Site Name: bwh002376.bwh.harvard.edu
Build Name: CIP-Darwin-13.4.0-x86_64-incr-SL-ON-SL-OFF (view notes)
Stamp: 20160806-0400-Nightly (related builds)
Time: 2016-08-06T23:06:52 EDT
Type: Nightly

OS Name: Mac OS X
OS Platform: x86_64
OS Release: 10.9.5
OS Version: 13F1808
CTest version: ctest-3.5.0-rc1

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Start Time: 2016-08-06T23:06:24 EDT
End Time: 2016-08-06T23:06:48 EDT
Configure Command: /Applications/CMake.app/Contents/bin/cmake -DCMAKE_BUILD_TYPE:STRING=Release "-GUnix Makefiles" "/Users/acil-user/Projects/CIP"
Configure Return Value: 0
Configure Output:
----------- ENTRY ------------
----------- PHASE 2 ------------
Configuring CIP...
-- VTK Built with BOOST Graph
----------- DONE ------------
Appending new list
-- 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: ReadParticlesWriteConnectedParticles
-- Configuring SEM CLI module: LabelAirwayParticlesByGeneration
-- Configuring SEM CLI module: GenerateStatisticsForAirwayGenerationLabeling
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/__init__.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/common
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/common/__init__.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/common/chest_conventions.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/common/chest_conventions_static.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/common/cipChestConventionsXmlParser.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/common/geometry_topology_data.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/common/paths.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/common/tests
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/common/tests/test_geometry_topology_data.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/__init__.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/apply_reader_labels.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/classify_image_subtypes.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/distance_feature_extractor.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/distance_feature_extractor_from_ROI.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/distance_feature_extractor_from_xmlpoints.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/emphysema_classification.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/get_ct_patch_from_center.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/hist_dist_knn.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/hist_dist_scikit_knn.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/kde_.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/kde_bandwidth.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/kde_histogram_feature_extractor.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/kde_histogram_feature_extractor_from_ROI.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/kde_histogram_feature_extractor_from_xmlpoints.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/lattice_classifier.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/local_histogram.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/tests
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_apply_reader_labels.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_classify_image_subtypes.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_distance_feature_extractor.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_distance_feature_extractor_from_ROI.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_distance_feature_extractor_from_xml_points.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_distance_histogram_extractors.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_get_ct_patch_from_center.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_hist_dist_knn.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_hist_dist_scikit_knn.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_kde_histogram_feature_extractor.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_kde_histogram_feature_extractor_from_ROI.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_kde_histogram_feature_extractor_from_xmlpoints.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/input_output
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/input_output/__init__.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/input_output/image_reader_writer.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/input_output/tests
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/input_output/tests/test_image_reader_writer.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/__init__.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/cip_convention_manager.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/cip_node.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/__init__.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/cip
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/cip/__init__.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/cip/base.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/cip/cip.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/cip/cip_python_interfaces.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/cip/generate_classes.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/cip/setup.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/unu
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/unu/__init__.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/interfaces/unu/unu.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflow_dispatcher.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/__init__.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/body_composition_workflow.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/cip_workflow.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/example.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/lung_lobe_segmentation_workflow.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/parenchyma_phenotype_workflow.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/parenchyma_phenotype_workflow_autocase.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/tests
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/tests/test_vessel_particles_mask_workflow.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/vessel_particles_mask_workflow.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/vessel_particles_workflow.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/particles
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/particles/__init__.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/particles/airway_particles.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/particles/chest_particles.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/particles/diaphragm_particles.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/particles/feature_strength_map.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/particles/fissure_particles.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/particles/multires_airway_particles.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/particles/multires_vessel_particles.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/particles/particle_metrics.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/particles/tests
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/particles/tests/test_airway_particles.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/particles/tests/test_fissure_particles.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/particles/tests/test_particle_metrics.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/particles/tests/test_vessel_particles.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/particles/vessel_particles.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/phenotypes
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/phenotypes/__init__.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/phenotypes/body_composition_phenotypes.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/phenotypes/bronchiectasis.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/phenotypes/diaphragm_thickness.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/phenotypes/emphysema_severity.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/phenotypes/gas_trapping.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/phenotypes/laa_phenotypes.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/phenotypes/parenchyma_phenotypes.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/phenotypes/phenotypes.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/phenotypes/tests
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/phenotypes/tests/test_body_composition_phenotypes.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/phenotypes/tests/test_emphysema_severity.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/phenotypes/tests/test_laa_phenotypes.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/phenotypes/tests/test_parenchyma_phenotypes.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/phenotypes/vasculature.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/phenotypes/vasculature_phenotypes.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/qualitycontrol
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/qualitycontrol/__init__.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/qualitycontrol/tests
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/qualitycontrol/vasculature_qc.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/qualitycontrol/xml_points_qc.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/registration
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/registration/__init__.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/registration/cip_registration.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/registration/tests
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/segmentation
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/segmentation/__init__.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/segmentation/chest_partition.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/segmentation/chest_partition_manager.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/segmentation/comput_image_similarity.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/segmentation/construct_chest_atlas.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/segmentation/construct_pec_atlas_from_filenames.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/segmentation/gaussian_rician.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/segmentation/grid_segmenter.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/segmentation/pectoralis_segmentor.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/segmentation/register_tobase_get_closest.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/segmentation/rind_vs_core_partition.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/segmentation/segment_chest_with_atlas.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/segmentation/slic_segmenter.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/segmentation/tests
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/segmentation/tests/test_grid_segmenter.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/segmentation/tests/test_rind_vs_core_partition.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/__init__.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/anonymize_dicom.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/apply_label_from_classification.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/cluster_particles.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/compute_dice_coefficient.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/feature_maps.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/generate_CLIs_description.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/generate_overlay_image.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/get_closest_cases.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/get_mi_similarity_vec.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/polynomial_feature_map.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/query_dicom_directories.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/quick_airway_vessel_segmentation.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/read_geometrytopologypoint_write_dataframe.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/read_nrrds_write_vtk.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/region_type_parser.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/remap_lm.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/tests
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/tests/test_anonymize_dicom.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/tests/test_compute_dice_coefficient.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/tests/test_feature_maps.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/tests/test_read_geometrytopologypoint_write_dataframe.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/tests/test_region_type_parser.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/tests/test_remap_lm.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/tests/test_weighted_feature_map_densities.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/weighted_feature_map_densities.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/utils/WeightedFeatureMapDensity.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/visualization
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/visualization/__init__.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/visualization/display_particles.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/visualization/display_particles_volume.py
-- Up-to-date: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/visualization/tests
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/acil-user/Projects/CIP-build/CIP-build

View Configure Summary

Build (50 errors, 6 warnings)

Build command: /Applications/CMake.app/Contents/bin/cmake --build . --config "Release" -- -i
Start Time: 2016-08-06T23:06:52 EDT
End Time: 2016-08-06T23:08:40 EDT


Build Log line 1598


File: Common/vtkCIPAirwayParticlesToConnectedAirwayParticlesFilter.cxx Line: 1110
-- Configuring done
-- Generating done
-- Build files have been written to: /.../CIP-build/CIP-build
[ 91%] Performing forcebuild step for 'CIP'
[ 92%] Performing build step for 'CIP'
[  0%] Built target copy-input-files
[  0%] Built target copy-external-files
[  1%] Built target CIPUtilities
[  1%] Built target generateChestConventions
[  1%] Building CXX object Common/CMakeFiles/CIPCommon.dir/vtkCIPAirwayParticlesToConnectedAirwayParticlesFilter.cxx.o
/.../CIP/Common/vtkCIPAirwayParticlesToConnectedAirwayParticlesFilter.cxx:1110:8: error: call to 'abs' is ambiguous
  if ( std::abs( arg ) > 1.0 )
       ^~~~~~~~
ar: CMakeFiles/CIPCommon.dir/vtkCIPAirwayParticlesToConnectedAirwayParticlesFilter.cxx.o: No such file or directory
[  9%] Built target CIPCommon
[ 10%] Built target CIPIO
[ 10%] Linking CXX executable cipLobeSurfaceModelTEST
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: unable to execute command: Segmentation fault: 11
clang: error: linker command failed due to signal (use -v to see invocation)
[ 10%] Built target cipLobeSurfaceModelTEST
[ 11%] Linking CXX executable cipNelderMeadSimplexOptimizerTEST
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: unable to execute command: Segmentation fault: 11
clang: error: linker command failed due to signal (use -v to see invocation)
[ 11%] Built target cipNelderMeadSimplexOptimizerTEST
[ 11%] Linking CXX executable itkCIPExtractChestLabelMapImageFilterTEST
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 11%] Built target itkCIPExtractChestLabelMapImageFilterTEST
[ 12%] Linking CXX executable itkCIPMergeChestLabelMapsImageFilterTEST
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 12%] Built target itkCIPMergeChestLabelMapsImageFilterTEST
[ 13%] Linking CXX executable cipHelperTEST
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 13%] Built target cipHelperTEST
[ 13%] Linking CXX executable cipLobeSurfaceModelIOTEST
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 13%] Built target cipLobeSurfaceModelIOTEST
[ 13%] Linking CXX executable cipChestRegionChestTypeLocationsIOTEST
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 13%] Built target cipChestRegionChestTypeLocationsIOTEST
[ 14%] Built target ConvertDicomLib
[ 14%] Linking CXX executable ../../bin/ConvertDicom
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: unable to execute command: Segmentation fault: 11
clang: error: linker command failed due to signal (use -v to see invocation)
[ 14%] Built target ConvertDicom
[ 14%] Linking CXX executable ../Testing/bin/ConvertDicomTest
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 14%] Built target ConvertDicomTest
[ 14%] Built target MergeParticleDataSetsLib
[ 15%] Linking CXX executable ../../bin/MergeParticleDataSets
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: unable to execute command: Segmentation fault: 11
clang: error: linker command failed due to signal (use -v to see invocation)
[ 15%] Built target MergeParticleDataSets
[ 15%] Linking CXX executable ../Testing/bin/MergeParticleDataSetsTest
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 15%] Built target MergeParticleDataSetsTest
[ 15%] Built target RemoveParticlesFromParticlesDataSetLib
[ 15%] Linking CXX executable ../../bin/RemoveParticlesFromParticlesDataSet
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 15%] Built target RemoveParticlesFromParticlesDataSet
[ 15%] Linking CXX executable ../Testing/bin/RemoveParticlesFromParticlesDataSetTest
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 16%] Built target RemoveParticlesFromParticlesDataSetTest
[ 16%] Built target ExtractParticlesFromChestRegionChestTypeLib
[ 16%] Linking CXX executable ../../bin/ExtractParticlesFromChestRegionChestType
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 17%] Built target ExtractParticlesFromChestRegionChestType
[ 18%] Linking CXX executable ../Testing/bin/ExtractParticlesFromChestRegionChestTypeTest
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 18%] Built target ExtractParticlesFromChestRegionChestTypeTest
[ 18%] Built target GenerateOtsuLungCastLib
[ 19%] Linking CXX executable ../../bin/GenerateOtsuLungCast
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: unable to execute command: Segmentation fault: 11
clang: error: linker command failed due to signal (use -v to see invocation)
[ 19%] Built target GenerateOtsuLungCast
[ 19%] Linking CXX executable ../Testing/bin/GenerateOtsuLungCastTest
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 19%] Built target GenerateOtsuLungCastTest
[ 20%] Built target GenerateAtlasConvexHullLib
[ 20%] Linking CXX executable ../Testing/bin/GenerateAtlasConvexHullTest
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 20%] Built target GenerateAtlasConvexHullTest
[ 20%] Linking CXX executable ../../bin/GenerateAtlasConvexHull
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 20%] Built target GenerateAtlasConvexHull
[ 21%] Built target RegisterLungAtlasLib
[ 21%] Linking CXX executable ../../bin/RegisterLungAtlas
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 21%] Built target RegisterLungAtlas
[ 21%] Linking CXX executable ../Testing/bin/RegisterLungAtlasTest
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 21%] Built target RegisterLungAtlasTest
[ 22%] Built target ResampleLabelMapLib
[ 22%] Linking CXX executable ../Testing/bin/ResampleLabelMapTest
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 22%] Built target ResampleLabelMapTest
[ 22%] Linking CXX executable ../../bin/ResampleLabelMap
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: unable to execute command: Segmentation fault: 11
clang: error: linker command failed due to signal (use -v to see invocation)
[ 22%] Built target ResampleLabelMap
[ 22%] Built target RescaleLabelMapLib
[ 22%] Linking CXX executable ../Testing/bin/RescaleLabelMapTest
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 22%] Built target RescaleLabelMapTest
[ 23%] Linking CXX executable ../../bin/RescaleLabelMap
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 23%] Built target RescaleLabelMap
[ 24%] Built target ResampleCTLib
[ 24%] Linking CXX executable ../../bin/ResampleCT
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 24%] Built target ResampleCT
[ 24%] Linking CXX executable ../Testing/bin/ResampleCTTest
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 24%] Built target ResampleCTTest
[ 25%] Built target QualityControlLib
[ 25%] Linking CXX executable ../Testing/bin/QualityControlTest
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 25%] Built target QualityControlTest
[ 25%] Linking CXX executable ../../bin/QualityControl
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: unable to execute command: Segmentation fault: 11
clang: error: linker command failed due to signal (use -v to see invocation)
[ 25%] Built target QualityControl
[ 25%] Built target RemoveChestTypeFromLabelMapUsingParticlesLib
[ 25%] Linking CXX executable ../../bin/RemoveChestTypeFromLabelMapUsingParticles
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 26%] Built target RemoveChestTypeFromLabelMapUsingParticles
[ 27%] Linking CXX executable ../Testing/bin/RemoveChestTypeFromLabelMapUsingParticlesTest
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 27%] Built target RemoveChestTypeFromLabelMapUsingParticlesTest
[ 27%] Built target SegmentLungLobesLib
[ 27%] Linking CXX executable ../../bin/SegmentLungLobes
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 28%] Built target SegmentLungLobes
[ 29%] Linking CXX executable ../Testing/bin/SegmentLungLobesTest
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 29%] Built target SegmentLungLobesTest
[ 30%] Built target ReadDicomWriteTagsLib
[ 30%] Linking CXX executable ../../bin/ReadDicomWriteTags
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 30%] Built target ReadDicomWriteTags
[ 30%] Linking CXX executable ../Testing/bin/ReadDicomWriteTagsTest
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 30%] Built target ReadDicomWriteTagsTest
[ 30%] Built target SplitLeftLungRightLungLib
[ 30%] Linking CXX executable ../../bin/SplitLeftLungRightLung
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 30%] Built target SplitLeftLungRightLung
[ 30%] Linking CXX executable ../Testing/bin/SplitLeftLungRightLungTest
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 31%] Built target SplitLeftLungRightLungTest
[ 32%] Built target ExtractChestLabelMapLib
[ 32%] Linking CXX executable ../../bin/ExtractChestLabelMap
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 32%] Built target ExtractChestLabelMap
[ 32%] Linking CXX executable ../Testing/bin/ExtractChestLabelMapTest
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 32%] Built target ExtractChestLabelMapTest
[ 33%] Built target LabelParticlesByChestRegionChestTypeLib
[ 33%] Linking CXX executable ../Testing/bin/LabelParticlesByChestRegionChestTypeTest
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 33%] Built target LabelParticlesByChestRegionChestTypeTest
[ 33%] Linking CXX executable ../../bin/LabelParticlesByChestRegionChestType
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[ 33%] Built target LabelParticlesByChestRegionChestType
[ 33%] Built target GenerateStenciledLabelMapFromParticlesLib
[ 34%] Linking CXX executable ../../bin/GenerateStenciledLabelMapFromParticles
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: unable to execute command: Segmentation fault: 11
clang: error: linker command failed due to signal (use -v to see invocation)
[ 34%] Built target GenerateStenciledLabelMapFromParticles
[ 35%] Linking CXX executable ../Testing/bin/GenerateStenciledLabelMapFromParticlesTest
ld: archive has no table of contents file '/.../CIP-build/lib/libCIPCommon.a' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
The maximum number of reported warnings or errors has been reached!!!
View Errors Summary

Build Warnings (6)
[ 99%] Linking CXX shared library ../../lib/libvtkViewsContext2D-6.3.dylib
[ 99%] Built target vtkViewsContext2D
[ 99%] Linking CXX shared library ../../lib/libvtkViewsInfovis-6.3.dylib
[100%] Built target vtkViewsInfovis
[ 54%] No install step for 'VTKv6'
[ 55%] Completed 'VTKv6'
[ 59%] Built target VTKv6
[ 60%] Performing update step for 'teem'
[ 61%] Performing configure step for 'teem'
loading initial cache file /.../CIP-build/teem-prefix/tmp/teem-cache-Release.cmake
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
  cmake-packages(7) manual for more.

This warning is for project developers.  Use -Wno-dev to suppress it.
-- Configuring done

-- Generating done
CMake Warning (dev):
  Policy CMP0042 is not set: MACOSX_RPATH is enabled by default.  Run "cmake
  --help-policy CMP0042" for policy details.  Use the cmake_policy command to
  set the policy and suppress this warning.

  MACOSX_RPATH is not specified for the following targets:

   teem

This warning is for project developers.  Use -Wno-dev to suppress it.
[100%] Linking CXX shared library ../../../../lib/libitkMGHIO-4.10.dylib
[100%] Built target MGHIO
[100%] Built target MGHIO-all
[ 74%] No install step for 'ITKv4'
[ 75%] Completed 'ITKv4'
[ 79%] Built target ITKv4
[ 80%] Performing update step for 'SlicerExecutionModel'
[ 81%] Performing configure step for 'SlicerExecutionModel'
loading initial cache file /.../CIP-build/SlicerExecutionModel-prefix/tmp/SlicerExecutionModel-cache-Release.cmake
-- Configuring done
CMake Warning (dev):
  Policy CMP0042 is not set: MACOSX_RPATH is enabled by default.  Run "cmake
  --help-policy CMP0042" for policy details.  Use the cmake_policy command to
  set the policy and suppress this warning.

  MACOSX_RPATH is not specified for the following targets:

   ModuleDescriptionParser

This warning is for project developers.  Use -Wno-dev to suppress it.

Build Log line 1601


File: /usr/include/stdlib.h Line: 129
/usr/include/stdlib.h:129:6: note: candidate function
int      abs(int) __pure2;
         ^

Build Log line 1604


File: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdlib Line: 159
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:159:44: note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long      abs(     long __x) _NOEXCEPT {return  labs(__x);}
                                           ^

Build Log line 1607


File: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdlib Line: 161
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:161:44: note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long long abs(long long __x) _NOEXCEPT {return llabs(__x);}
                                           ^
1 error generated.
[  1%] Linking CXX static library /.../CIP-build/lib/libCIPCommon.a

View Warnings Summary

Test (17 passed, 5 failed, 53 not run)
View Tests Summary