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----------- ENTRY ------------
----------- PHASE 2 ------------
Configuring CIP...
ChestConv: ON
----------- 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: 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: ReadVTKWriteNRRDs
-- 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: FindPatchMatch
-- Configuring SEM CLI module: TransferRegionAndTypeIndicesToFromPoints
-- 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: 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: 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 SEM CLI module: GenerateNLMFilteredImage
-- Configuring SEM CLI module: ComputeAirwayWallFromParticles
-- Configuring SEM CLI module: RegionTypeLocationsToROIVolume
-- Configuring SEM CLI module: ExtractFissureBoundaryFromLobeMap
-- Configuring SEM CLI module: ExecuteSystemCommand
Wrapping ChestConventions with Python in /home/ec2-user/Projects/CIP-build/CIPPython-install/bin/python
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ec2-user/Projects/CIP-build/CIP-build

[ 98%] Built target ITKIOPNG
[ 98%] Built target ITKIOPNG-all
[ 98%] Built target ITKIORAW-all
[ 98%] Built target ITKIOSiemens
[ 98%] Built target ITKIOSiemens-all
[ 98%] Built target ITKIOStimulate
[ 98%] Built target ITKIOStimulate-all
[ 98%] Building CXX object Modules/IO/TransformBase/src/CMakeFiles/ITKIOTransformBase.dir/itkTransformFactoryBase.cxx.o
virtual memory exhausted: Cannot allocate memory
Linking CXX shared library ../../../../lib/libITKIOTransformBase-4.8.so

c++: error: CMakeFiles/ITKIOTransformBase.dir/itkTransformFactoryBase.cxx.o: No such file or directory

[ 98%] Built target ITKIOTransformBase
[ 98%] Built target ITKIOTransformBase-all

gmake[5]: *** No rule to make target `lib/libITKIOTransformBase-4.8.so.1', needed by `lib/libITKIOTransformHDF5-4.8.so.1'.  Stop.

[ 98%] Built target ITKIOTransformHDF5
[ 98%] Built target ITKIOTransformHDF5-all

gmake[5]: *** No rule to make target `lib/libITKIOTransformBase-4.8.so.1', needed by `lib/libITKIOTransformInsightLegacy-4.8.so.1'.  Stop.

[ 98%] Built target ITKIOTransformInsightLegacy
[ 98%] Built target ITKIOTransformInsightLegacy-all

gmake[5]: *** No rule to make target `lib/libITKIOTransformBase-4.8.so.1', needed by `lib/libITKIOTransformMatlab-4.8.so.1'.  Stop.

[ 98%] Built target ITKIOTransformMatlab
[ 98%] Built target ITKIOTransformMatlab-all
[ 98%] Built target ITKIOVTK
[ 98%] Built target ITKIOVTK-all
[ 98%] Built target ITKImageFusion-all
[ 98%] Built target ITKImageNoise-all
[ 98%] Built target ITKIntegratedTest-all
[ 98%] Built target ITKKLMRegionGrowing
[ 98%] Built target ITKKLMRegionGrowing-all
[ 98%] Built target ITKLabelVoting-all

[ 99%] Built target ITKOpenJPEG-all
[ 99%] Built target ITKQuadEdgeMeshFiltering-all
[ 99%] Built target ITKRegionGrowing-all
[ 99%] Built target ITKRegistrationMethodsv4-all
[ 99%] Built target ITKSpatialFunction-all
[ 99%] Built target ITKVTK
[ 99%] Built target ITKVTK-all
[ 99%] Built target ITKVoronoi-all
[ 99%] Built target ITKWatersheds
[ 99%] Built target ITKWatersheds-all

gmake[5]: *** No rule to make target `lib/libITKIOTransformHDF5-4.8.so.1', needed by `lib/libITKReview-4.8.so.1'.  Stop.

[100%] Built target ITKReview
[100%] Built target ITKReview-all
[100%] Built target itkTestDriver
[100%] Built target ITKTestKernel-all
[100%] Built target ITKVideoCore
[100%] Built target ITKVideoCore-all
[100%] Built target ITKVideoFiltering-all
[100%] Built target ITKVideoIO
[100%] Built target ITKVideoIO-all
[100%] Built target ITKVtkGlue

    from .Visitor import CythonTransform
  File "Cython/Compiler/Visitor.py", line 13, in init Cython.Compiler.Visitor (/home/ilan/minonda/conda-bld/work/Cython-0.23.4/Cython/Compiler/Visitor.c:19299)
  File "/.../CIP-build/CIPPython-install/lib/python2.7/site-packages/Cython/Compiler/Builtin.py", line 16, in <module>
    iter_next_utility_code = UtilityCode.load("IterNext", "ObjectHandling.c")
[ 16%] Built target CIP_PYTHON
  File "Cython/Compiler/Code.py", line 253, in Cython.Compiler.Code.UtilityCodeBase.load (/home/ilan/minonda/conda-bld/work/Cython-0.23.4/Cython/Compiler/Code.c:8385)
  File "Cython/Compiler/Code.py", line 177, in Cython.Compiler.Code.UtilityCodeBase.load_utilities_from_file (/home/ilan/minonda/conda-bld/work/Cython-0.23.4/Cython/Compiler/Code.c:6279)
  File "/.../CIP-build/CIPPython-install/lib/python2.7/site-packages/Cython/Utils.py", line 276, in open_source_file
    stream = io.open(source_filename, mode=mode,
AttributeError: 'module' object has no attribute 'open'

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `Common/Testing/cipHelperTEST'.  Stop.

[ 16%] Built target cipHelperTEST

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `Common/Testing/cipLobeSurfaceModelTEST'.  Stop.

[ 17%] Built target cipLobeSurfaceModelTEST

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `Common/Testing/cipNelderMeadSimplexOptimizerTEST'.  Stop.

[ 17%] Built target cipNelderMeadSimplexOptimizerTEST

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `Common/Testing/itkCIPExtractChestLabelMapImageFilterTEST'.  Stop.

[ 17%] Built target itkCIPExtractChestLabelMapImageFilterTEST

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `Common/Testing/itkCIPMergeChestLabelMapsImageFilterTEST'.  Stop.

[ 18%] Built target itkCIPMergeChestLabelMapsImageFilterTEST

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `IO/Testing/cipChestRegionChestTypeLocationsIOTEST'.  Stop.

[ 19%] Built target cipChestRegionChestTypeLocationsIOTEST

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `IO/Testing/cipGeometryTopologyDataIOTEST'.  Stop.

[ 19%] Built target cipGeometryTopologyDataIOTEST

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `IO/Testing/cipLobeSurfaceModelIOTEST'.  Stop.

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

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/ConvertDicom'.  Stop.

[ 20%] Built target ConvertDicom

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/ConvertDicomTest'.  Stop.

[ 20%] Built target ConvertDicomTest
[ 21%] Built target MergeParticleDataSetsLib

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/MergeParticleDataSets'.  Stop.

[ 21%] Built target MergeParticleDataSets

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/MergeParticleDataSetsTest'.  Stop.

[ 21%] Built target MergeParticleDataSetsTest
[ 22%] Built target RemoveParticlesFromParticlesDataSetLib

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/RemoveParticlesFromParticlesDataSet'.  Stop.

[ 22%] Built target RemoveParticlesFromParticlesDataSet

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/RemoveParticlesFromParticlesDataSetTest'.  Stop.

[ 22%] Built target RemoveParticlesFromParticlesDataSetTest
[ 23%] Built target ExtractParticlesFromChestRegionChestTypeLib

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/ExtractParticlesFromChestRegionChestType'.  Stop.

[ 23%] Built target ExtractParticlesFromChestRegionChestType

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/ExtractParticlesFromChestRegionChestTypeTest'.  Stop.

[ 23%] Built target ExtractParticlesFromChestRegionChestTypeTest
[ 24%] Built target GenerateOtsuLungCastLib

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/GenerateOtsuLungCast'.  Stop.

[ 24%] Built target GenerateOtsuLungCast

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/GenerateOtsuLungCastTest'.  Stop.

[ 24%] Built target GenerateOtsuLungCastTest
[ 25%] Built target GenerateAtlasConvexHullLib

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/GenerateAtlasConvexHull'.  Stop.

[ 25%] Built target GenerateAtlasConvexHull

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/GenerateAtlasConvexHullTest'.  Stop.

[ 25%] Built target GenerateAtlasConvexHullTest
[ 25%] Built target RegisterLungAtlasLib

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/RegisterLungAtlas'.  Stop.

[ 25%] Built target RegisterLungAtlas

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/RegisterLungAtlasTest'.  Stop.

[ 26%] Built target RegisterLungAtlasTest
[ 26%] Built target ResampleLabelMapLib

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/ResampleLabelMap'.  Stop.

[ 27%] Built target ResampleLabelMap

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/ResampleLabelMapTest'.  Stop.

[ 27%] Built target ResampleLabelMapTest
[ 27%] Built target RescaleLabelMapLib

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/RescaleLabelMap'.  Stop.

[ 28%] Built target RescaleLabelMap

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/RescaleLabelMapTest'.  Stop.

[ 29%] Built target RescaleLabelMapTest
[ 30%] Built target ResampleCTLib

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/ResampleCT'.  Stop.

[ 30%] Built target ResampleCT

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/ResampleCTTest'.  Stop.

[ 30%] Built target ResampleCTTest
[ 31%] Built target QualityControlLib

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/QualityControl'.  Stop.

[ 31%] Built target QualityControl

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/QualityControlTest'.  Stop.

[ 31%] Built target QualityControlTest
[ 32%] Built target RemoveChestTypeFromLabelMapUsingParticlesLib

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/RemoveChestTypeFromLabelMapUsingParticles'.  Stop.

[ 32%] Built target RemoveChestTypeFromLabelMapUsingParticles

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/RemoveChestTypeFromLabelMapUsingParticlesTest'.  Stop.

[ 32%] Built target RemoveChestTypeFromLabelMapUsingParticlesTest
[ 33%] Built target SegmentLungLobesLib

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/SegmentLungLobes'.  Stop.

[ 33%] Built target SegmentLungLobes

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/SegmentLungLobesTest'.  Stop.

[ 33%] Built target SegmentLungLobesTest
[ 33%] Built target ReadDicomWriteTagsLib

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/ReadDicomWriteTags'.  Stop.

[ 34%] Built target ReadDicomWriteTags

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/ReadDicomWriteTagsTest'.  Stop.

[ 34%] Built target ReadDicomWriteTagsTest
[ 35%] Built target SplitLeftLungRightLungLib

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/SplitLeftLungRightLung'.  Stop.

[ 35%] Built target SplitLeftLungRightLung

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/SplitLeftLungRightLungTest'.  Stop.

[ 35%] Built target SplitLeftLungRightLungTest
[ 35%] Built target ExtractChestLabelMapLib

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/ExtractChestLabelMap'.  Stop.

[ 35%] Built target ExtractChestLabelMap

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/ExtractChestLabelMapTest'.  Stop.

[ 36%] Built target ExtractChestLabelMapTest
[ 36%] Built target LabelParticlesByChestRegionChestTypeLib

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/LabelParticlesByChestRegionChestType'.  Stop.

[ 37%] Built target LabelParticlesByChestRegionChestType

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/LabelParticlesByChestRegionChestTypeTest'.  Stop.

[ 37%] Built target LabelParticlesByChestRegionChestTypeTest
[ 37%] Built target GenerateStenciledLabelMapFromParticlesLib

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/GenerateStenciledLabelMapFromParticles'.  Stop.

[ 38%] Built target GenerateStenciledLabelMapFromParticles

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/GenerateStenciledLabelMapFromParticlesTest'.  Stop.

[ 39%] Built target GenerateStenciledLabelMapFromParticlesTest
[ 39%] Built target GenerateDistanceMapFromLabelMapLib

gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/GenerateDistanceMapFromLabelMap'.  Stop.

[ 40%] Built target GenerateDistanceMapFromLabelMap
gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/GenerateDistanceMapFromLabelMapTest'.  Stop.
[ 41%] Built target GenerateDistanceMapFromLabelMapTest
[ 42%] Built target FilterVesselParticleDataLib
gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/FilterVesselParticleData'.  Stop.
[ 42%] Built target FilterVesselParticleData
gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKIOTransformBase-4.8.so.1', needed by `CommandLineTools/Testing/bin/FilterVesselParticleDataTest'.  Stop.
[ 42%] Built target FilterVesselParticleDataTest
[ 43%] Built target FilterAirwayParticleDataLib
gmake[5]: *** No rule to make target `/.../CIP-build/ITKv4-build/lib/libITKReview-4.8.so.1', needed by `bin/FilterAirwayParticleData'.  Stop.
The maximum number of reported warnings or errors has been reached!!!

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