[ 30%] Built target RescaleLabelMap

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/RescaleLabelMapTest'.  Stop.

[ 31%] Built target RescaleLabelMapTest
[ 32%] Built target ResampleCT2DLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/ResampleCT2D'.  Stop.

[ 32%] Built target ResampleCT2D

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/ResampleCT2DTest'.  Stop.

[ 32%] Built target ResampleCT2DTest
[ 33%] Built target ResampleCT3DLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/ResampleCT3D'.  Stop.

[ 33%] Built target ResampleCT3D

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/ResampleCT3DTest'.  Stop.

[ 33%] Built target ResampleCT3DTest
[ 34%] Built target ResampleCTLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/ResampleCT'.  Stop.

[ 34%] Built target ResampleCT

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/ResampleCTTest'.  Stop.

[ 34%] Built target ResampleCTTest
[ 35%] Built target QualityControlLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/QualityControl'.  Stop.

[ 35%] Built target QualityControl

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/QualityControlTest'.  Stop.

[ 35%] Built target QualityControlTest
[ 35%] Built target RemoveChestTypeFromLabelMapUsingParticlesLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/RemoveChestTypeFromLabelMapUsingParticles'.  Stop.

[ 36%] Built target RemoveChestTypeFromLabelMapUsingParticles

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/RemoveChestTypeFromLabelMapUsingParticlesTest'.  Stop.

[ 36%] Built target RemoveChestTypeFromLabelMapUsingParticlesTest
[ 37%] Built target SegmentLungLobesLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/SegmentLungLobes'.  Stop.

[ 37%] Built target SegmentLungLobes

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/SegmentLungLobesTest'.  Stop.

[ 37%] Built target SegmentLungLobesTest
[ 37%] Built target ReadDicomWriteTagsLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/ReadDicomWriteTags'.  Stop.

[ 38%] Built target ReadDicomWriteTags

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/ReadDicomWriteTagsTest'.  Stop.

[ 39%] Built target ReadDicomWriteTagsTest
[ 40%] Built target SplitLeftLungRightLungLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/SplitLeftLungRightLung'.  Stop.

[ 40%] Built target SplitLeftLungRightLung

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/SplitLeftLungRightLungTest'.  Stop.

[ 40%] Built target SplitLeftLungRightLungTest
[ 41%] Built target ExtractChestLabelMapLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/ExtractChestLabelMap'.  Stop.

[ 41%] Built target ExtractChestLabelMap

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/ExtractChestLabelMapTest'.  Stop.

[ 41%] Built target ExtractChestLabelMapTest
[ 42%] Built target LabelParticlesByChestRegionChestTypeLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/LabelParticlesByChestRegionChestType'.  Stop.

[ 42%] Built target LabelParticlesByChestRegionChestType

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/LabelParticlesByChestRegionChestTypeTest'.  Stop.

[ 42%] Built target LabelParticlesByChestRegionChestTypeTest
[ 42%] Built target GenerateStenciledLabelMapFromParticlesLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/GenerateStenciledLabelMapFromParticles'.  Stop.

[ 43%] Built target GenerateStenciledLabelMapFromParticles

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/GenerateStenciledLabelMapFromParticlesTest'.  Stop.

[ 44%] Built target GenerateStenciledLabelMapFromParticlesTest
[ 45%] Built target GenerateDistanceMapFromLabelMapLib

gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/GenerateDistanceMapFromLabelMap'.  Stop.

[ 45%] Built target GenerateDistanceMapFromLabelMap
gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/GenerateDistanceMapFromLabelMapTest'.  Stop.
[ 45%] Built target GenerateDistanceMapFromLabelMapTest
[ 45%] Built target FilterVesselParticleDataLib
gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/FilterVesselParticleData'.  Stop.
[ 46%] Built target FilterVesselParticleData
gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `CommandLineTools/Testing/bin/FilterVesselParticleDataTest'.  Stop.
[ 46%] Built target FilterVesselParticleDataTest
[ 46%] Built target FilterAirwayParticleDataLib
gmake[5]: *** No rule to make target `/.../CIP-master-build/lib/libCIPUtilities.a', needed by `bin/FilterAirwayParticleData'.  Stop.
The maximum number of reported warnings or errors has been reached!!!

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