Site Name: ip-172-31-44-204.ec2.internal
Build Name: CIP-Linux-3.10.0-123.el7.x86_64-x86_64-incr-SL-ON (view notes)
Stamp: 20200309-0400-Nightly (related builds)
Time: 2020-03-09T00:03:39 EDT
Type: Nightly

OS Name: Linux
OS Platform: x86_64
OS Release: 3.10.0-123.el7.x86_64
OS Version: #1 SMP Mon May 5 11:16:57 EDT 2014
CTest version: ctest-3.9.0

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Stage: Update (0 errors, 0 warnings)

Start Time: 2020-03-09T00:03:18 EDT
End Time: 2020-03-09T00:03:19 EDT
Update Command: "/usr/bin/git" "fetch"
Update Type: GIT
Number of Updates: 0

Configure (0 errors, 0 warnings)

Start Time: 2020-03-09T00:03:20 EDT
End Time: 2020-03-09T00:03:38 EDT
Configure Command: /home/ec2-user/sw/cmake-3.9.0-Linux-x86_64/bin/cmake -DCMAKE_BUILD_TYPE:STRING=Release "-GUnix Makefiles" "/home/ec2-user/Projects/CIP"
Configure Return Value: 0
Configure Output: 
--  - C++11
----------- ENTRY ------------
----------- PHASE 2 ------------
Configuring CIP...
-- Using Infovis Boost
----------- DONE ------------
Appending new list
-- Configuring SEM CLI module: ExampleCLI
-- 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: 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: GenerateParenchymaPhenotypes
-- Configuring SEM CLI module: ComputeDistanceMap
-- 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
-- Configuring SEM CLI module: GraphCutsOptimization
-- Configuring SEM CLI module: SegmentLungAirways
-- Configuring SEM CLI module: ComputeStrainFromDeformationField
-- Configuring SEM CLI module: ComputeAirwayWallFromImages
-- Configuring SEM CLI module: FitBSplineToDeformationField
-- Configuring SEM CLI module: CreateVolumeFromSlices
-- Configuring SEM CLI module: ReadParticlesWriteConnectedParticles
-- Configuring SEM CLI module: LabelAirwayParticlesByGeneration
-- Configuring SEM CLI module: GenerateStatisticsForAirwayGenerationLabeling
-- Configuring SEM CLI module: TransferFieldDataToFromPointData
-- Configuring SEM CLI module: UpdateParticlesData
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/__init__.py
Wrapping GraphCutsOptimization with Python in /home/ec2-user/Projects/CIP-build/CIPPython-install/bin/python2.7 and flags   -fPIC  -Wno-array-bounds -msse2 
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/common
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/common/tests
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/common/tests/baseline
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/common/tests/test_example.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/common/tests/test_geometry_topology_data.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/common/chest_conventions_static.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/common/example_pythonCLI.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/common/paths.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/common/__init__.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/common/chest_conventions.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/common/geometry_topology_data.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/common/anatomic_structures_manager.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/common/cipChestConventionsXmlParser.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/distance_feature_extractor_from_ROI.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/get_ct_patch_from_center.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/lattice_classifier.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/tests
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_apply_reader_labels.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_distance_feature_extractor.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_distance_feature_extractor_from_ROI.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_distance_feature_extractor_from_xml_points.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_distance_histogram_extractors.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_get_ct_patch_from_center.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_hist_dist_knn.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_hist_dist_scikit_knn.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_kde_histogram_feature_extractor.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_kde_histogram_feature_extractor_from_ROI.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_kde_histogram_feature_extractor_from_xmlpoints.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_classify_image_subtypes.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/hist_dist_scikit_knn.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/kde_histogram_feature_extractor_from_ROI.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/kde_bandwidth.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/__init__.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/apply_reader_labels.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/distance_feature_extractor.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/distance_feature_extractor_from_xmlpoints.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/kde_.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/kde_histogram_feature_extractor.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/kde_histogram_feature_extractor_from_xmlpoints.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/local_histogram_emphysema.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/hist_dist_knn.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/localHistogramModel.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/localHistogramMapper.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/classification/classify_image_subtypes.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/tests
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/tests/test_image_reader_writer.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/data_operators
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/data_operators/data_operator.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/data_operators/uniform_similarity_3D_transform_with_coords_DO.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/data_operators/elastic_2D_transform_DO.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/data_operators/flipping_DO.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/data_operators/gaussian_noise_DO.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/data_operators/perspective_skew_2D_transform_DO.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/data_operators/rotation_DO.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/data_operators/shear_DO.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/data_operators/shifting_DO.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/data_operators/uniform_affine_2D_transform_DO.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/data_operators/__init__.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/data_operators/invert_intensities_DO.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/data_operators/transpose_2d_DO.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/__init__.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/volume_file.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/concat_full_h5s.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/concat_h5_datasets.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/h5_dataset_store.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/input_output/image_reader_writer.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/__init__.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/data
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/data/__init__.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/data/data_augmentor.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/data/data_processing.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/data/h5_manager.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/logic
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/logic/__init__.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/logic/metrics_manager.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/logic/network.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/logic/utils.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/logic/deep_learning_models_manager.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/logic/engine.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/projects
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/projects/__init__.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/projects/lung_segmenter
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/projects/lung_segmenter/__init__.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/projects/lung_segmenter/tests
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/projects/lung_segmenter/tests/baseline
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/projects/lung_segmenter/tests/test_lung_segmentation_dcnn.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/projects/lung_segmenter/lung_segmenter_dcnn.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/projects/low_to_high_dose_filter
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/projects/low_to_high_dose_filter/__init__.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/projects/low_to_high_dose_filter/low_to_high_dose_engine.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/projects/low_to_high_dose_filter/low_to_high_dose_filter_dcnn.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/projects/low_to_high_dose_filter/networks
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/projects/low_to_high_dose_filter/networks/__init__.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/projects/low_to_high_dose_filter/networks/low_to_high_dose_metrics_manager.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/projects/low_to_high_dose_filter/networks/low_to_high_dose_network.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/projects/low_to_high_dose_filter/tests
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/projects/low_to_high_dose_filter/tests/test_low_to_high_dose_filter_dcnn.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/example
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/example/__init__.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/example/av_segmentation_dataset_generator.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/example/dcnn_airway_flow
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/example/dcnn_airway_flow/BashScripts
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/example/dcnn_airway_flow/__init__.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/example/dcnn_airway_flow/airway_flow_engine.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/example/dcnn_airway_flow/airway_flow_generator.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/example/dcnn_airway_flow/airway_flow_neural_network.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/example/dcnn_airway_flow/airway_flow_run_training_testing.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/example/dcnn_airway_flow/utils
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/example/dcnn_airway_flow/utils/__init__.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/dcnn/example/dcnn_airway_flow/utils/custom_metrics.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/cip_convention_manager.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/cip
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/cip/base.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/cip/setup.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/cip/cip.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/cip/generate_classes.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/cip/cip_python_interfaces.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/cip/__init__.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/unu
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/unu/unu.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/unu/__init__.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/__init__.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflow_dispatcher.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/__init__.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/cip_workflow.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/example.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/parenchyma_phenotype_workflow.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/parenchyma_phenotype_workflow_autocase.py
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/tests
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-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/utils/feature_maps.py
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-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/visualization
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-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/common/tests/baseline
-- Up-to-date: /home/ec2-user/Projects/CIP-build/CIP-build/cip_python/common/tests/baseline/crop_ct_2slices.nrrd
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ec2-user/Projects/CIP-build/CIP-build

View Configure Summary

Build (21 errors, 5 warnings)

Build command: /home/ec2-user/sw/cmake-3.9.0-Linux-x86_64/bin/cmake --build . --config "Release" -- -i
Start Time: 2020-03-09T00:03:39 EDT
End Time: 2020-03-09T00:06:27 EDT

Build Log line 1068


  File: Utilities/GraphCutsOptimization/maxflow.cpp
  Line: 366 
/.../CIP/Utilities/GraphCutsOptimization/maxflow.cpp:366:30: error: ‘nullptr’ was not declared in this scope
  if ((i->parent = a0_min) != nullptr)
                              ^
/.../CIP/Utilities/GraphCutsOptimization/maxflow.cpp: In member function ‘void Graph<captype, tcaptype, flowtype>::process_sink_orphan(Graph<captype, tcaptype, flowtype>::node*)’:

Build Log line 1072


  File: Utilities/GraphCutsOptimization/maxflow.cpp
  Line: 443 
/.../CIP/Utilities/GraphCutsOptimization/maxflow.cpp:443:30: error: ‘nullptr’ was not declared in this scope
  if ((i->parent = a0_min) != nullptr)
                              ^
error: command '/usr/bin/cc' failed with exit status 1
[ 10%] Built target CIP_PYTHON
[ 11%] Linking CXX executable cipNelderMeadSimplexOptimizerTEST
[ 11%] Built target cipNelderMeadSimplexOptimizerTEST
[ 11%] Linking CXX executable itkCIPExtractChestLabelMapImageFilterTEST
[ 11%] Built target itkCIPExtractChestLabelMapImageFilterTEST
[ 11%] Linking CXX executable cipHelperTEST
[ 12%] Built target cipHelperTEST
Build Log line 1420


  File: CommandLineTools/ComputeFeatureStrength/ComputeFeatureStrength.cxx
  Line: 125 
[ 71%] Linking CXX executable ../Testing/bin/MergeChestLabelMapsTest
[ 71%] Built target MergeChestLabelMapsTest
[ 72%] Built target MaskOutLabelMapStructuresLib
[ 72%] Linking CXX executable ../Testing/bin/MaskOutLabelMapStructuresTest
[ 72%] Built target MaskOutLabelMapStructuresTest
[ 72%] Linking CXX executable ../../bin/MaskOutLabelMapStructures
Copying XML file 'MaskOutLabelMapStructures.xml' along side the executable
[ 72%] Built target MaskOutLabelMapStructures
[ 72%] Building CXX object CommandLineTools/ComputeFeatureStrength/CMakeFiles/ComputeFeatureStrengthLib.dir/ComputeFeatureStrength.cxx.o
/.../CIP/CommandLineTools/ComputeFeatureStrength/ComputeFeatureStrength.cxx: In function ‘int ModuleEntryPoint(int, char**)’:

/.../CIP/CommandLineTools/ComputeFeatureStrength/ComputeFeatureStrength.cxx:125:34: error: ‘itk::MultiThreaderBase’ has not been declared
   unsigned int maxThreads = itk::MultiThreaderBase::GetGlobalDefaultNumberOfThreads();
                                  ^

Build Log line 1423


  File: CommandLineTools/ComputeFeatureStrength/ComputeFeatureStrength.cxx
  Line: 132 
/.../CIP/CommandLineTools/ComputeFeatureStrength/ComputeFeatureStrength.cxx:132:8: error: ‘itk::MultiThreaderBase’ has not been declared
   itk::MultiThreaderBase::SetGlobalMaximumNumberOfThreads( maxThreads );
        ^
[ 72%] Linking CXX static library ../../bin/libComputeFeatureStrengthLib.a

/usr/bin/ar: CMakeFiles/ComputeFeatureStrengthLib.dir/ComputeFeatureStrength.cxx.o: No such file or directory
[ 73%] Built target ComputeFeatureStrengthLib

gmake[5]: *** No rule to make target `bin/libComputeFeatureStrengthLib.a', needed by `CommandLineTools/Testing/bin/ComputeFeatureStrengthTest'.  Stop.
[ 73%] Built target ComputeFeatureStrengthTest

gmake[5]: *** No rule to make target `bin/libComputeFeatureStrengthLib.a', needed by `bin/ComputeFeatureStrength'.  Stop.
[ 73%] Built target ComputeFeatureStrength
[ 73%] Built target LabelMapFromRegionAndTypePointsLib
[ 73%] Linking CXX executable ../../bin/LabelMapFromRegionAndTypePoints
Copying XML file 'LabelMapFromRegionAndTypePoints.xml' along side the executable
[ 73%] Built target LabelMapFromRegionAndTypePoints
[ 73%] Linking CXX executable ../Testing/bin/LabelMapFromRegionAndTypePointsTest
[ 74%] Built target LabelMapFromRegionAndTypePointsTest
[ 75%] Built target GenerateSimpleLungMaskLib
[ 75%] Linking CXX executable ../../bin/GenerateSimpleLungMask
Copying XML file 'GenerateSimpleLungMask.xml' along side the executable
Build Log line 1483


  File: CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx
  Line: 24 
[ 81%] Built target ComputeFissureFeatureVectors
[ 81%] Linking CXX executable ../Testing/bin/ComputeFissureFeatureVectorsTest
[ 81%] Built target ComputeFissureFeatureVectorsTest
[ 82%] Built target FitLobeSurfaceModelsToParticleDataLib
[ 82%] Linking CXX executable ../../bin/FitLobeSurfaceModelsToParticleData
Copying XML file 'FitLobeSurfaceModelsToParticleData.xml' along side the executable
[ 82%] Built target FitLobeSurfaceModelsToParticleData
[ 82%] Linking CXX executable ../Testing/bin/FitLobeSurfaceModelsToParticleDataTest
[ 82%] Built target FitLobeSurfaceModelsToParticleDataTest
[ 82%] Building CXX object CommandLineTools/GenerateLesionSegmentation/CMakeFiles/GenerateLesionSegmentationLib.dir/GenerateLesionSegmentation.cxx.o

/.../CIP/CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx:24:9: error: ‘LandmarkPointListType’ in ‘SeedSpatialObjectType {aka class itk::LandmarkSpatialObject<3u>}’ does not name a type
 typedef SeedSpatialObjectType::LandmarkPointListType   LandmarkPointListType;
         ^

Build Log line 1486


  File: CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx
  Line: 37 
/.../CIP/CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx:37:1: error: ‘LandmarkPointListType’ does not name a type
 LandmarkPointListType GetSeeds(std::vector<std::vector<float> > seeds,InputImageType *image)
 ^
/.../CIP/CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx: In function ‘int ModuleEntryPoint(int, char**)’:

Build Log line 1490


  File: CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx
  Line: 117 
/.../CIP/CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx:117:5: error: ‘LandmarkPointListType’ was not declared in this scope
     LandmarkPointListType seeds=GetSeeds(seedsFiducials,image);
     ^

Build Log line 1493


  File: CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx
  Line: 117 
/.../CIP/CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx:117:27: error: expected ‘;’ before ‘seeds’
     LandmarkPointListType seeds=GetSeeds(seedsFiducials,image);
                           ^

Build Log line 1496


  File: CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx
  Line: 118 
/.../CIP/CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx:118:5: error: ‘seeds’ was not declared in this scope
     seeds[0];
     ^
In file included from /.../CIP/CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx:12:0:
/.../CIP/Utilities/LesionSizingToolkit/itkLesionSegmentationImageFilter8.h: In instantiation of ‘class itk::LesionSegmentationImageFilter8<itk::Image<short int, 3u>, itk::Image<float, 3u> >’:
/.../CIP/CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx:194:25:   required from here

Build Log line 1502


  File: Utilities/LesionSizingToolkit/itkLesionSegmentationImageFilter8.h
  Line: 132 
/.../CIP/Utilities/LesionSizingToolkit/itkLesionSegmentationImageFilter8.h:132:67: error: no type named ‘LandmarkPointListType’ in ‘class itk::LandmarkSpatialObject<3u>’
   typedef typename SeedSpatialObjectType::LandmarkPointListType   LandmarkPointListType;
                                                                   ^

Build Log line 1505


  File: Utilities/LesionSizingToolkit/itkLesionSegmentationImageFilter8.h
  Line: 197 
/.../CIP/Utilities/LesionSizingToolkit/itkLesionSegmentationImageFilter8.h:197:59: error: no type named ‘LandmarkPointListType’ in ‘class itk::LandmarkSpatialObject<3u>’
   typename SeedSpatialObjectType::LandmarkPointListType   m_Seeds;
                                                           ^

Build Log line 1508


  File: CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx
  Line: 196 
/.../CIP/CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx:196:8: error: ‘itk::SmartPointer<itk::LesionSegmentationImageFilter8<itk::Image<short int, 3u>, itk::Image<float, 3u> > >::ObjectType’ has no member named ‘SetSeeds’
   seg->SetSeeds(GetSeeds(seedsFiducials,image));
        ^

Build Log line 1511


  File: CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx
  Line: 196 
/.../CIP/CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx:196:46: error: ‘GetSeeds’ was not declared in this scope
   seg->SetSeeds(GetSeeds(seedsFiducials,image));
                                              ^
In file included from /.../CIP/Utilities/LesionSizingToolkit/itkLesionSegmentationImageFilter8.h:207:0,
                 from /.../CIP/CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx:12:
/.../CIP/Utilities/LesionSizingToolkit/itkLesionSegmentationImageFilter8.hxx: In instantiation of ‘void itk::LesionSegmentationImageFilter8<TInputImage, TOutputImage>::GenerateData() [with TInputImage = itk::Image<short int, 3u>; TOutputImage = itk::Image<float, 3u>]’:
/.../CIP/CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx:266:1:   required from here

Build Log line 1518


  File: Utilities/LesionSizingToolkit/itkLesionSegmentationImageFilter8.hxx
  Line: 235 
/.../CIP/Utilities/LesionSizingToolkit/itkLesionSegmentationImageFilter8.hxx:235:3: error: using invalid field ‘itk::LesionSegmentationImageFilter8<TInputImage, TOutputImage>::m_Seeds’
   seedSpatialObject->SetPoints(m_Seeds);
   ^
In file included from /.../CIP/Utilities/LesionSizingToolkit/itkFastMarchingSegmentationModule.h:108:0,
                 from /.../CIP/Utilities/LesionSizingToolkit/itkFastMarchingAndGeodesicActiveContourLevelSetSegmentationModule.h:21,
                 from /.../CIP/Utilities/LesionSizingToolkit/itkLesionSegmentationImageFilter8.h:30,
                 from /.../CIP/CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx:12:
/.../CIP/Utilities/LesionSizingToolkit/itkFastMarchingSegmentationModule.hxx: In instantiation of ‘void itk::FastMarchingSegmentationModule<NDimension>::GenerateData() [with unsigned int NDimension = 3u]’:
/.../CIP/CommandLineTools/GenerateLesionSegmentation/GenerateLesionSegmentation.cxx:266:1:   required from here

Build Log line 1527


  File: Utilities/LesionSizingToolkit/itkFastMarchingSegmentationModule.hxx
  Line: 102 
/.../CIP/Utilities/LesionSizingToolkit/itkFastMarchingSegmentationModule.hxx:102:69: error: no type named ‘LandmarkPointListType’ in ‘class itk::LandmarkSpatialObject<3u>’
   typedef typename InputSpatialObjectType::LandmarkPointListType    LandmarkPointListType;
                                                                     ^
[ 82%] Linking CXX static library ../../bin/libGenerateLesionSegmentationLib.a

/usr/bin/ar: CMakeFiles/GenerateLesionSegmentationLib.dir/GenerateLesionSegmentation.cxx.o: No such file or directory
[ 83%] Built target GenerateLesionSegmentationLib

gmake[5]: *** No rule to make target `bin/libGenerateLesionSegmentationLib.a', needed by `bin/GenerateLesionSegmentation'.  Stop.
[ 83%] Built target GenerateLesionSegmentation

gmake[5]: *** No rule to make target `bin/libGenerateLesionSegmentationLib.a', needed by `CommandLineTools/Testing/bin/GenerateLesionSegmentationTest'.  Stop.
[ 83%] Built target GenerateLesionSegmentationTest
[ 84%] Built target RemapLabelMapLib
[ 84%] Linking CXX executable ../../bin/RemapLabelMap
Copying XML file 'RemapLabelMap.xml' along side the executable
[ 84%] Built target RemapLabelMap
[ 84%] Linking CXX executable ../Testing/bin/RemapLabelMapTest
[ 84%] Built target RemapLabelMapTest
[ 85%] Built target GenerateNLMFilteredImageLib
[ 85%] Linking CXX executable ../../bin/GenerateNLMFilteredImage
Copying XML file 'GenerateNLMFilteredImage.xml' along side the executable
View Errors Summary


Build Warnings (5)
-- Enabled ITKVideoIO, requested by ITK_BUILD_DEFAULT_MODULES.
-- Enabled ITKVoronoi, requested by ITK_BUILD_DEFAULT_MODULES.
-- Enabled ITKVtkGlue, requested by Module_ITKVtkGlue.
-- Enabled ITKWatersheds, requested by ITK_BUILD_DEFAULT_MODULES.
-- Enabled ITKZLIB, requested by ITK_BUILD_DEFAULT_MODULES.
-- Enabled MGHIO, requested by Module_MGHIO.
-- Performing Test ITK_PRIVATE_DYNAMIC_CAST - Success
-- Found ZLIB: /.../CIP-build/zlib-install/lib/libzlib.a (found version "1.2.3") 
-- Found ZLIB: /.../CIP-build/zlib-install/lib/libzlib.a  
-- Filter ZLIB is ON

CMake Warning (dev) at Modules/Remote/MGHIO/CMakeLists.txt:2 (project):
  Policy CMP0048 is not set: project() command manages VERSION variables.
  Run "cmake --help-policy CMP0048" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  The following variable(s) would be set to empty:

    PROJECT_VERSION
    PROJECT_VERSION_MAJOR
    PROJECT_VERSION_MINOR
    PROJECT_VERSION_PATCH
[ 69%] Built target ModuleDescriptionParser
[ 84%] Built target GenerateCLP
[100%] Built target GenerateCLPLauncher
[ 67%] No install step for 'SlicerExecutionModel'
[ 69%] Completed 'SlicerExecutionModel'
[ 73%] Built target SlicerExecutionModel
[ 75%] Performing update step for 'teem'
[ 76%] Performing configure step for 'teem'
loading initial cache file /.../CIP-build/teem-prefix/tmp/teem-cache-Release.cmake
-- Configuring done

CMake Warning (dev) at CMakeLists.txt:555 (install):
  Policy CMP0062 is not set: Disallow install() of export() result.  Run
  "cmake --help-policy CMP0062" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  The file

    /.../CIP-build/teem-build/TeemLibraryDepends.cmake

  was generated by the export() command.  It should not be installed with the
  install() command.  Use the install(EXPORT) mechanism instead.  See the
[  0%] Built target copy-external-files
[  0%] Built target copy-input-files
[  2%] Built target CIPUtilities
[  2%] Built target generateChestConventions
[  9%] Built target CIPCommon
[ 10%] Built target CIPIO
running build_ext
skipping '/.../CIP/cip_python/utils/gco_python/gco_python.cpp' Cython extension (up-to-date)
building 'pygco' extension
/usr/bin/cc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/.../CIP/Utilities/GraphCutsOptimization -I/.../CIP-build/CIPPython-install/lib/python2.7/site-packages/numpy/core/include -I/.../CIP-build/CIPPython-install/include/python2.7 -c /.../CIP/cip_python/utils/gco_python/gco_python.cpp -o build/temp.linux-x86_64-2.7/.../CIP/cip_python/utils/gco_python/gco_python.o

cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
In file included from /.../CIP-build/CIPPython-install/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0,
                 from /.../CIP-build/CIPPython-install/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /.../CIP-build/CIPPython-install/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /.../CIP/cip_python/utils/gco_python/gco_python.cpp:449:

Build Log line 1059


  File: CIPPython-install/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h
  Line: 17 
/.../CIP-build/CIPPython-install/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^
In file included from /.../CIP/Utilities/GraphCutsOptimization/GCoptimization.h:111:0,
                 from /.../CIP/cip_python/utils/gco_python/gco_python.cpp:451:

Build Log line 1064


  File: Utilities/GraphCutsOptimization/maxflow.cpp
  Line: 366 
/.../CIP/Utilities/GraphCutsOptimization/maxflow.cpp:366:2: warning: identifier ‘nullptr’ is a keyword in C++11 [-Wc++0x-compat]
  if ((i->parent = a0_min) != nullptr)
  ^
/.../CIP/Utilities/GraphCutsOptimization/maxflow.cpp: In member function ‘void Graph<captype, tcaptype, flowtype>::process_source_orphan(Graph<captype, tcaptype, flowtype>::node*)’:


View Warnings Summary


Test (95  passed, 2 failed, 0 not run)
 
View Tests Summary